SRX840720 GSM1584630 SRP052077 SRS817398 GSM1584630 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584630 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584630 gds 301584630 GEO Accession GSM1584630 SRX840721 GSM1584631 SRP052077 SRS817397 GSM1584631 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584631 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584631 gds 301584631 GEO Accession GSM1584631 SRX840722 GSM1584632 SRP052077 SRS817400 GSM1584632 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584632 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584632 gds 301584632 GEO Accession GSM1584632 SRX840723 GSM1584633 SRP052077 SRS817399 GSM1584633 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584633 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584633 gds 301584633 GEO Accession GSM1584633 SRX840724 GSM1584634 SRP052077 SRS817401 GSM1584634 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584634 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584634 gds 301584634 GEO Accession GSM1584634 SRX840725 GSM1584635 SRP052077 SRS817402 GSM1584635 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584635 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584635 gds 301584635 GEO Accession GSM1584635 SRX840726 GSM1584636 SRP052077 SRS817403 GSM1584636 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584636 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584636 gds 301584636 GEO Accession GSM1584636 SRX840727 GSM1584637 SRP052077 SRS817405 GSM1584637 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584637 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584637 gds 301584637 GEO Accession GSM1584637 SRX840728 GSM1584638 SRP052077 SRS817406 GSM1584638 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584638 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584638 gds 301584638 GEO Accession GSM1584638 SRX840729 GSM1584639 SRP052077 SRS817404 GSM1584639 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584639 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584639 gds 301584639 GEO Accession GSM1584639 SRX840730 GSM1584640 SRP052077 SRS817407 GSM1584640 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584640 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584640 gds 301584640 GEO Accession GSM1584640 SRX840731 GSM1584641 SRP052077 SRS817408 GSM1584641 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584641 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584641 gds 301584641 GEO Accession GSM1584641 SRX840732 GSM1584642 SRP052077 SRS817410 GSM1584642 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584642 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584642 gds 301584642 GEO Accession GSM1584642 SRX840733 GSM1584643 SRP052077 SRS817411 GSM1584643 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584643 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584643 gds 301584643 GEO Accession GSM1584643 SRX840734 GSM1584644 SRP052077 SRS817409 GSM1584644 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584644 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584644 gds 301584644 GEO Accession GSM1584644 SRX840735 GSM1584645 SRP052077 SRS817412 GSM1584645 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584645 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584645 gds 301584645 GEO Accession GSM1584645 SRX840736 GSM1584646 SRP052077 SRS817413 GSM1584646 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584646 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584646 gds 301584646 GEO Accession GSM1584646 SRX840737 GSM1584647 SRP052077 SRS817416 GSM1584647 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584647 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584647 gds 301584647 GEO Accession GSM1584647 SRX840738 GSM1584648 SRP052077 SRS817417 GSM1584648 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584648 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584648 gds 301584648 GEO Accession GSM1584648 SRX840739 GSM1584649 SRP052077 SRS817414 GSM1584649 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584649 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584649 gds 301584649 GEO Accession GSM1584649 SRX840740 GSM1584650 SRP052077 SRS817415 GSM1584650 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584650 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584650 gds 301584650 GEO Accession GSM1584650 SRX840741 GSM1584651 SRP052077 SRS817419 GSM1584651 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584651 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584651 gds 301584651 GEO Accession GSM1584651 SRX840742 GSM1584652 SRP052077 SRS817418 GSM1584652 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584652 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584652 gds 301584652 GEO Accession GSM1584652 SRX840743 GSM1584653 SRP052077 SRS817420 GSM1584653 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584653 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584653 gds 301584653 GEO Accession GSM1584653 SRX840744 GSM1584654 SRP052077 SRS817421 GSM1584654 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584654 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584654 gds 301584654 GEO Accession GSM1584654 SRX840745 GSM1584655 SRP052077 SRS817422 GSM1584655 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584655 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584655 gds 301584655 GEO Accession GSM1584655 SRX840746 GSM1584656 SRP052077 SRS817423 GSM1584656 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584656 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584656 gds 301584656 GEO Accession GSM1584656 SRX840747 GSM1584657 SRP052077 SRS817424 GSM1584657 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584657 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584657 gds 301584657 GEO Accession GSM1584657 SRX840748 GSM1584658 SRP052077 SRS817425 GSM1584658 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584658 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584658 gds 301584658 GEO Accession GSM1584658 SRX840749 GSM1584659 SRP052077 SRS817426 GSM1584659 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584659 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584659 gds 301584659 GEO Accession GSM1584659 SRX840750 GSM1584660 SRP052077 SRS817427 GSM1584660 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584660 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584660 gds 301584660 GEO Accession GSM1584660 SRX840751 GSM1584661 SRP052077 SRS817428 GSM1584661 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584661 