title: day3_D6__IM834-706-517_S171


title: day3_E1__IM834-701-518_S176

status: Public on Feb 21 2018

type: SRA

city: Stanford

first: Wanxin

last: Wang

state: CA

address: James H Clark Center, 318 Campus Drive, room E300

country: USA

institute: Stanford Univeristy

library_source: transcriptomic

data_processing:
STAR for alignment
Piccard for marking duplicates
HTSeq for quantification
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated file including HTSeq count for each cell

molecule: polyA RNA

organism: Mus musculus

source_name: primary resident immune cells in mouse kidney

extract_protocol:
Single cells were lysed following the Smartseq2 protocol
RNA libraries were prepared for sequencing using standard Illumina Nextera-XT protocols

tag: strain

tag: time

value: day 3


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title: day3_D11__IM834-714-517_S174


title: day3_D12__IM834-715-517_S175


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title: day3_C7__IM834-707-516_S163


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value: day 2


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title: day2_C5__IM793-705-516_S221


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title: day2_E5__IM793-705-518_S245


title: day2_B7__IM793-707-515_S211


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title: day2_A10__IM793-712-513_S202


title: day2_A1__IM793-701-513_S193


title: day1_H7__IM834-716-522_S257

value: day 1


title: day1_H9__IM834-719-522_S259


title: day2_A11__IM793-714-513_S203


title: day1_H4__IM834-720-511_S131


title: day2_B3__IM793-703-515_S207


title: day1_H5__IM834-721-511_S132


title: day2_B1__IM793-701-515_S205


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title: day1_H1__IM834-716-511_S128


title: day1_H2__IM834-718-511_S129


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title: day1_G7__IM834-716-521_S252


title: day1_G4__IM834-720-510_S125


title: day1_G9__IM834-719-521_S254


title: day1_H10__IM834-720-522_S260


title: day1_F5__IM834-721-508_S120


title: day1_F6__IM834-722-508_S121


title: day1_G2__IM834-718-510_S123


title: day1_F8__IM834-718-520_S247


title: day1_F1__IM834-716-508_S116


title: day1_F11__IM834-721-520_S250


title: day1_E5__IM834-721-507_S114


title: day1_E6__IM834-722-507_S115


title: day1_F7__IM834-716-520_S246


title: day1_F2__IM834-718-508_S117


title: day1_E3__IM834-719-507_S112


title: day1_G3__IM834-719-510_S124


title: day1_E1__IM834-716-507_S110


title: day1_H11__IM834-721-522_S261


title: day1_E11__IM834-721-518_S244


title: day1_D9__IM834-719-517_S236


title: day1_D7__IM834-716-517_S234


title: day1_D3__IM834-719-506_S106


title: day1_E12__IM834-722-518_S245


title: day1_D8__IM834-718-517_S235


title: day1_D6__IM834-722-506_S109


title: day1_D11__IM834-721-517_S238


title: day1_F3__IM834-719-508_S118


title: day1_C8__IM834-718-516_S229


title: day1_D10__IM834-720-517_S237


title: day1_D2__IM834-718-506_S105


title: day1_C9__IM834-719-516_S230


title: day1_F12__IM834-722-520_S251


title: day1_E7__IM834-716-518_S240


title: day1_C4__IM834-720-505_S101


title: day1_C6__IM834-722-505_S103


title: day1_C12__IM834-722-516_S233


title: day1_C2__IM834-718-505_S99


title: day1_C5__IM834-721-505_S102


title: day1_C7__IM834-716-516_S228


title: day1_F4__IM834-720-508_S119


title: day1_C1__IM834-716-505_S98


title: day1_B9__IM834-719-515_S224


title: day1_C10__IM834-720-516_S231


title: day1_C11__IM834-721-516_S232


title: day1_B8__IM834-718-515_S223


title: day1_D1__IM834-716-506_S104


title: day1_B7__IM834-716-515_S222


title: day1_B6__IM834-722-503_S97


title: day1_B5__IM834-721-503_S96


title: day1_B3__IM834-719-503_S94


title: day1_B12__IM834-722-515_S227


title: day1_B11__IM834-721-515_S226


title: day1_A8__IM834-718-513_S217


title: day2_C9__IM793-711-516_S225


title: day1_A7__IM834-716-513_S216


title: day1_A5__IM834-721-502_S90


title: day1_A6__IM834-722-502_S91


title: day1_A10__IM834-720-513_S219


title: day1_A3__IM834-719-502_S88


title: 6hour_G2__IM793-718-510_S170

value: 6 hour


title: day1_A2__IM834-718-502_S87


title: day1_C3__IM834-719-505_S100


title: day1_A12__IM834-722-513_S221


title: 6hour_G7__IM793-723-510_S175


title: 6hour_G8__IM793-724-510_S176


title: 6hour_F8__IM793-724-508_S164


title: 6hour_G4__IM793-720-510_S172


title: 6hour_F7__IM793-723-508_S163


title: 6hour_G3__IM793-719-510_S171


title: 6hour_G5__IM793-721-510_S173


title: day1_A11__IM834-721-513_S220


title: 6hour_G1__IM793-716-510_S169


title: day1_A1__IM834-716-502_S86


title: 6hour_F6__IM793-722-508_S162


title: 6hour_F5__IM793-721-508_S161


title: 6hour_F9__IM793-726-508_S165


title: 6hour_G6__IM793-722-510_S174


title: NIH3T3 Tcf-1 RV ChIP-seq H3K27ac Rep 1

city: Philadelphia

first: Herbert

middle: R

last: De'Broski

state: PA

address: 3800 Spruce St

institute: University of Pennsylvania

library_source: genomic

data_processing:
Quality assessment of raw reads was achieved with FastQC and contaminants were removed using Trimgalore with parameters ‘-q 15 --length 20 --stringency 5’. Human (GRCh37, November 17 2015) and mouse (GRCm38, May 23 2014) reference genomes were used in the alignment step. Bulk ATAC-seq samples were mapped to the reference genomes using Bowtie2 v2.2.9 with ‘-X2000’. STAR v2.5 was used for aligning single-cell ATAC-, RNA-, ChIP- and MNase-seq reads with parameters specifically optimized for each protocol. RNA-seq samples were analyzed with parameters ‘--outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignEndsType Local’. ChIP-seq raw reads were aligned with parameters ‘--alignSJDBoverhangMin 999 --alignSJoverhangMin 999 --alignIntronMax 1 --outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignEndsType Local’ to disable the usage of known and prevent calling novel splice junctions. The same parameters were also applied for mapping MNase-seq data combined with ‘--alignMatesGapMax 2000’. Reads aligned to the mitochondrial genome as well as reads mapping to multiple genomic loci were discarded. Picard minimized the PCR amplification bias in ATAC-, ChIP- and MNase-seq samples. In paired-end MNase-seq samples, fragments smaller than 75bp were filtered out.  For calling peaks in bulk ATAC-seq, macs2 with parameters ‘-p 1e-7 --nolambda --nomodel’ was used. Peak calling on merged single-cell ATAC-seq samples was facilitated with macs2 using parameters ‘-p 1e-3 --nolambda --nomodel’. Peaks for transcription factor ChIP-seq samples were called using macs2 with parameters ‘-p 1e-3 -q 0.05’. For calling reproducible peaks in Tcf-1 ChIP-seq samples from NIH3T3 Tcf-1 RV cells, macs2 was initially applied on each of the two replicates as well as after merging both replicates with parameters ‘--nomodel --extsize 300 --keep-dup all --call-summits -q 0.9’ using the Tcf-1 ChIP-seq on NIH3T3 Empty RV cells as control. The identified peaks were filtered with Irreproducible Discovery Rate (IDR) v2.0.2 using an IDR threshold of 2e-2.
Genome_build: mm10

