title: E6.5_P2_Cell_8_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_7_embryo4_single

status: Public on Jun 28 2017

type: SRA

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: G&T-Seq - (SMARTSEQ2)

library_source: transcriptomic

data_processing:
Libraries were sequenced with 2x100bp paired-end reads on a HiSeq2500 platform.
Reads were trimmed using Trim Galore v0.4.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the mouse GRCm38 genome assembly using HISAT2 v2.0.5. BAM files were imported to Seqmonk v1.37.0 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Raw read counts per transcript were calculated using the RNA-Seq quantitation pipeline.
Genome_build: GRCm38
Supplementary_files_format_and_content: The Quantitated RNA-Seq report file is tab delimited and contains the following columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (7) mRNA ID (Ensembl) (8) Gene ID (Ensembl) (9) Description (Ensembl); (10) Type; (11) Orientation; (12) Distance; (13-end) raw counts

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
E3.5 blastocysts were flushed from the uterus using M2 medium and the zonae removed by short incubation in Acid tyrodes solution. Embryos at E4.5 were dissected from nascent decidua. The trophectoderm was eliminated from E3.5 and E4.5 by immunosurgery (Solter and Knowles, 1975). Embryos were incubated for 15-30 min in 20% anti mouse anti serum in N2B27 (made in house), rinsed 3 times in N2B27 and transferred to 20% freshly thawed rat serum in N2B27 for 15-30 min. Lysed trophectoderm was removed manually by repeated aspiration using a mouth-controlled finely drawn Pasteur pipette just bigger than the ICM. Isolated ICMs were placed individually in 20 µL drops of AccutaseTM in a bacteriological dish for at least 5 min until they assumed a blackberry-like appearance. They were transferred to similar sized drops of M2 and aspirated repeatedly using a very finely drawn Pasteur pipette to separate the cells. Cells were immediately placed individually into wells of lysis buffer and frozen. E5.5 embryos were dissected manually and were observed to be early E5.5 cells lacking distinct thickening of the visceral endoderm (pre-AVE migration). The extra embryonic ectoderm was removed using the tip of a pulled Pasteur pipette. The epiblast was separated from overlying visceral endoderm by aspiration, distal end first, with a pulled Pasteur pipette with diameter just bigger than the epiblast. Both epiblast and visceral endoderm were separately disaggregated and plated into wells as described above for ICMs.  E6.5 embryos were visually staged as early streak (Downs and Davies, 1993) and dissected from decidua in PBS and placed into M2 solution to remove extra embryonic tissues. Differences in dissection may contribute to different proportions of primitive streak and epiblast cells obtained at E6.5. The embryonic ectodermal portion of the early streak embryo was dissociated in drops of AccutaseTM at room temperature and upon partial digestion was fully dissociated by repeated aspiration using a very finely drawn, mouth controlled, siliconised glass needle. Cells were assigned as single, doublets or multiples by visual inspection and placed directly into lysis solution and frozen prior to library generation.
mRNA from isolated single cells was isolated and amplified using the bead based capture and amplification previously described in the G&T-seq protocol which incorporates SMARTSEQ2.
Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol and 100bp paired end sequencing was performed on an Illumina Hiseq2500 instrument.

tag: developmental stage

tag: tissue

value: Mouse Embryo

tag: strain

tag: genotype

value: Wild Type


title: E6.5_P2_Cell_72_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_71_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_67_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_68_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_69_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_64_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_70_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_66_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_60_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_53_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_5_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_47_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_45_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_24_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_48_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_43_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_20_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell3_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_3_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_38_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_36_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_39_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_37_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_34_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_32_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_31_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_4_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_30_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_29_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_44_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_23_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_21_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_25_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_40_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_28_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P3_Cell_27_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_24_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_22_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_26_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_42_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_20_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_18_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell90_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell82_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_16_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_19_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_12_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell7_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_13_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_10_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell92_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell93_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell78_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell77_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell74_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell72_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell69_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell83_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell8_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell73_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell76_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P2_Cell_17_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell59_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell79_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell64_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell80_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell67_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell62_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell66_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell51_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell52_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell91_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell50_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell53_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell3_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell38_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell36_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell35_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell31_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.75_cell40_Embryo1_Single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell39_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell65_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell22_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell2_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell94_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell95_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell13_embryo1_double

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell85_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell91_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell84_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell96_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell82_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell80_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell72_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell70_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell71_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell68_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell58_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell59_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell46_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell47_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell44_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell36_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell43_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell48_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell41_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell39_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell34_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell52_embryo1_double

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell35_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell26_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell31_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell32_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell83_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell22_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell23_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell63_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell60_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell10_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell11_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell9_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell19_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell53_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell8_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell7_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell74_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell24_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell72_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell70_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell71_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell66_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_cell12_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell65_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell62_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell6_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell56_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell58_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell54_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell55_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell59_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell3_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell52_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell51_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell34_embryo3_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell33_embryo3_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell32_embryo3_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell30_embryo3_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell2_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell27_embryo3_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell73_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell26_embryo3_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell68_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell23_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell22_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell28_embryo3_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell20_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell21_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell181_embryo6_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell180_embryo6_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell182_embryo6_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell63_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell179_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell172_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell173_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell171_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell178_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell169_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell168_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell167_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell166_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell165_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell163_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell161_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell162_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell160_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell158_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell15_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell183_embryo6_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell174_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell157_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell156_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell155_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell175_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell14_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell153_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell145_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell13_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell150_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell148_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell125_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell146_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell12_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell118_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell99_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell10_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell11_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell164_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell8_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell6_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell55_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell7_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell4_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell48_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell47_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E6.5_P1_Cell81_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell44_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell39_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell31_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell36_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell30_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell2_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P7.P4.P5_cell151_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell25_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell18_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell27_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell19_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell20_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell1_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell21_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell5_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell15_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell14_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell148_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell146_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell144_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell143_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell141_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell142_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell140_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell145_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell139_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell136_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell135_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell137_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell133_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell134_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell23_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell131_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell130_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell147_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell129_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell128_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell127_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell125_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell126_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell123_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell120_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell119_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell117_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell115_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell132_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell100_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell112_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell101_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell108_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell10_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell8_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell110_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell7_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell5_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell46_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell45_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell43_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell47_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell42_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell44_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell41_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell121_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell40_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell3_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell39_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell37_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell9_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell35_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell111_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell33_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell36_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell34_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell32_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell27_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell26_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell21_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell30_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell22_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell25_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell24_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell20_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell17_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell16_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell1_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell14_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell15_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell19_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell38_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell10_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell98_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell99_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell96_embryo7_VE