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584661 gds 301584661 GEO Accession GSM1584661 SRX840752 GSM1584662 SRP052077 SRS817429 GSM1584662 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584662 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584662 gds 301584662 GEO Accession GSM1584662 SRX840753 GSM1584663 SRP052077 SRS817430 GSM1584663 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584663 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584663 gds 301584663 GEO Accession GSM1584663 SRX840754 GSM1584664 SRP052077 SRS817431 GSM1584664 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584664 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584664 gds 301584664 GEO Accession GSM1584664 SRX840755 GSM1584665 SRP052077 SRS817432 GSM1584665 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584665 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584665 gds 301584665 GEO Accession GSM1584665 SRX840756 GSM1584666 SRP052077 SRS817433 GSM1584666 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584666 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584666 gds 301584666 GEO Accession GSM1584666 SRX840757 GSM1584667 SRP052077 SRS817434 GSM1584667 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584667 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584667 gds 301584667 GEO Accession GSM1584667 SRX840758 GSM1584668 SRP052077 SRS817435 GSM1584668 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584668 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584668 gds 301584668 GEO Accession GSM1584668 SRX840759 GSM1584669 SRP052077 SRS817436 GSM1584669 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584669 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584669 gds 301584669 GEO Accession GSM1584669 SRX840760 GSM1584670 SRP052077 SRS817437 GSM1584670 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584670 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584670 gds 301584670 GEO Accession GSM1584670 SRX840761 GSM1584671 SRP052077 SRS817438 GSM1584671 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584671 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584671 gds 301584671 GEO Accession GSM1584671 SRX840762 GSM1584672 SRP052077 SRS817439 GSM1584672 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584672 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584672 gds 301584672 GEO Accession GSM1584672 SRX840763 GSM1584673 SRP052077 SRS817440 GSM1584673 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584673 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584673 gds 301584673 GEO Accession GSM1584673 SRX840764 GSM1584674 SRP052077 SRS817442 GSM1584674 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584674 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584674 gds 301584674 GEO Accession GSM1584674 SRX840765 GSM1584675 SRP052077 SRS817441 GSM1584675 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584675 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584675 gds 301584675 GEO Accession GSM1584675 SRX840766 GSM1584676 SRP052077 SRS817443 GSM1584676 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584676 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584676 gds 301584676 GEO Accession GSM1584676 SRX840767 GSM1584677 SRP052077 SRS817444 GSM1584677 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584677 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584677 gds 301584677 GEO Accession GSM1584677 SRX840768 GSM1584678 SRP052077 SRS817445 GSM1584678 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584678 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584678 gds 301584678 GEO Accession GSM1584678 SRX840769 GSM1584679 SRP052077 SRS817446 GSM1584679 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584679 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584679 gds 301584679 GEO Accession GSM1584679 SRX840770 GSM1584680 SRP052077 SRS817447 GSM1584680 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584680 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584680 gds 301584680 GEO Accession GSM1584680 SRX840771 GSM1584681 SRP052077 SRS817448 GSM1584681 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584681 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584681 gds 301584681 GEO Accession GSM1584681 SRX840772 GSM1584682 SRP052077 SRS817449 GSM1584682 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584682 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584682 gds 301584682 GEO Accession GSM1584682 SRX840773 GSM1584683 SRP052077 SRS817451 GSM1584683 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584683 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584683 gds 301584683 GEO Accession GSM1584683 SRX840774 GSM1584684 SRP052077 SRS817450 GSM1584684 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584684 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584684 gds 301584684 GEO Accession GSM1584684 SRX840775 GSM1584685 SRP052077 SRS817452 GSM1584685 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584685 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584685 gds 301584685 GEO Accession GSM1584685 SRX840776 GSM1584686 SRP052077 SRS817453 GSM1584686 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584686 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584686 gds 301584686 GEO Accession GSM1584686 SRX840777 GSM1584687 SRP052077 SRS817457 GSM1584687 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584687 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584687 gds 301584687 GEO Accession GSM1584687 SRX840778 GSM1584688 SRP052077 SRS817456 GSM1584688 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584688 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584688 gds 301584688 GEO Accession GSM1584688 SRX840779 GSM1584689 SRP052077 SRS817454 GSM1584689 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584689 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584689 gds 301584689 GEO Accession GSM1584689 SRX840780 GSM1584690 SRP052077 SRS817455 GSM1584690 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584690 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584690 gds 301584690 GEO Accession GSM1584690 SRX840781 GSM1584691 SRP052077 SRS817459 GSM1584691 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584691 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584691 gds 301584691 GEO Accession GSM1584691 SRX840782 GSM1584692 SRP052077 SRS817458 GSM1584692 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584692 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584692 gds 301584692 GEO Accession GSM1584692 SRX840783 GSM1584693 SRP052077 SRS817460 GSM1584693 