SRX1960867 GSM2242157 SRP078939 PRJNA330391 SRS1570864 SAMN05417333 RNA-Seq TRANSCRIPTOMIC cDNA RNA was extracted using a protocol described previously (Baugh,DeModena, and Sternberg, Science vol 324, pp 92-94, 2009) except that 10 µl of a 20 mg ml-1 glycogen solution was used as a carrier Libraries were prepared from 10 µg of total RNA. PolyA+ RNA was purified using the Dynabeads mRNA purification kit (Ambion, 610-06) and fragmented using Fragmentation Reagent (Ambion, AM8740). First strand cDNA was synthesized from polyA+ RNA using the SuperScript III Reverse Transcriptase Kit (Life Technologies, 18080044) with random primers (Life Technologies, 48190-011). Second strand cDNA synthesis was performed using Second Strand Synthesis buffer, DNA Pol I, and RNase H (Life Technologies, 10812014, 18010025, 18021014). cDNA libraries were prepared for sequencing using the mRNA TruSeq protocol (Illumina). Illumina HiSeq 2000 gds 302242157 GSM2242157 GEO Accession GSM2242157 SRX1960868 GSM2242158 SRP078939 PRJNA330391 SRS1570865 SAMN05417334 RNA-Seq TRANSCRIPTOMIC cDNA RNA was extracted using a protocol described previously (Baugh,DeModena, and Sternberg, Science vol 324, pp 92-94, 2009) except that 10 µl of a 20 mg ml-1 glycogen solution was used as a carrier Libraries were prepared from 10 µg of total RNA. PolyA+ RNA was purified using the Dynabeads mRNA purification kit (Ambion, 610-06) and fragmented using Fragmentation Reagent (Ambion, AM8740). First strand cDNA was synthesized from polyA+ RNA using the SuperScript III Reverse Transcriptase Kit (Life Technologies, 18080044) with random primers (Life Technologies, 48190-011). Second strand cDNA synthesis was performed using Second Strand Synthesis buffer, DNA Pol I, and RNase H (Life Technologies, 10812014, 18010025, 18021014). cDNA libraries were prepared for sequencing using the mRNA TruSeq protocol (Illumina). Illumina HiSeq 2000 gds 302242158 GSM2242158 GEO Accession GSM2242158 SRX1960869 GSM2242159 SRP078939 PRJNA330391 SRS1570866 SAMN05417335 RNA-Seq TRANSCRIPTOMIC cDNA RNA was extracted using a protocol described previously (Baugh,DeModena, and Sternberg, Science vol 324, pp 92-94, 2009) except that 10 µl of a 20 mg ml-1 glycogen solution was used as a carrier Libraries were prepared from 10 µg of total RNA. PolyA+ RNA was purified using the Dynabeads mRNA purification kit (Ambion, 610-06) and fragmented using Fragmentation Reagent (Ambion, AM8740). First strand cDNA was synthesized from polyA+ RNA using the SuperScript III Reverse Transcriptase Kit (Life Technologies, 18080044) with random primers (Life Technologies, 48190-011). Second strand cDNA synthesis was performed using Second Strand Synthesis buffer, DNA Pol I, and RNase H (Life Technologies, 10812014, 18010025, 18021014). cDNA libraries were prepared for sequencing using the mRNA TruSeq protocol (Illumina). Illumina HiSeq 2000 gds 302242159 GSM2242159 GEO Accession GSM2242159 SRX1960870 GSM2242160 SRP078939 PRJNA330391 SRS1570867 SAMN05417336 RNA-Seq TRANSCRIPTOMIC cDNA RNA was extracted using a protocol described previously (Baugh,DeModena, and Sternberg, Science vol 324, pp 92-94, 2009) except that 10 µl of a 20 mg ml-1 glycogen solution was used as a carrier Libraries were prepared from 10 µg of total RNA. PolyA+ RNA was purified using the Dynabeads mRNA purification kit (Ambion, 610-06) and fragmented using Fragmentation Reagent (Ambion, AM8740). First strand cDNA was synthesized from polyA+ RNA using the SuperScript III Reverse Transcriptase Kit (Life Technologies, 18080044) with random primers (Life Technologies, 48190-011). Second strand cDNA synthesis was performed using Second Strand Synthesis buffer, DNA Pol I, and RNase H (Life Technologies, 10812014, 18010025, 18021014). cDNA libraries were prepared for sequencing using the mRNA TruSeq protocol (Illumina). Illumina HiSeq 2000 gds 302242160 GSM2242160 GEO Accession GSM2242160 SRX1960871 GSM2242161 SRP078939 PRJNA330391 SRS1570868 SAMN05417337 RNA-Seq TRANSCRIPTOMIC cDNA RNA was extracted using a protocol described previously (Baugh,DeModena, and Sternberg, Science vol 324, pp 92-94, 2009) except that 10 