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell97_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell11_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell93_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell94_embryo7_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell23_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell89_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell92_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P1_cell2_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell84_embryo7_VE

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell85_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell77_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell80_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell82_embryo7_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell79_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell78_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell74_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell73_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell72_embryo7_VE

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell70_embryo7_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell6_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell67_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell65_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell66_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell64_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell61_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell62_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell60_embryo7_VE

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell54_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell53_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell58_embryo7_double

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell57_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell56_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell52_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell55_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell46_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell76_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell49_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell34_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell33_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell68_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell37_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell32_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell26_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell2_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell44_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell15_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell27_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell25_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell36_embryo7_VE

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell22_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell5_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell17_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell40_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell144_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell143_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell132_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell135_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell141_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell139_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell142_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell136_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell134_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell133_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell138_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell137_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell130_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell131_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell128_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell129_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell127_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell126_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell124_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell120_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell123_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell119_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell121_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell140_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell116_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell113_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell114_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell112_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell108_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell102_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell103_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell109_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell105_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell107_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell104_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell110_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell125_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell9_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell101_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell94_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell95_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell89_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell93_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell92_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell88_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell8_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell82_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell83_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell87_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell80_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell7_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell85_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell111_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell79_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell81_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P11.P6.P10_cell100_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E5.5_P2.P3_cell13_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell78_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell77_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell67_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell73_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell69_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell71_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell75_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell66_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell6_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell64_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell63_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell62_embryo3_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell61_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell57_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell59_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell5_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell53_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell54_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell50_embryo3_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell51_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell55_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell49_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell47_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell46_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell52_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell45_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell43_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell44_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell65_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell76_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell42_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell39_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell56_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell3_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell38_embryo3_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell35_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell33_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell37_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell40_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell30_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell2_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell31_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell28_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell29_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell23_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell25_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell15_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell14_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell16_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell13_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell11_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell19_embryo4_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell41_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell91_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell85_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell90_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell7_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell79_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell8_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell68_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell73_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell78_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell74_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell26_embryo3_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P2_Cell22_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell62_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell86_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell55_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell50_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell51_embryo1_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell38_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell92_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell37_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell33_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell67_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell32_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell2_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell28_embryo1_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell25_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell21_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell1_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell20_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell19_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell61_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell49_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell27_embryo1_double

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell90_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell92_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell89_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell8_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell94_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell87_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell44_embryo2_double

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell9_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell13_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell85_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell83_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E4.5_P1_Cell39_embryo1_double

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell86_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell81_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell80_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell78_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell77_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell74_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell73_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell75_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell70_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell6_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell69_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell68_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell82_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell66_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell65_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell63_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell61_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell52_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell62_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell5_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell54_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell59_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell4_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell50_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell58_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell53_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell56_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell49_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell45_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell46_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell71_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell47_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell42_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell41_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell40_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell39_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell3_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell36_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell37_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell57_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell38_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell35_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell34_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell51_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell30_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell33_embryo8_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell43_embryo7_double

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell22_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell25_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell27_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell23_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell26_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell24_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell16_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell29_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell28_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell1_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell14_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell17_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell15_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell13_embryo6_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell12_embryo9_double

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell10_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell11_embryo9_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P8_Cell91_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P8_Cell87_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P8_Cell80_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P8_Cell7_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P9_Cell18_embryo7_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P8_Cell70_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P8_Cell65_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: Riboseq_drpl9a_rep3

city: Basel

first: Joao

middle: C

last: Guimaraes

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rpl9a::kanMX4
rpko_expression_profiles.csv
rpko_ribseq_counts.csv

data_processing:
Library strategy: Ribo-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to transcriptome based on the CDS annotations from the yeast database (http://www.yeastgenome.org) and the 5’/3’UTR mappings from Ref. (Nagalakshmi et al., 2008) using segemehl v0.1.7-411 with parameters --accuracy 90
Transcript counts were calculated based on uniquely mapped reads and used to estimate differential expression by DESeq2. Ribosome density foldchange was calculated using the ratio Riboseq foldchange by mRNAseq foldchange.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include read counts and fold-change for each strain

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: Yeast was grown on YPD (1% yeast extract, 2% peptone and 2% glucose) medium at 30°C, 200 rpm unless otherwise stated. The cells were collected in mid-log phase at OD600 0.4-0.8.

extract_protocol:
A yeast cell pellet was resuspended in 1 ml of lysis buffer from Dynabeads® mRNA DIRECTTM Kit (61011, Life technologies) and lysed at 4°C with 1 volume of acid washed glass beads in a FastPrep instrument (Thermo Scientific) using 2 cycles with the following settings; 45 s at 6.5 speed with 3 min pause on ice between each cycle.
Libraries for mRNA sequencing were prepared using the “directional mRNAseq sample preparation” protocol from Illumina with minor modifications. Polysome profiling and sequencing of ribosome-protected mRNA fragments were performed according to protocol described in (Nedialkova and Leidel, 2015).

treatment_protocol: For ribosome profiling cells were treated with cycloheximide 100ug/ml for 1 minute.