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584693 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584693 gds 301584693 GEO Accession GSM1584693 SRX840784 GSM1584694 SRP052077 SRS817461 GSM1584694 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584694 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584694 gds 301584694 GEO Accession GSM1584694 SRX840785 GSM1584695 SRP052077 SRS817462 GSM1584695 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584695 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584695 gds 301584695 GEO Accession GSM1584695 SRX840786 GSM1584696 SRP052077 SRS817463 GSM1584696 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584696 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584696 gds 301584696 GEO Accession GSM1584696 SRX840787 GSM1584697 SRP052077 SRS817466 GSM1584697 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584697 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584697 gds 301584697 GEO Accession GSM1584697 SRX840788 GSM1584698 SRP052077 SRS817467 GSM1584698 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584698 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584698 gds 301584698 GEO Accession GSM1584698 SRX840789 GSM1584699 SRP052077 SRS817464 GSM1584699 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584699 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584699 gds 301584699 GEO Accession GSM1584699 SRX840790 GSM1584700 SRP052077 SRS817465 GSM1584700 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584700 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584700 gds 301584700 GEO Accession GSM1584700 SRX840791 GSM1584701 SRP052077 SRS817468 GSM1584701 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584701 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584701 gds 301584701 GEO Accession GSM1584701 SRX840792 GSM1584702 SRP052077 SRS817471 GSM1584702 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584702 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584702 gds 301584702 GEO Accession GSM1584702 SRX840793 GSM1584703 SRP052077 SRS817470 GSM1584703 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584703 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584703 gds 301584703 GEO Accession GSM1584703 SRX840794 GSM1584704 SRP052077 SRS817469 GSM1584704 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584704 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584704 gds 301584704 GEO Accession GSM1584704 SRX840795 GSM1584705 SRP052077 SRS817472 GSM1584705 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584705 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584705 gds 301584705 GEO Accession GSM1584705 SRX840796 GSM1584706 SRP052077 SRS817473 GSM1584706 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584706 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584706 gds 301584706 GEO Accession GSM1584706 SRX840797 GSM1584707 SRP052077 SRS817474 GSM1584707 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584707 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584707 gds 301584707 GEO Accession GSM1584707 SRX840798 GSM1584708 SRP052077 SRS817475 GSM1584708 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584708 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584708 gds 301584708 GEO Accession GSM1584708 SRX840799 GSM1584709 SRP052077 SRS817476 GSM1584709 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584709 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584709 gds 301584709 GEO Accession GSM1584709 SRX840800 GSM1584710 SRP052077 SRS817477 GSM1584710 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584710 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584710 gds 301584710 GEO Accession GSM1584710 SRX840801 GSM1584711 SRP052077 SRS817480 GSM1584711 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584711 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584711 gds 301584711 GEO Accession GSM1584711 SRX840802 GSM1584712 SRP052077 SRS817479 GSM1584712 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584712 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584712 gds 301584712 GEO Accession GSM1584712 SRX840803 GSM1584713 SRP052077 SRS817478 GSM1584713 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584713 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584713 gds 301584713 GEO Accession GSM1584713 SRX840804 GSM1584714 SRP052077 SRS817481 GSM1584714 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584714 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584714 gds 301584714 GEO Accession GSM1584714 SRX840805 GSM1584715 SRP052077 SRS817482 GSM1584715 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584715 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584715 gds 301584715 GEO Accession GSM1584715 SRX840806 GSM1584716 SRP052077 SRS817485 GSM1584716 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584716 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584716 gds 301584716 GEO Accession GSM1584716 SRX840807 GSM1584717 SRP052077 SRS817484 GSM1584717 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584717 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584717 gds 301584717 GEO Accession GSM1584717 SRX840808 GSM1584718 SRP052077 SRS817483 GSM1584718 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584718 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584718 gds 301584718 GEO Accession GSM1584718 SRX840809 GSM1584719 SRP052077 SRS817486 GSM1584719 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584719 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584719 gds 301584719 GEO Accession GSM1584719 SRX840810 GSM1584720 SRP052077 SRS817487 GSM1584720 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584720 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584720 gds 301584720 GEO Accession GSM1584720 SRX840811 GSM1584721 SRP052077 SRS817488 GSM1584721 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584721 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584721 gds 301584721 GEO Accession GSM1584721 SRX840812 GSM1584722 SRP052077 SRS817489 GSM1584722 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584722 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584722 gds 301584722 GEO Accession GSM1584722 SRX840813 GSM1584723 SRP052077 SRS817491 GSM1584723 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584723 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584723 gds 301584723 GEO Accession GSM1584723 SRX840814 GSM1584724 SRP052077 SRS817490 GSM1584724 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584724 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584724 gds 