µl of a 20 mg ml-1 glycogen solution was used as a carrier Libraries were prepared from 10 µg of total RNA. PolyA+ RNA was purified using the Dynabeads mRNA purification kit (Ambion, 610-06) and fragmented using Fragmentation Reagent (Ambion, AM8740). First strand cDNA was synthesized from polyA+ RNA using the SuperScript III Reverse Transcriptase Kit (Life Technologies, 18080044) with random primers (Life Technologies, 48190-011). Second strand cDNA synthesis was performed using Second Strand Synthesis buffer, DNA Pol I, and RNase H (Life Technologies, 10812014, 18010025, 18021014). cDNA libraries were prepared for sequencing using the mRNA TruSeq protocol (Illumina). Illumina HiSeq 2000 gds 302242161 GSM2242161 GEO Accession GSM2242161 SRX1960872 GSM2242162 SRP078939 PRJNA330391 SRS1570869 SAMN05417338 RNA-Seq TRANSCRIPTOMIC cDNA RNA was extracted using a protocol described previously (Baugh,DeModena, and Sternberg, Science vol 324, pp 92-94, 2009) except that 10 µl of a 20 mg ml-1 glycogen solution was used as a carrier Libraries were prepared from 10 µg of total RNA. PolyA+ RNA was purified using the Dynabeads mRNA purification kit (Ambion, 610-06) and fragmented using Fragmentation Reagent (Ambion, AM8740). First strand cDNA was synthesized from polyA+ RNA using the SuperScript III Reverse Transcriptase Kit (Life Technologies, 18080044) with random primers (Life Technologies, 48190-011). Second strand cDNA synthesis was performed using Second Strand Synthesis buffer, DNA Pol I, and RNase H (Life Technologies, 10812014, 18010025, 18021014). cDNA libraries were prepared for sequencing using the mRNA TruSeq protocol (Illumina). Illumina HiSeq 2000 gds 302242162 GSM2242162 GEO Accession GSM2242162 SRX1960873 GSM2242163 SRP078939 PRJNA330391 SRS1570870 SAMN05417339 RNA-Seq TRANSCRIPTOMIC cDNA RNA was extracted using a protocol described previously (Baugh,DeModena, and Sternberg, Science vol 324, pp 92-94, 2009) except that 10 µl of a 20 mg ml-1 glycogen solution was used as a carrier Libraries were prepared from 10 µg of total RNA. PolyA+ RNA was purified using the Dynabeads mRNA purification kit (Ambion, 610-06) and fragmented using Fragmentation Reagent (Ambion, AM8740). First strand cDNA was synthesized from polyA+ RNA using the SuperScript III Reverse Transcriptase Kit (Life Technologies, 18080044) with random primers (Life Technologies, 48190-011). Second strand cDNA synthesis was performed using Second Strand Synthesis buffer, DNA Pol I, and RNase H (Life Technologies, 10812014, 18010025, 18021014). cDNA libraries were prepared for sequencing using the mRNA TruSeq protocol (Illumina). Illumina HiSeq 2000 gds 302242163 GSM2242163 GEO Accession GSM2242163 SRX1960874 GSM2242164 SRP078939 PRJNA330391 SRS1570871 SAMN05417340 RNA-Seq TRANSCRIPTOMIC cDNA RNA was extracted using a protocol described previously (Baugh,DeModena, and Sternberg, Science vol 324, pp 92-94, 2009) except that 10 µl of a 20 mg ml-1 glycogen solution was used as a carrier Libraries were prepared from 10 µg of total RNA. PolyA+ RNA was purified using the Dynabeads mRNA purification kit (Ambion, 610-06) and fragmented using Fragmentation Reagent (Ambion, AM8740). First strand cDNA was synthesized from polyA+ RNA using the SuperScript III Reverse Transcriptase Kit (Life Technologies, 18080044) with random primers (Life Technologies, 48190-011). Second strand cDNA synthesis was performed using Second Strand Synthesis buffer, DNA Pol I, and RNase H (Life Technologies, 10812014, 18010025, 18021014). cDNA libraries were prepared for sequencing using the mRNA TruSeq protocol (Illumina). Illumina HiSeq 2000 gds 302242164 GSM2242164 GEO Accession GSM2242164 SRX2638355 GSM2536181 SRP078939 PRJNA330391 SRS2046343 SAMN06579153 Hi-C GENOMIC other DNA was purified as in Rao et al. (2014) and sheared in a 130 µl microTUBE (Covaris, 520045) using an S2 Covaris (Covaris 520045) for 55s with duty cycle 10%, intensity 4, and 200 cycles/burst. 