molecule: genomic DNA

source_name: NIH3T3 cells

extract_protocol:
RNA-seq: Total RNA was prepared from approximately 100,000-500,000 cells using an RNeasy Plus Micro Kit (Qiagen). RNA integrity numbers were determined using a TapeStation 2200 (Agilent) and all samples had RIN numbers above 9.5.
ChIP-seq: Cells were chemically cross-linked by 1% formaldehyde. Samples were sonicated and protein-DNA complexes were isolated with antibody.
ATAC-seq: ATAC-seq was performed as previously described with minor modifications (Buenrostro et al., Nature Methods, 2013). Fifty thousand cells from FACS or from cultur were pelleted at 550 x g and washed with 1 mL 1x PBS followed by lysis with 50 μL lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Accessible chromatin was tagmented with Tn5 transposase (FC-121-1030; Illumina) for 45-75 minutes depending on the cell-type in a 37°C waterbath.
scATAC-seq: Single cell ATAC-seq was performed as previously described with minor modifications (Buenrostro et al., Nature, 2015) using the C1 Single-Cell Auto Prep System with the C1 Open App program (Fluidigm). Cells were FACS sorted and stained with mammalian LIVE/DEAD Viability/Cytotoxicity Kit (Invitrogen) for 10 minutes on ice at a final concentration of 5 μM Ethidium homodimer-1 and 5 μM Calcein AM in 1x PBS. After staining, cells were diluted in RPMI-1640+1% FBS to a concentration of 400,000 cells per mL. C1 Cell Suspension Reagent (Fluidigm) was added to a final concentration of 20%. Cell capture was verified by light microscope (for Capture 1). Brightfield and fluorescent images of each capture site was taken with a Leica DMi8 (for Captures 2 and 3). The Lysis/Tagmention step in the C1 protocol was lengthened to a duration of 60 minutes using the Open App software (Fluidigm).
RNA-seq: RNA-seq libraries were prepared using the SMARTer High-Input Strand-Specific Total RNA-seq for Illumina kit (Clontech) and were single-end sequenced for 75 bp.
ChIP-seq: ChIP DNA was approximately 300 bp in length. Libraries were prepared using Ultra DNA Library Prep Kit (NEB) and single-end sequenced for 75 bp.
ATAC-seq: Tagmented DNA was amplified for 12 cycles of PCR, purified, and the prepared libraries were paired-end sequenced (38bp+37bp).
scATAC-seq: After single cell ATAC-seq chemistry was performed on the Fluidigm C1, tagmented DNA from single cell libraries were harvested and amplified for 14 PCR cycles. Libraries were pooled and paired-end sequenced (38bp+37bp).

tag: passages

value: NIH/Swiss

tag: chip antibody

value: Active Motif 39133


title: NIH3T3 Tcf-1 RV ChIP-seq H3K9me3 Rep 1

value: Active Motif 39161


title: NIH3T3 Tcf-1 RV ChIP-seq H3K9me3 Rep 2


title: 6hour_F4__IM793-720-508_S160


title: day1_B2__IM834-718-503_S93


title: NIH3T3 Tcf-1 RV ChIP-seq H3K27ac Rep 2


title: 6hour_F3__IM793-719-508_S159


title: NIH3T3 Tcf-1 RV ChIP-seq H3K27me3 Rep 2


title: 6hour_F2__IM793-718-508_S158


title: 6hour_F11__IM793-728-508_S167


title: NIH3T3 Tcf-1 RV ChIP-seq H3K27me3 Rep 1


title: DP scATAC-seq Capture 3 H11

source_name: CD4+CD8+ T cells

tag: cell type

value: CD4+CD8+ T cells (in vivo FACS purified cells)