301584724 GEO Accession GSM1584724 SRX840815 GSM1584725 SRP052077 SRS817494 GSM1584725 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584725 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584725 gds 301584725 GEO Accession GSM1584725 SRX840816 GSM1584726 SRP052077 SRS817492 GSM1584726 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584726 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584726 gds 301584726 GEO Accession GSM1584726 SRX840817 GSM1584727 SRP052077 SRS817495 GSM1584727 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584727 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584727 gds 301584727 GEO Accession GSM1584727 SRX840818 GSM1584728 SRP052077 SRS817493 GSM1584728 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584728 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584728 gds 301584728 GEO Accession GSM1584728 SRX840819 GSM1584729 SRP052077 SRS817496 GSM1584729 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584729 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584729 gds 301584729 GEO Accession GSM1584729 SRX840820 GSM1584730 SRP052077 SRS817497 GSM1584730 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584730 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584730 gds 301584730 GEO Accession GSM1584730 SRX840821 GSM1584731 SRP052077 SRS817500 GSM1584731 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584731 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584731 gds 301584731 GEO Accession GSM1584731 SRX840822 GSM1584732 SRP052077 SRS817499 GSM1584732 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584732 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584732 gds 301584732 GEO Accession GSM1584732 SRX840823 GSM1584733 SRP052077 SRS817498 GSM1584733 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584733 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584733 gds 301584733 GEO Accession GSM1584733 SRX840824 GSM1584734 SRP052077 SRS817501 GSM1584734 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584734 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584734 gds 301584734 GEO Accession GSM1584734 SRX840825 GSM1584735 SRP052077 SRS817502 GSM1584735 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584735 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584735 gds 301584735 GEO Accession GSM1584735 SRX840826 GSM1584736 SRP052077 SRS817504 GSM1584736 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584736 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584736 gds 301584736 GEO Accession GSM1584736 SRX840827 GSM1584737 SRP052077 SRS817503 GSM1584737 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584737 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584737 gds 301584737 GEO Accession GSM1584737 SRX840828 GSM1584738 SRP052077 SRS817505 GSM1584738 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584738 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584738 gds 301584738 GEO Accession GSM1584738 SRX840829 GSM1584739 SRP052077 SRS817506 GSM1584739 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584739 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584739 gds 301584739 GEO Accession GSM1584739 SRX840830 GSM1584740 SRP052077 SRS817507 GSM1584740 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584740 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584740 gds 301584740 GEO Accession GSM1584740 SRX840831 GSM1584741 SRP052077 SRS817509 GSM1584741 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584741 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584741 gds 301584741 GEO Accession GSM1584741 SRX840832 GSM1584742 SRP052077 SRS817508 GSM1584742 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584742 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584742 gds 301584742 GEO Accession GSM1584742 SRX840833 GSM1584743 SRP052077 SRS817511 GSM1584743 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584743 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584743 gds 301584743 GEO Accession GSM1584743 SRX840834 GSM1584744 SRP052077 SRS817510 GSM1584744 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584744 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584744 gds 301584744 GEO Accession GSM1584744 SRX840835 GSM1584745 SRP052077 SRS817513 GSM1584745 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584745 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584745 gds 301584745 GEO Accession GSM1584745 SRX840836 GSM1584746 SRP052077 SRS817512 GSM1584746 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584746 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584746 gds 301584746 GEO Accession GSM1584746 SRX840837 GSM1584747 SRP052077 SRS817514 GSM1584747 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584747 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584747 gds 301584747 GEO Accession GSM1584747 SRX840838 GSM1584748 SRP052077 SRS817515 GSM1584748 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584748 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584748 gds 301584748 GEO Accession GSM1584748 SRX840839 GSM1584749 SRP052077 SRS817516 GSM1584749 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584749 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584749 gds 301584749 GEO Accession GSM1584749 SRX840840 GSM1584750 SRP052077 SRS817519 GSM1584750 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584750 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584750 gds 301584750 GEO Accession GSM1584750 SRX840841 GSM1584751 SRP052077 SRS817518 GSM1584751 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584751 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584751 gds 301584751 GEO Accession GSM1584751 SRX840842 GSM1584752 SRP052077 SRS817517 GSM1584752 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584752 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584752 gds 301584752 GEO Accession GSM1584752 SRX840843 GSM1584753 SRP052077 SRS817520 GSM1584753 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584753 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584753 gds 301584753 GEO Accession GSM1584753 SRX840844 GSM1584754 SRP052077 SRS817522 GSM1584754 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584754 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584754 gds 301584754 GEO Accession GSM1584754 SRX840845 GSM1584755 SRP052077 SRS817521 GSM1584755 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps. The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. Illumina HiSeq 2000 GEO Sample GSM1584755 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1584755 gds 301584755 GEO Accession GSM1584755