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rpl9a::kanMX4


title: E3.5_P8_Cell79_embryo4_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P8_Cell61_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P8_Cell63_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P8_Cell5_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P8_Cell3_embryo2_single

description: G&T-Seq - (SMARTSEQ2)


title: Riboseq_drpl9a_rep2


title: Riboseq_drps27b_rep3

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rps27b::kanMX4
rpko_expression_profiles.csv
rpko_ribseq_counts.csv

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rps27b::kanMX4


title: Riboseq_drps27b_rep2


title: E3.5_P8_Cell2_embryo1_single

description: G&T-Seq - (SMARTSEQ2)


title: Riboseq_drpl7a_rep2

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rpl7a::kanMX4
rpko_expression_profiles.csv
rpko_ribseq_counts.csv

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rpl7a::kanMX4


title: Riboseq_drps27b_rep1


title: E3.5_P8_Cell58_embryo5_double

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P8_Cell22_embryo5_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P8_Cell25_embryo1_double

description: G&T-Seq - (SMARTSEQ2)


title: Riboseq_drpl9a_rep1


title: E3.5_P11.P6.P10_cell189_embryo_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P11.P6.P10_cell190_embryo_single

description: G&T-Seq - (SMARTSEQ2)


title: Riboseq_drpl6a_rep2

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rpl6a::kanMX4
rpko_expression_profiles.csv
rpko_ribseq_counts.csv

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rpl6a::kanMX4


title: Riboseq_drpl7a_rep1


title: Riboseq_drpl15b_rep3

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rpl15b::kanMX4
rpko_expression_profiles.csv
rpko_ribseq_counts.csv

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rpl15b::kanMX4


title: E3.5_P8_Cell77_embryo3_single

description: G&T-Seq - (SMARTSEQ2)


title: Riboseq_drpl15b_rep2


title: Riboseq_drpl15b_rep1


title: E3.5_P11.P6.P10_cell186_embryo_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P11.P6.P10_cell184_embryo_single

description: G&T-Seq - (SMARTSEQ2)


title: E3.5_P11.P6.P10_cell185_embryo_single

description: G&T-Seq - (SMARTSEQ2)


title: Riboseq_drpl7a_rep3


title: E3.5_P11.P6.P10_cell183_embryo_single

description: G&T-Seq - (SMARTSEQ2)


title: Riboseq_wt_rep3

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0
rpko_expression_profiles.csv
rpko_ribseq_counts.csv

source_name: wt

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: Riboseq_wt_rep2


title: Riboseq_wt_rep1


title: E3.5_P11.P6.P10_cell181_embryo_single

description: G&T-Seq - (SMARTSEQ2)


title: VV FST Lo TRAP

city: New York

first: Jordan

last: Marrocco

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

description: High and Low E2 Stress Raw Counts.xlsx

data_processing:
Library strategy: TRAP-Seq
Raw reads were trimmed to remove sequencing artefacts (10bp from 5’ end) and filtered to remove low quality reads (read with a quality score < 20 in more than 10% of bases were discarded)
Aligned to mouse genome (mm10) using TopHat2
Differential expression analysis was conducted with Strand NGS software (Agilent Technologies,USA), in which DESeq was used to quantify transcript reads and obtain Z scores and fold change values for individual genes. Genes with p<0.001, Benjamini-Hochberg corrected and fold change greater than 1.5 were selected for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: "Male Female BDNF Stress Raw Counts.xlsx" and "High and Low E2 Stress Raw Counts.xlsx" report Raw counts of genes.  The two .xlsx files represent two separate analyses with some samples overlapping.

source_name: Hippocampus - CA3

extract_protocol:
After a 40-minute recovery period, mice were cervical dislocated, immediately decapitated, brains were removed and hippocampi were fresh dissected and prepared for TRAP protocol.Translating Ribosome Affinity Purification (TRAP)  of CA3 Neurons was performed as described by Heiman et al
A total of 200ng of RNA per group was prepared for sequencing by The Rockefeller University Genomics Core Facility using the TrueSeq RNA Sample Preparation Kit v2 (Illumina, USA). The samples were barcoded to allow for multiplexing within a flow cell lane. Barcoded cDNA libraries were sequenced on an Illumina HiSeq 2500 in a single lane to obtain 100-bp single-end reads at an approximate sequencing depth of 25–35 million reads per sample.

treatment_protocol: Mice were subjected to a six-minute swimming task in a 4L-graduated cylinder containing 2500 mL of room-temperature water. Control mice were left undisturbed in their home cage.

value: Hippocampus

tag: cell type

value: CA3 neurons

tag: Sex

value: Female

tag: stress protocol

value: FST

tag: estradiol level

value: Low (metestrus)


title: M VM TRAP

description: Male Female BDNF Stress Raw Counts.xlsx

value: Male

value: BDNF Met/+


title: Riboseq_drpl6a_rep1


title: E3.5_P11.P6.P10_cell187_embryo_single

description: G&T-Seq - (SMARTSEQ2)


title: M VM FST TRAP

description: Male Female BDNF Stress Raw Counts.xlsx


title: T3_To_r3

city: Lausanne

first: Dominique

last: Sanglard

address: Rue Bugnon 48

institute: University of Lausanne and University Hospital Center

data_processing:
Sequencing data were processed using Illumina Pipeline software. Reads were filtered, trimmed, and counts align to the SC5314 C. albicans reference genome using CLC workbench pipeline. The numbers of read counts per gene locus was extracted
Data normalization and gene expression analysis were performed in R (v3.2.3), using Bioconductor packages. The read count data were normalized using TMM (trimmed mean of M-values) method available in the R package edgeR and transformed into log2 counts per million by Voom method from R package Limma. This package was then used to apply a linear model with one factor per condition (4 conditions: untreated 1h, tomatidine-treated 1h, untreated 3h, tomatidine-treated 3h (all in triplicates)) to the transformed data. Two contrasts representing the difference between tomatidine-treated and untreated cells at each drug exposure time (1- and 3 h) were extracted from the linear model to result in a moderated t statistic for all genes expressed.
Genome_build: SC5314 C. albicans reference genome
Supplementary_files_format_and_content: Excel data sheets; Gene counts, Voom normalized gene expression, 1- and 3-h tomatidine treatment

organism: Candida albicans

source_name: Tomatidine-treated 3 h

growth_protocol: Overnight YPD culture of C. albicans SC5314 strain was diluted 1:200 in 5 ml YPD media and incubated under agitation at 30° C until early exponential growth phase (OD540 = 0.3).