tag: strain/genotype


title: 6hour_F1__IM793-716-508_S157


title: DP scATAC-seq Capture 3 H12


title: 6hour_E8__IM793-724-507_S152


title: 6hour_E9__IM793-726-507_S153


title: 6hour_F12__IM793-729-508_S168


title: DP scATAC-seq Capture 3 H10


title: DP scATAC-seq Capture 3 H9


title: DP scATAC-seq Capture 3 H8


title: 6hour_E7__IM793-723-507_S151


title: DP scATAC-seq Capture 3 H7


title: DP scATAC-seq Capture 3 H6


title: 6hour_E6__IM793-722-507_S150


title: DP scATAC-seq Capture 3 H4


title: 6hour_E2__IM793-718-507_S146


title: 6hour_E1__IM793-716-507_S145


title: DP scATAC-seq Capture 3 H1


title: 6hour_F10__IM793-727-508_S166


title: DP scATAC-seq Capture 3 G12


title: 6hour_E11__IM793-728-507_S155


title: 6hour_E10__IM793-727-507_S154


title: 6hour_D9__IM793-726-506_S141


title: 6hour_E4__IM793-720-507_S148


title: DP scATAC-seq Capture 3 G10


title: 6hour_E5__IM793-721-507_S149


title: 6hour_E12__IM793-729-507_S156


title: 6hour_D8__IM793-724-506_S140


title: DP scATAC-seq Capture 3 G9


title: DP scATAC-seq Capture 3 G8


title: 6hour_D7__IM793-723-506_S139


title: DP scATAC-seq Capture 3 H2


title: 6hour_D4__IM793-720-506_S136


title: DP scATAC-seq Capture 3 G7


title: DP scATAC-seq Capture 3 H3


title: 6hour_D2__IM793-718-506_S134


title: DP scATAC-seq Capture 3 G6


title: DP scATAC-seq Capture 3 G3


title: DP scATAC-seq Capture 3 G2


title: DP scATAC-seq Capture 3 G4


title: 6hour_E3__IM793-719-507_S147


title: DP scATAC-seq Capture 3 G11


title: day1_D12__IM834-722-517_S239


title: 6hour_D1__IM793-716-506_S133


title: 6hour_D12__IM793-729-506_S144


title: DP scATAC-seq Capture 3 F12


title: DP scATAC-seq Capture 3 G1


title: 6hour_D10__IM793-727-506_S142


title: 6hour_C9__IM793-726-505_S129


title: DP scATAC-seq Capture 3 F11


title: 6hour_C7__IM793-723-505_S127


title: 6hour_C8__IM793-724-505_S128


title: DP scATAC-seq Capture 3 F10


title: DP scATAC-seq Capture 3 F7


title: 6hour_C4__IM793-720-505_S124


title: DP scATAC-seq Capture 3 F8


title: DP scATAC-seq Capture 3 F2


title: 6hour_C2__IM793-718-505_S122


title: DP scATAC-seq Capture 3 F6


title: 6hour_C12__IM793-729-505_S132


title: 6hour_C3__IM793-719-505_S123


title: DP scATAC-seq Capture 3 F1


title: DP scATAC-seq Capture 3 F3


title: DP scATAC-seq Capture 3 E11


title: DP scATAC-seq Capture 3 F9


title: 6hour_C6__IM793-722-505_S126


title: 6hour_C5__IM793-721-505_S125


title: DP scATAC-seq Capture 3 E12


title: 6hour_C10__IM793-727-505_S130


title: DP scATAC-seq Capture 3 E10


title: 6hour_D11__IM793-728-506_S143


title: 6hour_B9__IM793-726-503_S117


title: DP scATAC-seq Capture 3 E9


title: 6hour_B8__IM793-724-503_S116


title: DP scATAC-seq Capture 3 E8


title: 6hour_B7__IM793-723-503_S115


title: 6hour_B6__IM793-722-503_S114


title: DP scATAC-seq Capture 3 E7


title: 6hour_C11__IM793-728-505_S131


title: DP scATAC-seq Capture 3 E3


title: DP scATAC-seq Capture 3 E6


title: 6hour_B3__IM793-719-503_S111


title: DP scATAC-seq Capture 3 E4


title: DP scATAC-seq Capture 3 F4


title: DP scATAC-seq Capture 3 E1


title: 6hour_B5__IM793-721-503_S113


title: 6hour_B1__IM793-716-503_S109


title: DP scATAC-seq Capture 3 E2


title: 6hour_B11__IM793-728-503_S119


title: 6hour_B12__IM793-729-503_S120


title: 6hour_A9__IM793-726-502_S105


title: 6hour_B2__IM793-718-503_S110


title: DP scATAC-seq Capture 3 D12


title: DP scATAC-seq Capture 3 D8


title: DP scATAC-seq Capture 3 D10


title: 6hour_A7__IM793-723-502_S103


title: DP scATAC-seq Capture 3 D6


title: DP scATAC-seq Capture 3 D7


title: 6hour_A5__IM793-721-502_S101


title: 6hour_A6__IM793-722-502_S102


title: DP scATAC-seq Capture 3 D5


title: 6hour_A3__IM793-719-502_S99


title: 6hour_A4__IM793-720-502_S100


title: DP scATAC-seq Capture 3 D3


title: 6hour_B4__IM793-720-503_S112


title: DP scATAC-seq Capture 3 D4


title: DP scATAC-seq Capture 3 D2


title: 6hour_A2__IM793-718-502_S98


title: DP scATAC-seq Capture 3 D9


title: DP scATAC-seq Capture 3 D1


title: 6hour_A11__IM793-728-502_S107


title: 6hour_A1__IM793-716-502_S97


title: DP scATAC-seq Capture 3 D11


title: DP scATAC-seq Capture 3 C5


title: 6hour_B10__IM793-727-503_S118


title: DP scATAC-seq Capture 3 C3


title: DP scATAC-seq Capture 3 C12


title: DP scATAC-seq Capture 3 C9


title: DP scATAC-seq Capture 3 C10


title: 6hour_A8__IM793-724-502_S104


title: DP scATAC-seq Capture 3 C8


title: 6hour_A12__IM793-729-502_S108


title: DP scATAC-seq Capture 3 C7


title: DP scATAC-seq Capture 3 C6


title: DP scATAC-seq Capture 3 B11


title: DP scATAC-seq Capture 3 C2


title: DP scATAC-seq Capture 3 B9


title: DP scATAC-seq Capture 3 B8


title: DP scATAC-seq Capture 3 C4


title: DP scATAC-seq Capture 3 B7


title: DP scATAC-seq Capture 3 B6


title: DP scATAC-seq Capture 3 B2


title: DP scATAC-seq Capture 3 B5


title: DP scATAC-seq Capture 3 B12


title: DP scATAC-seq Capture 3 B1


title: DP scATAC-seq Capture 3 C1


title: DP scATAC-seq Capture 3 B4


title: DP scATAC-seq Capture 3 B3


title: DP scATAC-seq Capture 3 C11


title: 6hour_A10__IM793-727-502_S106


title: DP scATAC-seq Capture 3 A11


title: DP scATAC-seq Capture 3 A12


title: DP scATAC-seq Capture 3 A9


title: DP scATAC-seq Capture 3 A5


title: DP scATAC-seq Capture 3 A4


title: DP scATAC-seq Capture 3 B10


title: DP scATAC-seq Capture 3 A7


title: DP scATAC-seq Capture 3 A10


title: DP scATAC-seq Capture 3 A1


title: DP scATAC-seq Capture 3 A8


title: DP scATAC-seq Capture 3 A3


title: DP scATAC-seq Capture 3 A2


title: DP scATAC-seq Capture 3 A6


title: DP scATAC-seq Capture 2 H10


title: DP scATAC-seq Capture 2 H11


title: DP scATAC-seq Capture 2 H12


title: DP scATAC-seq Capture 2 H7


title: DP scATAC-seq Capture 2 H8


title: DP scATAC-seq Capture 2 H9


title: DP scATAC-seq Capture 2 H5


title: DP scATAC-seq Capture 2 H3


title: DP scATAC-seq Capture 2 H4


title: DP scATAC-seq Capture 2 H6


title: DP scATAC-seq Capture 2 G12


title: DP scATAC-seq Capture 2 G10


title: DP scATAC-seq Capture 2 G7


title: DP scATAC-seq Capture 2 G5


title: DP scATAC-seq Capture 2 G6


title: DP scATAC-seq Capture 2 G9


title: DP scATAC-seq Capture 2 H1


title: DP scATAC-seq Capture 2 G8


title: DP scATAC-seq Capture 2 G11


title: DP scATAC-seq Capture 2 F12


title: DP scATAC-seq Capture 2 F10


title: DP scATAC-seq Capture 2 F9


title: DP scATAC-seq Capture 2 F11


title: DOXO 2.5μM (sample B1)

city: Singapore

first: Manvendra

middle: K.

last: Singh

address: 8 College Road

department: Programme in Cardiovascular & Metabolic Disorders

country: Singapore

institute: Duke-NUS MEDICAL SCHOOL

data_processing:
Fastqc V0.11.3 was used to check the quality of the bases in the reads
Sequence reads were mapped to hg19 reference genome using Tophat2 and BAM files were generated
The aligned reads were assembled and estimated their abundance in FPKM using Cufflinks2
EdgeR is deployed to find out differentially expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited files with FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Stem cells derived cardimyocytes

growth_protocol: hESCs were differentiated into cardiomyocytes using the protocol described by Lian et al., PNAS, 2013. hESCs-derived cardiomyocytes were cultivated in RPMI/B27

extract_protocol:
Total RNA was extracted from control and doxorubicin-treated cardiomyocytes using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hESCs-derived cardiomyocytes were treated with vehicle only, 1 μM or 2 μM of doxorubicin for 16 hours

tag: engineered stem cell genotype

value: NKx2-5 eGFP/w

tag: derived from

value: hESCs

value: Stem cells derived cardimyocytes


title: DP scATAC-seq Capture 2 G3


title: DP scATAC-seq Capture 2 G2


title: DOXO 2.5μM (sample B2)


title: DOXO 2.5μM (sample A1)


title: DP scATAC-seq Capture 2 G4


title: DP scATAC-seq Capture 2 H2


title: DP scATAC-seq Capture 2 F7


title: DOXO 1μM (sample A1)


title: DOXO 1μM (sample B1)


title: DP scATAC-seq Capture 2 F8


title: DOXO 1μM (sample B2)


title: DOXO 1μM (sample A2)


title: DP scATAC-seq Capture 2 F6


title: DOXO 2.5μM (sample A2)


title: DP scATAC-seq Capture 2 F3


title: DP scATAC-seq Capture 2 G1


title: DOXO 0μM (sample B2)


title: DP scATAC-seq Capture 2 F4


title: DOXO 0μM (sample B1)


title: DP scATAC-seq Capture 2 F2


title: DOXO 0μM (sample A2)


title: DOXO 0μM (sample A1)


title: DP scATAC-seq Capture 2 E9


title: DP scATAC-seq Capture 2 F1


title: DP scATAC-seq Capture 2 F5


title: DP scATAC-seq Capture 2 E8


title: DP scATAC-seq Capture 2 E7


title: DP scATAC-seq Capture 2 E10


title: DP scATAC-seq Capture 2 E4


title: DP scATAC-seq Capture 2 E2


title: DP scATAC-seq Capture 2 E1


title: DP scATAC-seq Capture 2 E5


title: DP scATAC-seq Capture 2 D8


title: DP scATAC-seq Capture 2 E6


title: DP scATAC-seq Capture 2 E12


title: DP scATAC-seq Capture 2 D10


title: DP scATAC-seq Capture 2 D11


title: DP scATAC-seq Capture 2 D12


title: DP scATAC-seq Capture 2 D7


title: DP scATAC-seq Capture 2 D9


title: DP scATAC-seq Capture 2 D6


title: DP scATAC-seq Capture 2 E11


title: DP scATAC-seq Capture 2 D5


title: DP scATAC-seq Capture 2 D1


title: DP scATAC-seq Capture 2 D4


title: DP scATAC-seq Capture 2 D3


title: DP scATAC-seq Capture 2 D2


title: DP scATAC-seq Capture 2 C12


title: DP scATAC-seq Capture 2 C11


title: DP scATAC-seq Capture 2 E3


title: AMD_PRC_8.TR-32

first: Venkata

middle: Ramana Murthy

last: Chavali

address: 3620 Hamilton Walk

description: Sample name: TR-32

data_processing:
RNA-Seq reads from each sample were aligned to hg19 using STAR (version 2.5.1b).
Data were normalized at the read level, prior to quantification, using a resampling strategy PORT (v0.8.2a-beta) (https://github.com/itmat/Normalization).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

source_name: Peripheral RPE-Choroid-Sclera

extract_protocol:
collection protocol: For each donor eye, the retina (PR) and RPE-Choroid-Sclera (PRCS) samples were dissected from the peripheral region of the posterior eye globes using a 10mm-biopsy punch followed by a 8mm-punch in the middle of the 10mm-punch to minimize the sample contamination.
A total of 32 RNA samples were prepared using the AllPrep DNA/RNA Mini kit (Qiagen).
Library preparation and sequencing was done using the TruSeq Stranded total RNA with RiboZero Gold kit (Illumina, CA) protocol with a total RNA (800ng) as the starting material.

tag: donor id

tag: tissue

value: Peripheral RPE-Choroid-Sclera

tag: eye histological phenotype

value: Early Age-related maculopathy

tag: age

tag: Sex

value: Female

tag: race

value: Caucasian


title: AMD_PR_7.TR-29

description: Sample name: TR-29

source_name: Peripheral Retina

value: Peripheral Retina

value: Late non-exudative Age-related maculopathy


title: AMD_PR_8.TR-31

description: Sample name: TR-31


title: AMD_PRC_7.TR-30

description: Sample name: TR-30


title: AMD_PRC_5.TR-26

description: Sample name: TR-26


title: DP scATAC-seq Capture 2 C7


title: DP scATAC-seq Capture 2 C9


title: AMD_PR_6.TR-27

description: Sample name: TR-27

value: Other (RPEcell epithelial dystrophy (suspected))


