SRX818465 GSM1569033 SRP051376 SRS798519 GSM1569033 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569033 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569033 gds 301569033 GEO Accession GSM1569033 SRX818466 GSM1569034 SRP051376 SRS798520 GSM1569034 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569034 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569034 gds 301569034 GEO Accession GSM1569034 SRX818467 GSM1569035 SRP051376 SRS798521 GSM1569035 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569035 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569035 gds 301569035 GEO Accession GSM1569035 SRX818468 GSM1569036 SRP051376 SRS798522 GSM1569036 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569036 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569036 gds 301569036 GEO Accession GSM1569036 SRX818469 GSM1569037 SRP051376 SRS798523 GSM1569037 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569037 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569037 gds 301569037 GEO Accession GSM1569037 SRX818470 GSM1569038 SRP051376 SRS798524 GSM1569038 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569038 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569038 gds 301569038 GEO Accession GSM1569038 SRX818471 GSM1569039 SRP051376 SRS798525 GSM1569039 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569039 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569039 gds 301569039 GEO Accession GSM1569039 SRX818472 GSM1569040 SRP051376 SRS798526 GSM1569040 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569040 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569040 gds 301569040 GEO Accession GSM1569040 SRX818473 GSM1569041 SRP051376 SRS798527 GSM1569041 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569041 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569041 gds 301569041 GEO Accession GSM1569041 SRX818474 GSM1569042 SRP051376 SRS798528 GSM1569042 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569042 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569042 gds 301569042 GEO Accession GSM1569042 SRX818475 GSM1569043 SRP051376 SRS798529 GSM1569043 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569043 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569043 gds 301569043 GEO Accession GSM1569043 SRX818476 GSM1569044 SRP051376 SRS798530 GSM1569044 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569044 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569044 gds 301569044 GEO Accession GSM1569044 SRX818477 GSM1569045 SRP051376 SRS798531 GSM1569045 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569045 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569045 gds 301569045 GEO Accession GSM1569045 SRX818478 GSM1569046 SRP051376 SRS798532 GSM1569046 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569046 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569046 gds 301569046 GEO Accession GSM1569046 SRX818479 GSM1569047 SRP051376 SRS798533 GSM1569047 RNA-Seq TRANSCRIPTOMIC cDNA The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA). Illumina HiSeq 2000 GEO Sample GSM1569047 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1569047 gds 301569047 GEO Accession GSM1569047