extract_protocol:
Total RNA was extracted after 1 h or 3 h tomatidine/solvent exposure by mechanical disruption of the cells with glass beads. Experiments were carried out in triplicates with 12 samples
Total RNA extracts were treated with DNase using the DNA-free kit (Ambion-Life Technologies, Zug, Switzerland) and RNA quality and integrity was verified with Fragment Analyzer™ Automated CE System (Advanced Analytical). One µg of RNA was used to create sequencing libraries through standard Illumina TruSeq stranded mRNA protocol. Each library (sample) received a different index enabling several libraries to be multiplexed. Before RNA sequencing, libraries were analyzed with a fragment analyzer to assess quality and fragment size and with a Qubit fluorometer (Invitrogen) to determine cDNA concentration. Libraries were kept at −20°C until sequencing. The 12 libraries were run on Illumina HiSeq platerform (HiSeq2500)

treatment_protocol: Fifty µl of solvent (DMSO) or 250 µM tomatidine (diluted in DMSO) were added to the culture to reach a concentration 1% DMSO and 2.5 µM tomatidine

tag: exposure time


title: VV TRAP Lo

description: High and Low E2 Stress Raw Counts.xlsx


title: T1_To_r3

source_name: Tomatidine-treated 1 h


title: T3_To_r2


title: VV FST TRAP

description:
Male Female BDNF Stress Raw Counts.xlsx
High and Low E2 Stress Raw Counts.xlsx


title: T3_nt_r3

source_name: Untreated for 3 h


title: T1_To_r2


title: VV TRAP


title: T3_To_r1


title: T1_To_r1


title: T3_nt_r2


title: VM Hi TRAP

description: Male Female BDNF Stress Raw Counts.xlsx

value: High (estrus)


title: VV FST Hi TRAP


title: F Hi VM FST TRAP

description: Male Female BDNF Stress Raw Counts.xlsx


title: VV TRAP Hi


title: E3.5_P11.P6.P10_cell182_embryo_single

description: G&T-Seq - (SMARTSEQ2)


title: T1_nt_r3

source_name: Untreated for 1 h


title: AGM3_84

city: Madiosn

first: Jue

last: Zhang

state: WI

address: 330 N orchard st

institute: Morgridge Institute for Research

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38593
Barcode: GTAGAGGA-AAGGAGTA

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed for adapter sequence and quality. Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing a matrix of RNA expression estimates reported by RSEM in Transcripts Per Million (TPM)

source_name: CD31+CD144+CD41-CD45- cells were isolated from E11.5 mouse AGM

extract_protocol:
Single-cell suspensions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system.
diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina). Libraries were multiplexed at 24 libraries per lane, and single-end reads of 67-bp sequencing was performed on an Illumina HiSeq 2500 system.

tag: facs sorting


title: AGM3_83

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38592
Barcode: AAGAGGCA-AAGGAGTA


title: T1_nt_r2


title: T1_nt_r1


title: AGM3_81

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38590
Barcode: GCTACGCT-AAGGAGTA


title: ESCs rep2_RNA-seq

city: Shanghai

first: Jian

last: Hu

address: 1239,Siping Road

country: China

institute: Tongji University

data_processing:
Illumina software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 genome assembly using Tophat v2.0.13 with default parameters
Uniquely mapped pairs were retained using the following commond: samtools view -hf 0x2 accepted_hits.bam |perl -ne 'print if (/^@/||/NM:i:(\d+)/ &&$1<5);'|samtools view -bS - >paired_uniq.bam
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a Cufflinks v2.2.1. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files include FPKM values for each Sample

source_name: Embryonic stem cells

growth_protocol: Mouse ESCs, 4F-iPSCs and CiPSCs were maintained on feeder layers of mitomycin C-treated MEFs in an ESC culture medium containing DMEM high glucose (Gibco),15%fetal bovine serum (FBS,Gicco), 1% GlutaMAXTM-I (Invitrogen), 1% nonessential amino acids (NEAA, Invitrogen), sodium pyruvate, 0.055 mM 2-mercaptoethanol (Invitrogen), 1%penicillin-streptomycin (Invitrogen) ,1,000 U/ml leukemia inhibitory factor (LIF, Millipore) and supplemented with 2i (3 μM CHIR99021 and 1 μM PD0325901)

extract_protocol:
Total RNA  was collected using the TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The feeder layers were removed on gelatin-coated plates before collecting cells.

value: Mouse embryonic stem cells E14

tag: gender

value: male

tag: passage


title: AGM3_80

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38589
Barcode: CAGAGAGG-AAGGAGTA


title: 4F-iPSCs rep1_RNA-seq

value: Transcriptional factors induced pluripotent stem cells from mouse fibroblasts


title: AGM3_79

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38588
Barcode: CTCTCTAC-AAGGAGTA


title: AGM3_82

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38591
Barcode: CGAGGCTG-AAGGAGTA


title: CiPSCs rep2_RNA-seq

source_name: Chemical induced pluripotent stem cells

value: Chemical induced pluripotent stem cells from mouse fibroblasts


title: AGM3_78

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38587
Barcode: TAGGCATG-AAGGAGTA


title: AGM3_77

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38586
Barcode: GGACTCCT-AAGGAGTA


title: T3_nt_r1


title: AGM3_76

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38585
Barcode: TCCTGAGC-AAGGAGTA


title: ESCs rep1_RNA-seq


title: 4F-iPSCs rep2_RNA-seq

source_name: Transcriptional factors induced pluripotent stem cells


title: AGM3_72

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38581
Barcode: GTAGAGGA-ACTGCATA


title: AGM3_71

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38580
Barcode: AAGAGGCA-ACTGCATA


title: AGM3_73

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38582
Barcode: TAAGGCGA-AAGGAGTA


title: nsRNA_seq_TRPexp_aB_ETO_TRIPTOLIDE

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

library_source: genomic

data_processing:
Library strategy: nascent RNA-seq
Reads were aligned to the GRCm38p2/mm10 genome assembly
Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 3 -m1 -l 50
Peaks were called using the parameters: --nolambda,-- nomodel.
Genome_build: GRCm38p2/mm10
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