title: DP scATAC-seq Capture 2 C5


title: DP scATAC-seq Capture 2 C10


title: DP scATAC-seq Capture 2 C4


title: AMD_PR_4.TR-23

description: Sample name: TR-23

value: Late exudative Age-related maculopathy

value: Male


title: AMD_PRC_4.TR-24

description: Sample name: TR-24


title: AMD_PR_5.TR-25

description: Sample name: TR-25


title: DP scATAC-seq Capture 2 C6


title: AMD_PR_3.TR-21

description: Sample name: TR-21


title: AMD_PRC_3.TR-22

description: Sample name: TR-22


title: AMD_PRC_1.TR-18

description: Sample name: TR-18


title: AMD_PRC_2.TR-20

description: Sample name: TR-20


title: DP scATAC-seq Capture 2 C2


title: DP scATAC-seq Capture 2 C1


title: DP scATAC-seq Capture 2 C3


title: DP scATAC-seq Capture 2 B11


title: AMD_PR_1.TR-17

description: Sample name: TR-17


title: AMD_PR_2.TR-19

description: Sample name: TR-19


title: DP scATAC-seq Capture 2 B12


title: DP scATAC-seq Capture 2 B9


title: DP scATAC-seq Capture 2 B10


title: DP scATAC-seq Capture 2 B8


title: Normal_PR_8.TR15

description: Sample name: TR15

value: Normal


title: AMD_PRC_6.TR-28

description: Sample name: TR-28


title: DP scATAC-seq Capture 2 C8


title: Normal_PRC_8.TR16

description: Sample name: TR16


title: Normal_PR_7.TR13_reseq

description: Sample name: TR13_reseq


title: DP scATAC-seq Capture 2 B7


title: Normal_PRC_7.TR14

description: Sample name: TR14


title: Normal_PR_6.TR11

description: Sample name: TR11


title: DP scATAC-seq Capture 2 B5


title: Normal_PRC_6.TR12

description: Sample name: TR12


title: DP scATAC-seq Capture 2 B4


title: DP scATAC-seq Capture 2 B3


title: Normal_PRC_4.TR08

description: Sample name: TR08


title: Normal_PR_5.TR09

description: Sample name: TR09


title: Normal_PRC_3.TR06

description: Sample name: TR06


title: Normal_PR_3.TR05

description: Sample name: TR05


title: Normal_PR_4.TR07

description: Sample name: TR07


title: DP scATAC-seq Capture 2 A12


title: Normal_PR_2.TR03

description: Sample name: TR03


title: DP scATAC-seq Capture 2 A11


title: Normal_PRC_1.TR02

description: Sample name: TR02


title: DP scATAC-seq Capture 2 A10


title: DP scATAC-seq Capture 2 B6


title: DP scATAC-seq Capture 2 A8


title: DP scATAC-seq Capture 2 A5


title: DP scATAC-seq Capture 2 A6


title: Normal_PR_1.TR01_reseq

description: Sample name: TR01_reseq


title: DP scATAC-seq Capture 2 A9


title: DP scATAC-seq Capture 2 B2


title: DP scATAC-seq Capture 2 A3


title: DP scATAC-seq Capture 2 A7


title: DP scATAC-seq Capture 2 A4


title: Normal_PRC_5.TR10

description: Sample name: TR10


title: DP scATAC-seq Capture 2 B1


title: DP scATAC-seq Capture 1 H9


title: DP scATAC-seq Capture 2 A2


title: DP scATAC-seq Capture 1 H12


title: DP scATAC-seq Capture 1 H8


title: DP scATAC-seq Capture 1 H11


title: DP scATAC-seq Capture 2 A1


title: DP scATAC-seq Capture 1 H3


title: DP scATAC-seq Capture 1 H5


title: DP scATAC-seq Capture 1 H6


title: DP scATAC-seq Capture 1 H10


title: DP scATAC-seq Capture 1 H7


title: DP scATAC-seq Capture 1 H1


title: DP scATAC-seq Capture 1 H4


title: DP scATAC-seq Capture 1 G9


title: DP scATAC-seq Capture 1 G10


title: DP scATAC-seq Capture 1 G6


title: DP scATAC-seq Capture 1 G12


title: DP scATAC-seq Capture 1 G2


title: DP scATAC-seq Capture 1 G5


title: DP scATAC-seq Capture 1 G3


title: DP scATAC-seq Capture 1 H2


title: DP scATAC-seq Capture 1 G4


title: DP scATAC-seq Capture 1 G8


title: DP scATAC-seq Capture 1 G1


title: DP scATAC-seq Capture 1 G11


title: DP scATAC-seq Capture 1 F12


title: DP scATAC-seq Capture 1 F11


title: DP scATAC-seq Capture 1 F10


title: DP scATAC-seq Capture 1 F9


title: DP scATAC-seq Capture 1 F8


title: DP scATAC-seq Capture 1 F7


title: DP scATAC-seq Capture 1 F6


title: DP scATAC-seq Capture 1 F5


title: DP scATAC-seq Capture 1 F3


title: DP scATAC-seq Capture 1 G7


title: DP scATAC-seq Capture 1 E12


title: DP scATAC-seq Capture 1 F4


title: DP scATAC-seq Capture 1 F1


title: DP scATAC-seq Capture 1 E11


title: DP scATAC-seq Capture 1 E9


title: DP scATAC-seq Capture 1 E10


title: DP scATAC-seq Capture 1 E7


title: DP scATAC-seq Capture 1 E5


title: DP scATAC-seq Capture 1 E3


title: DP scATAC-seq Capture 1 E6


title: DP scATAC-seq Capture 1 E1


title: DP scATAC-seq Capture 1 D11


title: DP scATAC-seq Capture 1 D10


title: DP scATAC-seq Capture 1 D12


title: DP scATAC-seq Capture 1 D9


title: DP scATAC-seq Capture 1 D8


title: DP scATAC-seq Capture 1 D7


title: DP scATAC-seq Capture 1 F2


title: DP scATAC-seq Capture 1 D5


title: DP scATAC-seq Capture 1 D6


title: DP scATAC-seq Capture 1 D4


title: DP scATAC-seq Capture 1 E4


title: DP scATAC-seq Capture 1 E8


title: DP scATAC-seq Capture 1 C12


title: DP scATAC-seq Capture 1 D1


title: DP scATAC-seq Capture 1 D2


title: DP scATAC-seq Capture 1 E2


title: DP scATAC-seq Capture 1 C8


title: DP scATAC-seq Capture 1 C7


title: DP scATAC-seq Capture 1 C10


title: DP scATAC-seq Capture 1 C4


title: DP scATAC-seq Capture 1 C5


title: DP scATAC-seq Capture 1 C6


title: DP scATAC-seq Capture 1 C2


title: DP scATAC-seq Capture 1 C1


title: DP scATAC-seq Capture 1 C3


title: DP scATAC-seq Capture 1 B12


title: DP scATAC-seq Capture 1 B11


title: DP scATAC-seq Capture 1 B9


title: DP scATAC-seq Capture 1 B7


title: DP scATAC-seq Capture 1 B6


title: DP scATAC-seq Capture 1 B8


title: DP scATAC-seq Capture 1 B5


title: DP scATAC-seq Capture 1 D3


title: DP scATAC-seq Capture 1 B4


title: DP scATAC-seq Capture 1 B2


title: DP scATAC-seq Capture 1 B3


title: DP scATAC-seq Capture 1 B1


title: DP scATAC-seq Capture 1 C11


title: DP scATAC-seq Capture 1 C9


title: DP scATAC-seq Capture 1 A12


title: DP scATAC-seq Capture 1 A11


title: DP scATAC-seq Capture 1 A10


title: DP scATAC-seq Capture 1 A9


title: DP scATAC-seq Capture 1 A8


title: DP scATAC-seq Capture 1 A7


title: DP scATAC-seq Capture 1 A6


title: DP scATAC-seq Capture 1 A4


title: DP scATAC-seq Capture 1 A3


title: DP scATAC-seq Capture 1 A1


title: DP scATAC-seq Capture 1 A5


title: DP scATAC-seq Capture 1 A2


title: Tcf-1 KO DP RNA-seq Rep 2

value: TCF-1-/- deltaVII


title: DP scATAC-seq Capture 1 B10


title: NIH3T3 Tcf-1 RV RNA-seq Rep 3

value: NIH/Swiss

tag: cell line


title: NIH3T3 Tcf-1 RV RNA-seq Rep 2


title: NIH3T3 Empty RV RNA-seq Rep 3


title: Tcf-1 KO DP RNA-seq Rep 1


title: NIH3T3 Empty RV RNA-seq Rep 2


title: NIH3T3 Tcf-1 RV RNA-seq Rep 1


title: NIH3T3 Empty RV RNA-seq Rep 1


title: DP RNA-seq Rep 2


title: NIH3T3 ChIP-seq H3K9me3 Rep 2

description: ChIP antibody: Active Motif 39161


title: NIH3T3 ChIP-seq Input


title: NIH3T3 Empty RV Tcf-1 ChIP-seq Rep 1

description: ChIP antibody: CST C46C7


title: NIH3T3 Tcf-1 RV Tcf-1 ChIP-seq Rep 1

description:
ChIP antibody: CST C46C7
Supplementary file on Series record: mTCF1_CST2206S_Day2_NIH3T3_Merged.Overlap.With.IDR.0.02.Summits.bed