300-500bp fragments were selected as in Rao et al. (2014), except that 40 µl of AMPure XP beads were used for the second size selection step. Biotinylated fragments were pulled down according to Rao et al. (2014) and Dynabeads were washed in 100 ul 1X End-It DNA End-Repair Kit (Lucigen, ER81050) End-Repair buffer. Beads were resuspended in 100 µl of End-Repair Mix (10 µl 10X End-Repair buffer, 10 µl 2.4mM dNTP mix, 10 µl 10mM ATP, 2 µl End-Repair enzyme mix, 68 µl water) and incubated at room temperature for 45 min with gentle rotation. A-tailing and adapter ligation were performed as in Rao et al. (2014) using 2 µl NEXTflex DNA Barcode (Bioo Scientific, 514101). To avoid PCR inhibition, the beads were divided between seven 50 µl PCRs and amplified for 4-6 cycles using Phusion polymerase (Thermo Fischer Scientific, F-530L) and NEXTflex Primer Mix (Bioo Scientific, 514107-48). The final library was purified according to Rao et al. (2014). To verify successful Hi-C, 1 µl of the library was cloned using a Zero Blunt TOPO PCR cloning kit (Life Technologies, 450245), and 20-50 colonies were amplified and sequenced. If at least 50% of the fragments contained informative ligations, the library was sequenced using 100 bp paired end reads on a HiSeq4000 platform. A step-by-step version of this protocol will be available on our website. Illumina HiSeq 4000 gds 302536181 GSM2536181 GEO Accession GSM2536181 SRX2638356 GSM2536182 SRP078939 PRJNA330391 SRS2046348 SAMN06579154 Hi-C GENOMIC other DNA was purified as in Rao et al. (2014) and sheared in a 130 µl microTUBE (Covaris, 520045) using an S2 Covaris (Covaris 520045) for 55s with duty cycle 10%, intensity 4, and 200 cycles/burst. 300-500bp fragments were selected as in Rao et al. (2014), except that 40 µl of AMPure XP beads were used for the second size selection step. Biotinylated fragments were pulled down according to Rao et al. (2014) and Dynabeads were washed in 100 ul 1X End-It DNA End-Repair Kit (Lucigen, ER81050) End-Repair buffer. Beads were resuspended in 100 µl of End-Repair Mix (10 µl 10X End-Repair buffer, 10 µl 2.4mM dNTP mix, 10 µl 10mM ATP, 2 µl End-Repair enzyme mix, 68 µl water) and incubated at room temperature for 45 min with gentle rotation. A-tailing and adapter ligation were performed as in Rao et al. (2014) using 2 µl NEXTflex DNA Barcode (Bioo Scientific, 514101). To avoid PCR inhibition, the beads were divided between seven 50 µl PCRs and amplified for 4-6 cycles using Phusion polymerase (Thermo Fischer Scientific, F-530L) and NEXTflex Primer Mix (Bioo Scientific, 514107-48). The final library was purified according to Rao et al. (2014). To verify successful Hi-C, 1 µl of the library was cloned using a Zero Blunt TOPO PCR cloning kit (Life Technologies, 450245), and 20-50 colonies were amplified and sequenced. If at least 50% of the fragments contained informative ligations, the library was sequenced using 100 bp paired end reads on a HiSeq4000 platform. A step-by-step version of this protocol will be available on our website. Illumina HiSeq 4000 gds 302536182 GSM2536182 GEO Accession GSM2536182 SRX2958247 GSM2685183 SRP078939 PRJNA330391 SRS2315379 SAMN07279110 ChIP-Seq GENOMIC ChIP The embryo extract was prepared and the immunoprecipitation was perfromed as in Kruesi et al. (2013). For each sample, 6 μg of H4K20me1 antibody was used for 2 mg embryo extract. The library construction was performed as in Kruesi et al. (2013). Illumina HiSeq 4000 gds 302685183 GSM2685183 GEO Accession GSM2685183 SRX2958248 GSM2685184 SRP078939 PRJNA330391 SRS2315380 SAMN07279115 ChIP-Seq GENOMIC ChIP The embryo extract was prepared and the immunoprecipitation was perfromed as in Kruesi et al. (2013). For each sample, 6 μg of H4K20me1 antibody was used for 2 mg embryo extract. The library construction was performed as in Kruesi et al. (2013). Illumina HiSeq 4000 gds 302685184 GSM2685184 GEO Accession GSM2685184 SRX2958249 GSM2685185 SRP078939 PRJNA330391 SRS2315381 SAMN07279114 ChIP-Seq GENOMIC ChIP The embryo extract was prepared and the immunoprecipitation was perfromed as in Kruesi et al. (2013). For each sample, 6 μg of H4K20me1 antibody was used for 2 mg embryo extract. The library construction was performed as in Kruesi et al. (2013). Illumina HiSeq 4000 gds 302685185 GSM2685185 GEO Accession GSM2685185