molecule: genomic DNA

source_name: Activated primary B cells

extract_protocol:
B cell cultures stimulated for 12 hours and T cell cultures for 4 hours. Resting B cells were incubated in media without stimulation. 4 million labeled with 0.5 mM 5-ethynyl uridine (EU) for 30 minutes at 37°C. For B-cells DRB (D-ribofuranosylbenzimidazole) (150 μM) or Triptolide (3 μM) was added to 90 minutes prior to EU labeling, and etoposide was present in the medium 5 minutes before and during the EU labeling (30 minutes). Total RNA extraction was performed using TRIzol (Ambion) and 1 ug of RNA as used. Ribosomal RNA was depleted using the NEBNext rRNA Depletion kit (human/mouse/rat) (New England Biosciences), prior to biotinylation by the Click-it reaction (Click-iT Nascent RNA Capture Kit, ThermoFisher C10365). First-strand cDNA synthesis of the captured nascent RNA was done using SuperScript VILO cDNA synthesis kit (Invitrogen), second-strand cDNA was synthesized with 10 mM dNTPs in the presence of RNase H, E. coli DNA polymerase I (Invitrogen) and sequencing libraries were prepared following the TruSeq RNA sample prep protocol (Illumina).
libraries were prepared and sequenced following standard Illumina protocols

value: Activated primary B cells

value: WT


title: nsRNA_seq_TRPexp_aB_ETO


title: AGM3_68

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38577
Barcode: CAGAGAGG-ACTGCATA


title: AGM3_67

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38576
Barcode: CTCTCTAC-ACTGCATA


title: AGM3_69

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38578
Barcode: GCTACGCT-ACTGCATA


title: nsRNA_seq_T_NT_2

source_name: primary T cells

value: primary T cells


title: nsRNA_seq_rB_NT

source_name: Resting primary B cells

value: Resting primary B cells


title: nsRNA_seq_T_NT_1


title: AGM3_66

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38575
Barcode: TAGGCATG-ACTGCATA


title: AGM3_74

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38583
Barcode: CGTACTAG-AAGGAGTA


title: AGM3_65

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38574
Barcode: GGACTCCT-ACTGCATA


title: CiPSCs rep1_RNA-seq


title: nsRNA_seq_DRBexp_aB_NT_DRB


title: nsRNA_seq_DRBexp_aB_NT


title: nsRNA_seq_TRPexp_aB_NT


title: AGM3_70

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38579
Barcode: CGAGGCTG-ACTGCATA


title: ChIP_seq_TOP2B_MEF_top2bKO

data_processing:
Reads were aligned to the GRCm38p2/mm10 genome assembly.
Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 2 -m1 -l 50
ChIP-seq peaks were called againts input samples using default parameters.
Genome_build: GRCm38p2/mm10
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

source_name: Mouse embryonic fibroblasts

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 2 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using the Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or using the Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. Ten microgram of respective antibody was incubated with 40 μl of Dynabeads Protein A (or G) for 15 min at room temperature. Antibody-bound beads were added to 1 ml of sonicated chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo). The library was prepared using the Ovation SP Ultralow library system (Nugen). 75 cycles of sequencing data were acquired on and Nextseq550 (Illumina). Antibodies for ChiP-seq were: anti-RAD21 (ab992, Abcam), anti-CTCF (07-729, Millipore), Topo IIβ Antibody (H-286) (sc13059, SantaCruz) and Topoisomerase II alpha antibody (EP1102Y) (ab52934, Abcam)
libraries were prepared and sequenced following standard Illumina protocols

value: Mouse embryonic fibroblasts


title: AGM3_61

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38570
Barcode: TAAGGCGA-ACTGCATA


title: nsRNA_seq_DRBexp_aB_ETO_DRB


title: ChIP_seq_TOP2B_aB24h


title: AGM3_64

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38573
Barcode: TCCTGAGC-ACTGCATA


title: AGM3_62

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38571
Barcode: CGTACTAG-ACTGCATA


title: AGM3_60

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38569
Barcode: GTAGAGGA-GTAAGGAG


title: AGM3_59

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38568
Barcode: AAGAGGCA-GTAAGGAG


title: AGM3_63

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38572
Barcode: AGGCAGAA-ACTGCATA


title: nsRNA_seq_DRBexp_aB_ETO


title: AGM3_58

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38567
Barcode: CGAGGCTG-GTAAGGAG


title: ChIP_seq_TOP2A_MEF_top2bKO


title: ChIP_seq_TOP2B_aB12h


title: ChIP_seq_TOP2B_MEF


title: AGM3_57

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38566
Barcode: GCTACGCT-GTAAGGAG


title: AGM3_55

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38564
Barcode: CTCTCTAC-GTAAGGAG


title: ChIP_seq_TOP2A_aB24h


title: ChIP_seq_TOP2A_MEF


title: ChIP_seq_TOP2A_aB12h


title: AGM3_56

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38565
Barcode: CAGAGAGG-GTAAGGAG


title: AGM3_75

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38584
Barcode: AGGCAGAA-AAGGAGTA


title: AGM3_54

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38563
Barcode: TAGGCATG-GTAAGGAG


title: ChIP_seq_RAD21_T

source_name: Primary T cells

value: Primary T cells


title: AGM3_53

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38562
Barcode: GGACTCCT-GTAAGGAG


title: ChIP_seq_RAD21_MEF


title: ChIP_seq_RAD21_rB


title: AGM3_52

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38561
Barcode: TCCTGAGC-GTAAGGAG


title: AGM3_51

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38560
Barcode: AGGCAGAA-GTAAGGAG


title: ChIP_seq_RAD21_aB


title: AGM3_49

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38558
Barcode: TAAGGCGA-GTAAGGAG


title: AGM3_48

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38557
Barcode: GTAGAGGA-AGAGTAGA


title: ChIP_seq_CTCF_T


title: AGM3_46

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38555
Barcode: CGAGGCTG-AGAGTAGA


title: AGM3_45

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38554
Barcode: GCTACGCT-AGAGTAGA


title: AGM3_50

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38559
Barcode: CGTACTAG-GTAAGGAG


title: AGM3_47

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38556
Barcode: AAGAGGCA-AGAGTAGA