title: NIH3T3 Empty RV Tcf-1 ChIP-seq Rep 2

description: ChIP antibody: CST C46C7


title: NIH3T3 Tcf-1 RV Tcf-1 ChIP-seq Rep 2


title: NIH3T3 ChIP-seq H3K27me3 Rep 1

description: ChIP antibody: EMD 07-449


title: NIH3T3 ChIP-seq H3K27me3 Rep 2

description: ChIP antibody: EMD 07-449


title: NIH3T3 ChIP-seq H3K9me3 Rep 1

description: ChIP antibody: Active Motif 39161


title: NIH3T3 Tcf-1 RV ATAC-seq Rep 3


title: NIH3T3 Tcf-1 RV ATAC-seq Rep 2


title: NIH3T3 Empty RV ATAC-seq Rep 1


title: NIH3T3 Empty RV ATAC-seq Rep 3


title: NIH3T3 Empty RV ATAC-seq Rep 2


title: DP ATAC-seq Rep 2


title: NIH3T3 Tcf-1 RV ATAC-seq Rep 1


title: Tcf-1 KO DP ATAC-seq Rep 2


title: DP ATAC-seq Rep 1


title: NIH3T3 Empty RV ATAC-seq Rep 4


title: Tcf-1 KO DP ATAC-seq Rep 1


title: DP RNA-seq Rep 1


title: Q344X.SL135812

city: Birmingham

first: Katie

middle: Leigh

last: Bales

state: AL

address: 1825 University Blvd

department: Optometry

institute: University of Alabama at Birmingham

description: polyA RNA

data_processing:
Quality and control of the FASTQ files was accessed using FastQC, and trimming of the bases with quality scores of less than 20 was performed with Trim_Galore! (v 0.4.4). The reads were aligned with STAR to the mm10 genome (v 2.5.2a; on --runMode genomeGenerate, the option --sjdbOverhang was set to 49. On --runMode alignReads, the following were set: --outSAMattributes NH HI AS nM NM MD; --outSAMtype BAM SortedByCoordinate; --runThreadN 12; additional options were kept as default). Gene-level counts were generated using featureCounts in R (Rsubread, v 1.26.1) and differential expression was quantified with DESeq2 (v 1.16.1) in R.
Genome_build: mm10
Supplementary_files_format_and_content: normalized_counts-Gross-STAR.csv: Comma-separated values file which contains the normalized gene-level counts for each biological sample.

source_name: Retina

extract_protocol:
The retinas were extracted from 3-week-old mice (n=3 Q344X, n=2  WT) and placed in stabilization reagent (RNAlater, QIAGEN; Catalog no. 76104). Total RNA was extracted using the RNeasy kit (QIAGEN; Catalog no. 74104).
Total RNA was poly-A selected and the libraries were constructed using the NEBNext Directional RNA Library kit at the HudsonAlpha Institute for Biotechnology. Sequencing was performed with the Illumina HiSeq 2500 system.

tag: phenotype


title: WT.SL135811

description: polyA RNA

value: WT


title: Treated stem cells_12 (T12)

city: Osakasayama

first: Seiichi

last: Omura

state: Osaka

address: 377-2 Ohnohigashi

department: Department of Microbiology

country: Japan

institute: Kindai University Faculty of Medicine

description: Barcode: ATCTCAGG-ACTGCATA

data_processing:
The raw sequences obtained were subject to quality trim and adaptor removal, using trimmomatic-0.32.
Within the CLCbio software environment (CLC genomics workbench 8.0.3, CLC Genomics Server 7.0.3), the trimmed sequences were aligned to reference genome, Mus musculus GRCm38.75, downloaded from ENSEMBLE (http://www.ensembl.org/).
Exon read count data of 12 samples were normalized with two methods: 1) read counts per kilobase (RPK) and 2) tag count comparison (TCC), using “R”
Genome_build: GRCm38.75
Supplementary_files_format_and_content: An Excel file includes normalized read count values and fold changes compared with naïve stem cells.

source_name: murine hematopoietic stem/progenitor cells

growth_protocol: Male mice (4-5 wk old, 15-17 g) were euthanized and femurs and tibias removed. Bones were flushed through with sterile Hank’s Buffered Saline Solution using a 25 G needle. BM was dissociated mechanically, filtered through a 70 μm gauze, centrifuged for 10 min at 450 g, resuspended in 10 ml PBS then counted using a cell counter.  After BMCs were extracted, hematopoietic stem/progenitor (Lin-) cells (HPSC) were negatively selected using magnetic beads, according to the manufacturer’s instructions of a hematopoietic cell selection kit. The lineage cocktail used to removed unwanted/differentiated cells consisted of: CD45R (B cells), CD11b (granulocytes, macrophages, and natural killer cells), CD3e (T cells), Ly-6G (lymphocytes), TER119 (erythrocytes).

extract_protocol:
cDNA was directly synthesized from cell lysate and amplified by PCR, using SMARTer Ultra Low Input RNA kit for sequencing-v3 (Clontech Laboratories, Mountain View, CA).
The Illumina Nextera XT DNA sample Prep Kit (Illumina, San Diego, CA) was used to generate sequencing libraries from the cDNA.  Sequencing libraries were validated, using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), and quantified, using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as real-time PCR (Applied Biosystems, Carlsbad, CA).  The sequencing libraries were sequenced on the Illumina HiSeq 2500 instrument, according to manufacturer’s instruction.

treatment_protocol: HPSCs (1 x 10e6) in 100 μl PBS were injected to mice i.v. and isolated from the brain 24 hours post injection. Non-treated HPSCs were used as naïve stem cell samples.

tag: treatment

value: Injected to a mouse i.v. and isolated from the brain 24 hours post injection

value: Treated stem cells


title: Treated stem cells_10 (T10)

description: Barcode: GTAGAGGA-TATCCTCT

tag: strain


title: Naïve stem cells_8 (N8)

description: Barcode: CGAGGCTG-TCTCTCCG

value: no treatment

value: Naive stem cells


title: NIH3T3 Tcf-1 RV ATAC-seq Rep 4


title: Treated stem cells_4 (T4)

description: Barcode: TCCTGAGC-ACTGCATA


title: Treated stem cells_5 (T5)

description: Barcode: GGACTCCT-AAGGAGTA


title: Naïve stem cells_7 (N7)

description: Barcode: CTCTCTAC-CGTCTAAT


title: Treated stem cells_6 (T6)

description: Barcode: TAGGCATG-CTAAGCCT


title: Naïve stem cells_2 (N2)

description: Barcode: CGTACTAG-TATCCTCT


title: Naïve stem cells_1 (N1)

description: Barcode: TAAGGCGA-CTCTCTAT


title: Naïve stem cells_9 (N9)

description: Barcode: AAGAGGCA-CTCTCTAT


title: 7d-SIG_rep2

city: East Lansing

first: Sookyung

last: Oh

state: MI

address: 612 Wilson Road, Rm. 322

department: Plant Research Laboratories

institute: Michigan State Univ.

data_processing:
We employed a massively parallel sequencing-by-synthesis four-dye approach to generate billions of bases of high-quality DNA sequence per run (Mardis, 2008) and yields >120 million reads of 55 nucleotides in length.
Cufflinks and Cuffdiff were used for the analysis.
Genome_build: The Arabidopsis Information Resource (TAIR) genome 10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: sigma factor 2-2 mutant

growth_protocol: Arabidopsis thaliana Col-0 ecotype as wild-type (WT), and T-DNA insertion mutant lines sig2-2 (SALK_045706) were used. Arabidopsis seeds were planted on growth medium containing 1× Murashige and Skoog (MS) salts, 1 % (w/v) Sucrose, and 0.7 % (w/v) Phytablend. Seeds on solid medium were stratified for four days at 4°C in the dark and were then incubated in a Percival model E-30LED growth chamber (Percival) with constant red (Rc) illumination for one (1 d) or seven days (7 d) at 22°C.