title: ChIP_seq_CTCF_MEF


title: ChIP_seq_CTCF_aB


title: END_seq_TRPexp_aB12h_NT

data_processing:
Library strategy: END-seq
mouse and human END-seq reads were aligned to the GRCm38p2/mm10 and  GRCh37/hg19 genome assemblies,respectively.
Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 3 -k1 -l 50
END-seq peaks were called using the parameters: --nolambda,-- nomodel and –keep-dup=all (keep all redundant reads). For Etoposide-treated END-seq data peak calling, we used the corresponding non-treated samples as control, keeping >10 fold-enriched peaks.
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

extract_protocol:
Single cell suspensions of B-cells (15 million per agarose plug), pre-B cells (40 million per agarose plug), T-cells (15 million per agarose plug), MEFS (4 million per agarose plug), neurons (5 million per agarose plug), MCF7 (5 million per agarose plug) and Nalm6 (15 million per agarose plug) were washed in PBS, embedded in agarose and transferred into plug molds (Bio-Rad CHEF Mammalian Genomic DNA plug kit) and processed as previously described (Canela et al., 2016). Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).
libraries were prepared and sequenced following standard Illumina protocols


title: END_seq_TRPexp_aB12h_TRIPTOLIDE


title: END_seq_TRPexp_aB12h_ETO_TRIPTOLIDE

description: Control: aB12h_TRIPTOLIDE


title: AGM3_43

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38552
Barcode: CTCTCTAC-AGAGTAGA


title: AGM3_42

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38551
Barcode: TAGGCATG-AGAGTAGA


title: AGM3_41

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38550
Barcode: GGACTCCT-AGAGTAGA


title: END_seq_TRPexp_aB12h_ETO

description: Control: aB12h_NT


title: END_seq_T_ETO

description: Control: T_NT


title: END_seq_T_NT


title: END_seq_Species_Mus_aB12h_NT


title: AGM3_38

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38547
Barcode: CGTACTAG-AGAGTAGA


title: ChIP_seq_CTCF_rB


title: AGM3_39

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38548
Barcode: AGGCAGAA-AGAGTAGA


title: END_seq_Species_Mus_aB12h_ETO

description: Control: Mus_aB12h_NT


title: AGM3_37

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38546
Barcode: TAAGGCGA-AGAGTAGA


title: END_seq_rB_ETO

description: Control: rB_NT


title: AGM3_36

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38545
Barcode: GTAGAGGA-TATCCTCT


title: END_seq_rB_NT


title: AGM3_35

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38544
Barcode: AAGAGGCA-TATCCTCT


title: AGM3_33

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38542
Barcode: GCTACGCT-TATCCTCT


title: AGM3_44

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38553
Barcode: CAGAGAGG-AGAGTAGA


title: AGM3_32

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38541
Barcode: CAGAGAGG-TATCCTCT


title: END_seq_NRN_ETO

description: Control: NRN_NT

source_name: Cortical neurons

value: Cortical neurons


title: END_seq_MEF_top2ko_NT

value: TOP2B -/-


title: END_seq_PB_ETO

description: Control: pre-B NT

source_name: Abelson-transformed pre-B cell

value: Abelson-transformed pre-B cell


title: AGM3_31

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38540
Barcode: CTCTCTAC-TATCCTCT


title: AGM3_34

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38543
Barcode: CGAGGCTG-TATCCTCT


title: END_seq_MEF_top2ko_ETO

description: Control: MEF TOP2B -/- NT


title: AGM3_40

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38549
Barcode: TCCTGAGC-AGAGTAGA


title: END_seq_MEF_NT


title: END_seq_MEF_ETO

description: Control: MEF_NT


title: AGM3_29

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38538
Barcode: GGACTCCT-TATCCTCT


title: AGM3_28

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38537
Barcode: TCCTGAGC-TATCCTCT


title: AGM3_30

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38539
Barcode: TAGGCATG-TATCCTCT


title: AGM3_27

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38536
Barcode: AGGCAGAA-TATCCTCT


title: END_seq_DRBexp_aB12h_ETO

description: Control: DRBexp_aB12h_NT


title: END_seq_DRBexp_aB12h_NT


title: AGM3_26

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38535
Barcode: CGTACTAG-TATCCTCT


title: END_seq_DRBexp_aB12h_ETO_DRB

description: Control: DRBexp_aB12h_DRB


title: END_seq_PB_NT


title: AGM3_25

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38534
Barcode: TAAGGCGA-TATCCTCT


title: END_seq_DRBexp_aB12h_DRB


title: AGM3_24

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38533
Barcode: GTAGAGGA-CTCTCTAT


title: AGM3_23

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38532
Barcode: AAGAGGCA-CTCTCTAT


title: END_seq_NRN_NT


title: END_seq_aB24h_NT


title: END_seq_aB24h_ETO

description: Control: aB24h_NT


title: AGM3_22

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38531
Barcode: CGAGGCTG-CTCTCTAT


title: AGM3_21

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38530
Barcode: GCTACGCT-CTCTCTAT


title: END_seq_aB12h_NT


title: END_seq_aB12h_ETO

description: Control: aB12h_NT


title: AGM3_17

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38526
Barcode: GGACTCCT-CTCTCTAT


title: AGM3_16

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38525
Barcode: TCCTGAGC-CTCTCTAT


title: AGM3_18

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38527
Barcode: TAGGCATG-CTCTCTAT


title: AGM3_19

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38528
Barcode: CTCTCTAC-CTCTCTAT


title: AGM3_14

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38523
Barcode: CGTACTAG-CTCTCTAT


title: AGM3_15

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38524
Barcode: AGGCAGAA-CTCTCTAT


title: AGM3_13

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38522
Barcode: TAAGGCGA-CTCTCTAT


title: AGM3_11

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38520
Barcode: AAGAGGCA-TAGATCGC


title: AGM3_10

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38519
Barcode: CGAGGCTG-TAGATCGC


title: AGM3_08

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38517
Barcode: CAGAGAGG-TAGATCGC


title: AGM3_12

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38521
Barcode: GTAGAGGA-TAGATCGC


title: AGM3_09

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38518
Barcode: GCTACGCT-TAGATCGC


title: AGM3_06

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38515
Barcode: TAGGCATG-TAGATCGC


title: AGM3_05

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38514
Barcode: GGACTCCT-TAGATCGC


title: AGM3_02

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38511
Barcode: CGTACTAG-TAGATCGC


title: AGM3_01

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38510
Barcode: TAAGGCGA-TAGATCGC