extract_protocol:
Total RNA was isolated from 1- or 7-d-old whole seedlings grown in Rc illumination (50 µmol m-2 s-1) as described above using an RNeasy® Plant Minikit (Qiagen).
RNA-seq samples were prepared using the Illumina TruSeq mRNA prep kit with standard Illumina protocols. RNA-seq was performed by the Research Technology. Support Facility at Michigan State University using the Illumina sequencing system

tag: ecotype/background

value: whole seedling

tag: genotype/variation

value: sigma factor 2-2 mutant

tag: light environment

value: grown under 50 uE of Red light

tag: growth condition

value: MS medium (1X MS salt, 1% sucrose, 0.7 % agar)-grown


title: 7d-SIG_rep3


title: Naïve stem cells_3 (N3)

description: Barcode: AGGCAGAA-GTAAGGAG

tag: cell type


title: WT.SL135813

description: polyA RNA


title: Treated stem cells_11 (T11)

description: Barcode: GCTCATGA-GTAAGGAG


title: 7d-WT_rep2

source_name: Col-0 wild-type (WT)


title: 1d-SIG_rep3


title: 1d-WT_rep1


title: 7d-SIG_rep1


title: Q344X.SL135814

description: polyA RNA


title: 1d-SIG_rep1


title: 1d-WT_rep3


title: 1d-SIG_rep2


title: 1d-WT_rep2


title: 7d-WT_rep3


title: EOMES KO+SOX17, day4, MS102Y92

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description:
Sample 226
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh SOX17 overexpression line, harvested at day4, BTAG-sorted

data_processing:
Samples were sequenced by four separate runs with different conditions, 3 runs on NextSeq 500 and 1 run on HiSeq 2500 with length between 76 and 134 bases (detail available on GEO records). For equal comparison between these samples, all bases longer than 76 bases from read data were trimmed from 3'-end by trimmomatic v0.35 (Bolger et.al., 2014).
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the human genome hg19 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and hg19 reference gene annotations with extended TTSs. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements

source_name: day4, from 585B1 hiPSC line

growth_protocol: 585B1 hiPSCs (XY) was cultured with AK03N medium on iMatrix coated plate as reported previously (Sasaki and Yokobayashi et al., 2015).

extract_protocol:
The cells were pelleted down and snap frozen until use.  RNA samples were extracted with RNeasy kit following manufacturer's protocol.
For 3'-seq analysis, cDNA synthesis / amplification from RNA samples and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60].

treatment_protocol:
The iMeLC induction was induced from iPSC cultured in above condition, passaged to fibronectin coated plate with Activin A (50 ng/ml), CHIR99021 (3µM) and Y27632 (10µM) in GMEM containing 15% KSR, and cultured for 44 to 48 hours.
Above iMeLCs were then dissociated and replated to low-adherent V-bottom plates to form aggregates with BMP4 (200 ng/ml), SCF (100 ng/ml), EGF (50 ng/ml), LIF(1000U/ml), and Y27632 (10µM) in GMEM containing 15% KSR, until the harvest day.

tag: sampled time point

value: day4 PGCLC

tag: transgenes

value: Blimp1-tdTomato, TFAP2C-EGFP

value: EOMES-/- +SOX17

tag: differentiation series

value: Series 4, EOMES and SOX17 over expressions


title: EOMES KO+SOX17, day4, MS102Y89

description:
Sample 227
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh SOX17 overexpression line, harvested at day4, BTAG-sorted


title: EOMES KO+SOX17, day4, MS102Y94

description:
Sample 228
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh SOX17 overexpression line, harvested at day4, BTAG-sorted


title: HIC1_ChIPSeq Replicate 2

city: Turku

first: Kartiek

last: Kanduri

address: Tykistokatu 6

country: Finland

institute: Turku Centre for Biotechnology

data_processing:
Base calling was done using Casava 1.8.2
Read alignment was performed using bowtie2-2.2.9 to hg19 version of genome
Peak calling was done using macs2-2.1.0.20140616
Genome_build: hg19
Supplementary_files_format_and_content: bed files contain peaks with scores representing -log10(p.value)

source_name: human iTreg cells

growth_protocol: Mononuclear cells were isolated from the cord blood of healthy neonates at Turku University Central Hospital using Ficoll-Paque PLUS (GE Healthcare, Fairfield, CT, USA). CD4+ T cells were then isolated using a bead-based positive isolation kit (Dynal, Invitrogen, Carlsbad, CA, USA). CD25 depletion was performed using LD columns and a CD25 depletion kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). CD4+CD25- cells from multiple donors (three or more) were either activated directly or were pooled before activation with plate-bound anti-CD3 (500 ng/24-well culture plate well; Immu-notech, Marseille, France) and soluble anti-CD28 (500 ng /mL; Immunotech) in a density of 2× 106 cells/mL of X-vivo 15 serum-free medium (Lonza, Bazel, Switzerland). For iTreg differentiation, the medium was supplemented with IL-2 (12ng/mL), TGF-β (10 ng/mL) (both from R&D systems, Minneapolis, MN, USA), All-trans retinoic acid (ATRA) (10nM) (Sigma-Aldrich, Dorse, UK), human serum (10%) and cultured at 37°C in 5% CO2. Control Th0 cells were stimulated with plate bound anti-CD3 soluble anti-CD28 in X-vivo 15 serum-free media without cytokines.

extract_protocol:
Lysates were clarified from sonicated nuclei and HIC1 protein-DNA complexes were isolated with antibody.
The DNA libraries were prepared as per the guidelines from Illumina by Fasteris Life Sciences (Plan-les-Ouates, Switzerland). Input DNA was sequenced and used as a control. DNA libraries were se-quenced on Illumina HiSeq2500 producing from 25 to 35 million reads per sample. The 50 nucleotide reads were aligned to hg19 build of human reference genome using bowtie2 (version 2.2.9)

tag: tissue

value: cord blood

value: iTreg cells

tag: antibody

value: HIC-1 antibody (Santa Cruz, sc-271499)


title: EOMES KO+SOX17, day4, MS102Y85

description:
Sample 225
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh SOX17 overexpression line, harvested at day4, BTAG-sorted


title: Input DNA Replicate 2


title: EOMES KO+EOMES, day4, MS102Y93

description:
Sample 224
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh EOMES overexpression line, harvested at day4, BTAG-sorted

value: EOMES-/- +EOMES


title: EOMES KO+EOMES, day4, MS102Y86

description:
Sample 223
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh EOMES overexpression line, harvested at day4, BTAG-sorted


title: HIC1_ChIPSeq Replicate 1


title: EOMES KO+EOMES, day4, MS102Y91

description:
Sample 222
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh EOMES overexpression line, harvested at day4, BTAG-sorted


title: Input DNA Replicate 1


title: 7d-WT_rep1

value: WT

tag: age


title: BLIMP1 KO, day4, MS081Y18

description:
Sample 194
Transcriptome of amplified cDNA from PGCLC induction of BLIMP1-/- line, harvested at day4, BTAG-sorted

value: Series 6, BLIMP1 KO


title: BLIMP1 KO, day4, MS081Y17

description:
Sample 193
Transcriptome of amplified cDNA from PGCLC induction of BLIMP1-/- line, harvested at day4, BTAG-sorted


title: Ctrl_BLIMP1, day4, MS081Y21

description:
Sample 192
Transcriptome of amplified cDNA from PGCLC induction of control for BLIMP1 KO line, harvested at day4, BTAG-sorted

value: WT control


title: Ctrl_EOMES KO+EOMES/SOX17, day4, MS102Y90

description:
Sample 219
Transcriptome of amplified cDNA from PGCLC induction of control for EOMES KO +EOMES and +SOX17 lines, harvested at day4, BTAG-sorted

value: Control BTAG


title: Ctrl_BLIMP1, day4, MS081Y20

description:
Sample 191
Transcriptome of amplified cDNA from PGCLC induction of control for BLIMP1 KO line, harvested at day4, BTAG-sorted


title: EOMES KO+SOX17, day2, MS102Y80

description:
Sample 189
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh SOX17 overexpression line, harvested at day2, BTAG-sorted

source_name: day2, from 585B1 hiPSC line

value: day2 PGCLC


title: BLIMP1 KO, day2, MS081Y12

description:
Sample 137
Transcriptome of amplified cDNA from PGCLC induction of BLIMP1-/- line, harvested at day2, BTAG-sorted


title: Ctrl_BLIMP1, day2, MS081Y16

description:
Sample 136
Transcriptome of amplified cDNA from PGCLC induction of control for BLIMP1 KO line, harvested at day2, BTAG-sorted


title: EOMES KO+SOX17, day2, MS102Y87

description:
Sample 188
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh SOX17 overexpression line, harvested at day2, BTAG-sorted


title: EOMES KO+SOX17, day2, MS102Y78

description:
Sample 187
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh SOX17 overexpression line, harvested at day2, BTAG-sorted


title: Ctrl_BLIMP1, day2, MS081Y15

description:
Sample 135
Transcriptome of amplified cDNA from PGCLC induction of control for BLIMP1 KO line, harvested at day2, BTAG-sorted


title: EOMES KO+EOMES, day2, MS102Y79

description:
Sample 185
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh EOMES overexpression line, harvested at day2, BTAG-sorted


title: EOMES KO+EOMES, day2, MS102Y76

description:
Sample 184
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh EOMES overexpression line, harvested at day2, BTAG-sorted


title: Ctrl_BLIMP1, iPSC, MS081Y11

description:
Sample 3
Transcriptome of amplified cDNA from PGCLC induction of control for BLIMP1 KO line, harvested at iPSC, non-sorted

source_name: iPSC, from 585B1 hiPSC line

value: iPSC


title: BLIMP1 KO, day2, MS081Y13

description:
Sample 138
Transcriptome of amplified cDNA from PGCLC induction of BLIMP1-/- line, harvested at day2, BTAG-sorted


title: Ctrl_BLIMP1, iPSC, MS081Y10

description:
Sample 2
Transcriptome of amplified cDNA from PGCLC induction of control for BLIMP1 KO line, harvested at iPSC, non-sorted


title: BLIMP1 KO, iPSC, MS081Y08

description:
Sample 5
Transcriptome of amplified cDNA from PGCLC induction of BLIMP1-/- line, harvested at iPSC, non-sorted


title: EOMES KO+EOMES, day2, MS102Y77

description:
Sample 183
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh EOMES overexpression line, harvested at day2, BTAG-sorted


title: EOMES KO+EOMES, day2, MS102Y74

description:
Sample 182
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh EOMES overexpression line, harvested at day2, BTAG-sorted


title: EOMES KO+EOMES, day4, MS102Y84

description:
Sample 221
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh EOMES overexpression line, harvested at day4, BTAG-sorted


title: BLIMP1 KO, iPSC, MS081Y07

description:
Sample 4
Transcriptome of amplified cDNA from PGCLC induction of BLIMP1-/- line, harvested at iPSC, non-sorted


title: Ctrl_WT, day8, MS081Y06

description:
Sample 230
Transcriptome of amplified cDNA from PGCLC induction of BTAG control line, harvested at day8, BTAG-sorted

source_name: day8, from 585B1 hiPSC line

value: day8 PGCLC

value: Series 5,WT


title: Ctrl_EOMES KO+EOMES/SOX17, day2, MS102Y81

description:
Sample 181
Transcriptome of amplified cDNA from PGCLC induction of control for EOMES KO +EOMES and +SOX17 lines, harvested at day2, BTAG-sorted


title: EOMES KO+SOX17, iMeLC, MS102Y70

description:
Sample 108
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh SOX17 overexpression line, harvested at iMeLC, non-sorted

source_name: iMeLC, from 585B1 hiPSC line

value: iMeLC


title: Ctrl_WT, day4, MS081Y04

description:
Sample 190
Transcriptome of amplified cDNA from PGCLC induction of BTAG control line, harvested at day4, BTAG-sorted

value: day4 PGCLC


title: Ctrl_WT, day6, MS081Y05

description:
Sample 229
Transcriptome of amplified cDNA from PGCLC induction of BTAG control line, harvested at day6, BTAG-sorted

source_name: day6, from 585B1 hiPSC line

value: day6 PGCLC

value: Blimp1-tdTomato, TFAP2C-EGFP


title: Ctrl_EOMES KO+EOMES/SOX17, day4, MS102Y95

description:
Sample 220
Transcriptome of amplified cDNA from PGCLC induction of control for EOMES KO +EOMES and +SOX17 lines, harvested at day4, BTAG-sorted

value: Series 4, EOMES and SOX17 over expressions


title: Ctrl_WT, day2, MS081Y03

description:
Sample 134
Transcriptome of amplified cDNA from PGCLC induction of BTAG control line, harvested at day2, BTAG-sorted


title: EOMES KO+SOX17, iMeLC, MS102Y65

description:
Sample 107
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh SOX17 overexpression line, harvested at iMeLC, non-sorted

value: EOMES-/- +SOX17


title: EOMES KO+SOX17, iMeLC, MS102Y68

description:
Sample 106
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh SOX17 overexpression line, harvested at iMeLC, non-sorted


title: EOMES KO+SOX17, iMeLC, MS102Y63

description:
Sample 105
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh SOX17 overexpression line, harvested at iMeLC, non-sorted


title: Ctrl_WT, iMeLC, MS081Y02

description:
Sample 57
Transcriptome of amplified cDNA from PGCLC induction of BTAG control line, harvested at iMeLC, non-sorted


title: Ctrl_WT, iPSC, MS081Y01

description:
Sample 1
Transcriptome of amplified cDNA from PGCLC induction of BTAG control line, harvested at iPSC, non-sorted


title: EOMES KO+SOX17, day2, MS102Y75

description:
Sample 186
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh SOX17 overexpression line, harvested at day2, BTAG-sorted


title: EOMES KO+EOMES, iMeLC, MS102Y69

description:
Sample 104
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh EOMES overexpression line, harvested at iMeLC, non-sorted


title: T KO, day4, MS081Y35

description:
Sample 208
Transcriptome of amplified cDNA from PGCLC induction of T-/-#27 line, harvested at day4, BT-sorted

value: Series 2, TFAP2C KO and T KO


title: T KO, day4, MS081Y41

description:
Sample 209
Transcriptome of amplified cDNA from PGCLC induction of T-/-#27 line, harvested at day4, BT-sorted


title: T KO, day4, MS081Y71

description:
Sample 207
Transcriptome of amplified cDNA from PGCLC induction of T-/-#19 line, harvested at day4, BT-sorted


title: EOMES KO+EOMES, iMeLC, MS102Y64

description:
Sample 103
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh EOMES overexpression line, harvested at iMeLC, non-sorted


title: EOMES KO+EOMES, iMeLC, MS102Y62

description:
Sample 101
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh EOMES overexpression line, harvested at iMeLC, non-sorted


title: T KO, day4, MS081Y56

description:
Sample 206
Transcriptome of amplified cDNA from PGCLC induction of T-/-#19 line, harvested at day4, BT-sorted


title: Ctrl_EOMES KO+EOMES/SOX17, iMeLC, MS102Y71

description:
Sample 100
Transcriptome of amplified cDNA from PGCLC induction of control for EOMES KO +EOMES and +SOX17 lines, harvested at iMeLC, non-sorted


title: T KO, day4, MS081Y34

description:
Sample 205
Transcriptome of amplified cDNA from PGCLC induction of T-/-#19 line, harvested at day4, BT-sorted


title: EOMES KO+SOX17, iPSC, MS102Y53

description:
Sample 55
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh SOX17 overexpression line, harvested at iPSC, non-sorted


title: TFAP2C KO, day4, MS081Y94

description:
Sample 202
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#2 line, harvested at day4, BT-sorted


title: TFAP2C KO, day4, MS081Y25

description:
Sample 203
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#7 line, harvested at day4, BT-sorted


title: EOMES KO+SOX17, iPSC, MS102Y58

description:
Sample 56
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh SOX17 overexpression line, harvested at iPSC, non-sorted


title: EOMES KO+SOX17, iPSC, MS102Y56

description:
Sample 54
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh SOX17 overexpression line, harvested at iPSC, non-sorted


title: TFAP2C KO, day4, MS081Y95

description:
Sample 204
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#7 line, harvested at day4, BT-sorted


title: EOMES KO+SOX17, iPSC, MS102Y51

description:
Sample 53
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh SOX17 overexpression line, harvested at iPSC, non-sorted


title: EOMES KO+EOMES, iPSC, MS102Y52

description:
Sample 51
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh EOMES overexpression line, harvested at iPSC, non-sorted


title: TFAP2C KO, day4, MS081Y64

description:
Sample 201
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#2 line, harvested at day4, BT-sorted


title: Ctrl_EOMES KO+EOMES/SOX17, day2, MS102Y88

description:
Sample 180
Transcriptome of amplified cDNA from PGCLC induction of control for EOMES KO +EOMES and +SOX17 lines, harvested at day2, BTAG-sorted


title: TFAP2C KO, day4, MS081Y24

description:
Sample 200
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#2 line, harvested at day4, BT-sorted


title: Ctrl_TFAP2C/T, day4, MS081Y57

description:
Sample 198
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at day4, BT-sorted


title: EOMES KO+EOMES, iPSC, MS102Y57

description:
Sample 52
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 wirh EOMES overexpression line, harvested at iPSC, non-sorted


title: Ctrl_TFAP2C/T, day4, MS081Y36

description:
Sample 197
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at day4, BT-sorted


title: Ctrl_TFAP2C/T, day4, MS081Y72

description:
Sample 199
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at day4, BT-sorted


title: EOMES KO+EOMES, iPSC, MS102Y50

description:
Sample 49
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh EOMES overexpression line, harvested at iPSC, non-sorted


title: Ctrl_EOMES KO+EOMES/SOX17, iPSC, MS102Y59

description:
Sample 48
Transcriptome of amplified cDNA from PGCLC induction of control for EOMES KO +EOMES and +SOX17 lines, harvested at iPSC, non-sorted