title: ESCs rep2_RRBS

data_processing:
Illumina software was used for basecalling.
RRBS reads were trimmed for adaptor and low-quanlity seqnences, then were aligned to the mm10 genome assembly using BSMAP version 2.90 with parameters -D C-CGG -s 12 -v 0.08 -p 4 -r 0;Only unique mapped pairs were retained.
Methylation ratios of CpGs were called using MOABS version 1.3.2 with parameters -a 1  --reportCpX=G --reportCHX=G
Genome_build: mm10
Supplementary_files_format_and_content: bed files including methylation ratios were generated using MOABS version 1.3.2

extract_protocol:
Genomic DNA was extracted using  using TIANamp Genomic DNA Kit according to the manufacturer’s protocol.
RRBS libraries were prepared for sequencing using standard Illumina protocols


title: ESCs rep1_RRBS


title: 4F-iPSCs rep2_RRBS


title: CiPSCs rep2_RRBS


title: 4F-iPSCs rep1_RRBS


title: AGM3_20

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38529
Barcode: CAGAGAGG-CTCTCTAT


title: mRNA-RORa WT_HFD_1 liver

city: Seoul

first: Young Suk

last: Yu

address: 1-Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
WT_HFD_1
PolyA RNA
Processed data file: FPKM.txt

data_processing:
Illumina CASAVA1.8.2 software used for basecalling. Sequenced reads were filtered for low-quality sequence, trimmed for adaptor sequence, trimmed 3' ends of the resulting reads for which PHRED quality scores were lower than 20 using Cutadapt v.1.0, and then mapped to mouse reference genome (GRCm38) using TopHat v2.0.7. Raw read counts for each gene were calculated using Cufflinks.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM for each sample.

source_name: RORa WT liver, high-fat diet

extract_protocol:
Total RNA extraction was performed using Trizol (Invitrogen).
RNA-seq library was generated using the Illumina TruSeq method according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina TruSeq RNA sample prep kit v2, according to the manufacturer’s protocol. TruSeq universal adapter sequence is 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'. TruSeq adapter sequences for each sample are following: 1) WT_CD_1: 5’- GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG-3'; 2) WT_CD_2: 5’-GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG-3'; 3) WT_HFD_1: 5’-GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG-3'; 4) WT_HFD_2: 5’-GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG-3'; 5) KO_CD_1: 5’-GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTG-3'; 6) KO_CD_2: 5’-GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTG-3'; 7) KO_HFD_1: 5’-GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG-3'; 8) KO_HFD_2: 5’-GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG-3'

treatment_protocol: Control diet or high-fat-diet.

tag: strain/background

tag: genotype/variation

value: RORa f/f

value: liver

tag: treatment

value: high-fat diet


title: mRNA-RORa WT_HFD_2 liver

description:
WT_HFD_2
PolyA RNA
Processed data file: FPKM.txt


title: Untransduced cells at time 48h, replicate 3

city: Milano

first: Davide

last: Cittaro

address: via Olgettina 58

department: Center for Traslational Genomics and Bioinformatics

country: Italy

institute: Ospedale San Raffaele

description: Sample name: mock_t48_3

data_processing:
Base calling was performed using CASAVA 1.8.2
Reads were aligned to reference genome using STAR v2.3.0
Features were counted using htseq-count; EnsEMBL genes v72 was used as gene model; reads were summarized at gene level
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements: raw read counts over genes

organism: Homo sapiens

source_name: Bone Marrow derived CD34+

extract_protocol:
Total RNA was extracted with the RNeasy Plus Micro kit (Qiagen) according manufacturer’s indications. RNA integrity was analyzed with the Agilent 2100 Bioanalyzer
Libraries, prepared starting from 100ng of total RNA/sample with the Illumina TruSeq RNA Sample Prep kit v2 procedure, were quantified by the Qubit BR assay and the Agilent 2100

tag: cell markers

value: bone marrow


title: mRNA-RORa WT_CD_2 liver

description:
WT_CD_2
PolyA RNA
Processed data file: FPKM.txt

source_name: RORa WT liver, control diet

value: control diet


title: mRNA-RORa WT_CD_1 liver

description:
WT_CD_1
PolyA RNA
Processed data file: FPKM.txt


title: Untransduced cells at time 24h, replicate 2

description: Sample name: mock_t24_2


title: Untransduced cells at time 24h, replicate 1

description: Sample name: mock_t24_1


title: mRNA-RORa KO_HFD_1 liver

description:
KO_HFD_1
PolyA RNA
Processed data file: FPKM.txt

source_name: RORa KO liver, high-fat diet

value: Alb-cre;RORa f/f


title: AGM3_07

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38516
Barcode: CTCTCTAC-TAGATCGC


title: Untransduced cells at time 24h, replicate 3

description: Sample name: mock_t24_3


title: mRNA-RORa KO_CD_1 liver

description:
KO_CD_1
PolyA RNA
Processed data file: FPKM.txt

source_name: RORa KO liver, control diet


title: mRNA-RORa KO_CD_2 liver

description:
KO_CD_2
PolyA RNA
Processed data file: FPKM.txt


title: Untransduced cells at time 18h, replicate 3

description: Sample name: mock_t18_3


title: Untransduced cells at time 18h, replicate 2

description: Sample name: mock_t18_2


title: AGM3_03

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38512
Barcode: AGGCAGAA-TAGATCGC


title: Untransduced cells at time 18h, replicate 1

description: Sample name: mock_t18_1


title: Rnasenf/f Cre replicate 2

first: Benjamin

last: tenOever

address: 1468 Madison Avenue

department: Microbiology

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Libraries were run on an Illumina MiSeq.
Fastq files were uploaded to Illumina's BaseSpace cloud computing environment.
Alignment and statistical analysis was performed using the RNAExpress application on BaseSpace.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing gene ID,  gene symbol and raw read numbers for each gene in each sample

source_name: Rnasen f/f primary fibroblasts

extract_protocol:
Total RNA was extracted from cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used to prepare 1 ug of total RNA for the sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: primary fibroblast

tag: adeno vector

value: Cre

value: Drosha depletion

tag: agent

value: IFNB


title: Rnasenf/f Cre replicate 1


title: Untransduced cells at time 6h, replicate 3

description: Sample name: mock_t06_3

tag: tissue


title: CiPSCs rep1_RRBS

value: Chemical induced pluripotent stem cells from mouse fibroblasts

value: male


title: Untransduced cells at time 6h, replicate 2

description: Sample name: mock_t06_2


title: Rnasenf/f GFP replicate 2

value: GFP

value: control


title: Rnasenf/f GFP replicate 1


title: Untransduced cells at time 6h, replicate 1

description: Sample name: mock_t06_1


title: Untransduced cells at time 48h, replicate 2

description: Sample name: mock_t48_2


title: Untransduced cells at time 48h, replicate 1

description: Sample name: mock_t48_1


title: mRNA-RORa KO_HFD_2 liver

description:
KO_HFD_2
PolyA RNA
Processed data file: FPKM.txt


title: Untransduced cells at time 3h, replicate 3

description: Sample name: mock_t03_3


title: AS_ShCtrl_R3

city: Stockholm

first: Johan

last: Holmberg

address: Nobels väg 3

department: Department of Cell- and Molecular Biology, Ludwig Institute for Cancer Research

country: Sweden

institute: Karolinska Institute

description:
Sample 68
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
RA treated Tumor 3 EP.
RNA-seq 50 bp single read.

data_processing:
Samples 1-54: Sequenced reads were mapped to hg19 using STAR v2.3.0 with default settings.
Samples 55-68: Sequenced reads were mapped to hg19 using Subread.
Samples 1-54: RPKM per gene were calculated using rpkmforgenes.py.
Samples 55-68: RPKM per gene were calculated using the “featureCounts” function in Subread.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include RPKM values and mapped reads for each gene (samples 1-54) or mapped reads for each gene (samples 55-68).
Supplementary_files_format_and_content: supplementary1.txt: Tab-delimited text file; Matrix table with RPKMs (samples 1-55).
Supplementary_files_format_and_content: supplementary2.txt: Tab-delimited text file; Matrix table with RPKMs (samples 56-68).

source_name: Neuroblastoma

extract_protocol:
Mice were sacrificed and tumors were dissected and snapfrozen on dry ice.
TruSeq (Illumina) according to protocol.

treatment_protocol: Adult female Crl:Nu (Ncr)-Foxn1 nu (nude mice) were injected subcutaneous with 2x10^6 cells in the right flank (day 0) and received daily i.p. injections from day 8 with vehicle (DMSO; CTRL), 10mg/kg/day Retinoic acid (RA), 0.1mg/kg/day 5-Aza-deoxycytidine (AZA), or AZA combined with RA (AZA+RA). Tumors were harvested at day 10, day 14 or EP (1000mm3).

tag: injected cells

value: SK-N-AS

value: RA

tag: time point

value: EP

value: Tumor


title: Untransduced cells at time 3h, replicate 2

description: Sample name: mock_t03_2


title: Untransduced cells at time 3h, replicate 1

description: Sample name: mock_t03_1


title: Untransduced cells at time 0h, replicate 3

description: Sample name: mock_t00_3


title: Untransduced cells at time 0h, replicate 2

description: Sample name: mock_t00_2


title: AGM3_04

description:
Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM
Sample.38513
Barcode: TCCTGAGC-TAGATCGC

source_name: CD31+CD144+CD41-CD45- cells were isolated from E11.5 mouse AGM


title: Cells exposed to poly (I:C) at time 48h, replicate 3

description: Sample name: Poly_IC_t48_3


title: AS_ShCtrl_C3

description:
Sample 65
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Tumor 3 EP.
RNA-seq 50 bp single read.

value: DMSO (CTRL)


title: AS_ShCtrl_C1

description:
Sample 63
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Tumor 1 EP.
RNA-seq 50 bp single read.


title: AS_ShCtrl_R2

description:
Sample 67
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
RA treated Tumor 2 EP.
RNA-seq 50 bp single read.


title: Cells exposed to poly (I:C) at time 48h, replicate 2

description: Sample name: Poly_IC_t48_2


title: nsRNA_seq_TRPexp_aB_TRIPTOLIDE

tag: cell type

value: Activated primary B cells

tag: genotype

value: WT

tag: strain


title: Cells exposed to poly (I:C) at time 48h, replicate 1

description: Sample name: Poly_IC_t48_1

value: bone marrow


title: AS_ShCtrl_AR3

description:
Sample 60
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Tumor 3 EP.
RNA-seq 50 bp single read.

value: AZA + RA


title: AS_ShCtrl_AR6

description:
Sample 61
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Tumor 6 EP.
RNA-seq 50 bp single read.


title: AS_ShCtrl_AR2

description:
Sample 59
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Tumor 2 EP.
RNA-seq 50 bp single read.


title: AS_ShCtrl_AR0

description:
Sample 58
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Tumor 0 EP.
RNA-seq 50 bp single read.


title: Cells exposed to poly (I:C) at time 24h, replicate 3

description: Sample name: Poly_IC_t24_3


title: AS_ShCtrl_C0

description:
Sample 62
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Tumor 0 EP.
RNA-seq 50 bp single read.


title: Cells exposed to poly (I:C) at time 24h, replicate 1

description: Sample name: Poly_IC_t24_1


title: Cells exposed to poly (I:C) at time 24h, replicate 2

description: Sample name: Poly_IC_t24_2


title: AS_ShCtrl_A5

description:
Sample 57
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA treated Tumor 5 EP.
RNA-seq 50 bp single read.

value: AZA


title: AS_ShCtrl_R0

description:
Sample 66
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
RA treated Tumor 0 EP.
RNA-seq 50 bp single read.


title: AS_ShCtrl_A2

description:
Sample 55
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA treated Tumor 2 EP.
RNA-seq 50 bp single read.


title: Cells exposed to poly (I:C) at time 18h, replicate 3

description: Sample name: Poly_IC_t18_3


title: Cells exposed to poly (I:C) at time 18h, replicate 1

description: Sample name: Poly_IC_t18_1


title: AS_ShCtrl_A4

description:
Sample 56
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA treated Tumor 4 EP.
RNA-seq 50 bp single read.


title: Cells exposed to poly (I:C) at time 18h, replicate 2

description: Sample name: Poly_IC_t18_2


title: Cells exposed to poly (I:C) at time 6h, replicate 3

description: Sample name: Poly_IC_t06_3


title: Lan1_R3

description:
Sample 53
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
RA treated Tumor 3 EP.
RNA-seq 50 bp single read.


title: AS_ShCtrl_C2

description:
Sample 64
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Tumor 2 EP.
RNA-seq 50 bp single read.