title: EOMES KO+EOMES, iMeLC, MS102Y67

description:
Sample 102
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh EOMES overexpression line, harvested at iMeLC, non-sorted


title: Ctrl_TFAP2C/T, day4, MS081Y96

description:
Sample 196
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at day4, BT-sorted


title: Ctrl_TFAP2C/T, day4, MS081Y63

description:
Sample 195
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at day4, BT-sorted


title: Ctrl_EOMES KO+EOMES/SOX17, iMeLC, MS102Y66

description:
Sample 99
Transcriptome of amplified cDNA from PGCLC induction of control for EOMES KO +EOMES and +SOX17 lines, harvested at iMeLC, non-sorted


title: MIXL1 KO, day4, MS089Y60

description:
Sample 218
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at day4, BTAG-sorted

value: Series 3, MIXL1 KO


title: MIXL1 KO, day4, MS089Y45

description:
Sample 217
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at day4, BTAG-sorted


title: MIXL1 KO, day4, MS089Y30

description:
Sample 216
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at day4, BTAG-sorted


title: Ctrl_EOMES KO+EOMES/SOX17, iPSC, MS102Y54

description:
Sample 47
Transcriptome of amplified cDNA from PGCLC induction of control for EOMES KO +EOMES and +SOX17 lines, harvested at iPSC, non-sorted


title: Ctrl_MIXL1, day4, MS089Y92

description:
Sample 212
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at day4, BTAG-sorted


title: Ctrl_MIXL1, day4, MS089Y47

description:
Sample 213
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at day4, BTAG-sorted


title: Ctrl_MIXL1, day4, MS089Y17

description:
Sample 211
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at day4, BTAG-sorted


title: MIXL1 KO, day2, MS089Y57

description:
Sample 179
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at day2, BTAG-sorted


title: MIXL1 KO, day2, MS089Y42

description:
Sample 178
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at day2, BTAG-sorted


title: MIXL1 KO, day4, MS089Y15

description:
Sample 215
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at day4, BTAG-sorted


title: EOMES KO+EOMES, iPSC, MS102Y55

description:
Sample 50
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 wirh EOMES overexpression line, harvested at iPSC, non-sorted

value: EOMES-/- +EOMES


title: MIXL1 KO, day2, MS089Y88

description:
Sample 176
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at day2, BTAG-sorted


title: Ctrl_MIXL1, day2, MS089Y59

description:
Sample 175
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at day2, BTAG-sorted


title: MIXL1 KO, day2, MS089Y27

description:
Sample 177
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at day2, BTAG-sorted


title: Ctrl_MIXL1, day4, MS089Y62

description:
Sample 214
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at day4, BTAG-sorted


title: Ctrl_MIXL1, day2, MS089Y44

description:
Sample 174
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at day2, BTAG-sorted


title: Ctrl_MIXL1, day2, MS089Y29

description:
Sample 173
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at day2, BTAG-sorted


title: MIXL1 KO, day1, MS089Y39

description:
Sample 132
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at day1, non-sorted

source_name: day1, from 585B1 hiPSC line

value: day1 PGCLC


title: MIXL1 KO, day1, MS089Y91

description:
Sample 131
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at day1, non-sorted


title: MIXL1 KO, day1, MS089Y54

description:
Sample 133
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at day1, non-sorted


title: Ctrl_TFAP2C/T, day2, MS081Y55

description:
Sample 159
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at day2, BT-sorted


title: T KO, day2, MS081Y69

description:
Sample 168
Transcriptome of amplified cDNA from PGCLC induction of T-/-#19 line, harvested at day2, BT-sorted


title: Ctrl_TFAP2C/T, day2, MS081Y70

description:
Sample 160
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at day2, BT-sorted


title: T KO, iMeLC, MS081Y67

description:
Sample 90
Transcriptome of amplified cDNA from PGCLC induction of T-/-#27 line, harvested at iMeLC, non-sorted


title: Ctrl_TFAP2C/T, day2, MS081Y39

description:
Sample 158
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at day2, BT-sorted


title: TFAP2C KO, day2, MS081Y62

description:
Sample 162
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#2 line, harvested at day2, BT-sorted


title: Ctrl_TFAP2C/T, day2, MS081Y93

description:
Sample 157
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at day2, BT-sorted


title: T KO, day2, MS081Y99

description:
Sample 171
Transcriptome of amplified cDNA from PGCLC induction of T-/-#27 line, harvested at day2, BT-sorted


title: TFAP2C KO, day2, MS081Y91

description:
Sample 163
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#2 line, harvested at day2, BT-sorted


title: TFAP2C KO, day2, MS081Y92

description:
Sample 165
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#7 line, harvested at day2, BT-sorted


title: Ctrl_TFAP2C/T, day2, MS081Y86

description:
Sample 156
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at day2, BT-sorted


title: T KO, day2, MS081Y38

description:
Sample 169
Transcriptome of amplified cDNA from PGCLC induction of T-/-#27 line, harvested at day2, BT-sorted


title: T KO, iMeLC, MS081Y66

description:
Sample 87
Transcriptome of amplified cDNA from PGCLC induction of T-/-#19 line, harvested at iMeLC, non-sorted


title: T KO, iMeLC, MS081Y32

description:
Sample 88
Transcriptome of amplified cDNA from PGCLC induction of T-/-#27 line, harvested at iMeLC, non-sorted


title: T KO, day2, MS081Y54

description:
Sample 170
Transcriptome of amplified cDNA from PGCLC induction of T-/-#27 line, harvested at day2, BT-sorted


title: T KO, day2, MS081Y37

description:
Sample 166
Transcriptome of amplified cDNA from PGCLC induction of T-/-#19 line, harvested at day2, BT-sorted


title: T KO, iMeLC, MS081Y51

description:
Sample 86
Transcriptome of amplified cDNA from PGCLC induction of T-/-#19 line, harvested at iMeLC, non-sorted


title: TFAP2C KO, day2, MS081Y23

description:
Sample 164
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#7 line, harvested at day2, BT-sorted


title: T KO, day2, MS081Y53

description:
Sample 167
Transcriptome of amplified cDNA from PGCLC induction of T-/-#19 line, harvested at day2, BT-sorted


title: T KO, iMeLC, MS081Y31

description:
Sample 85
Transcriptome of amplified cDNA from PGCLC induction of T-/-#19 line, harvested at iMeLC, non-sorted


title: TFAP2C KO, iMeLC, MS081Y89

description:
Sample 84
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#7 line, harvested at iMeLC, non-sorted


title: Ctrl_MIXL1, day1, MS089Y93

description:
Sample 129
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at day1, non-sorted


title: Ctrl_MIXL1, day2, MS089Y94

description:
Sample 172
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at day2, BTAG-sorted


title: T KO, iMeLC, MS081Y40

description:
Sample 89
Transcriptome of amplified cDNA from PGCLC induction of T-/-#27 line, harvested at iMeLC, non-sorted


title: Ctrl_MIXL1, day1, MS089Y41

description:
Sample 128
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at day1, non-sorted


title: TFAP2C KO, iMeLC, MS081Y88

description:
Sample 82
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#2 line, harvested at iMeLC, non-sorted


title: Ctrl_MIXL1, day1, MS089Y26

description:
Sample 127
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at day1, non-sorted


title: TFAP2C KO, iMeLC, MS081Y60

description:
Sample 81
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#2 line, harvested at iMeLC, non-sorted


title: Ctrl_MIXL1, day1, MS089Y87

description:
Sample 126
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at day1, non-sorted


title: TFAP2C KO, iMeLC, MS081Y22

description:
Sample 80
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#2 line, harvested at iMeLC, non-sorted


title: MIXL1 KO, iMeLC, MS089Y51

description:
Sample 98
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at iMeLC, non-sorted


title: MIXL1 KO, iMeLC, MS089Y36

description:
Sample 97
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at iMeLC, non-sorted


title: Ctrl_MIXL1, iMeLC, MS089Y53

description:
Sample 94
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at iMeLC, non-sorted


title: MIXL1 KO, iMeLC, MS089Y85

description:
Sample 95
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at iMeLC, non-sorted


title: Ctrl_TFAP2C/T, iMeLC, MS081Y52

description:
Sample 78
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at iMeLC, non-sorted


title: T KO, iPSC, MS081Y97

description:
Sample 35
Transcriptome of amplified cDNA from PGCLC induction of T-/-#19 line, harvested at iPSC, non-sorted


title: Ctrl_TFAP2C/T, iMeLC, MS081Y33

description:
Sample 77
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at iMeLC, non-sorted


title: T KO, iPSC, MS081Y98

description:
Sample 38
Transcriptome of amplified cDNA from PGCLC induction of T-/-#27 line, harvested at iPSC, non-sorted


title: Ctrl_MIXL1, iMeLC, MS089Y23

description:
Sample 92
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at iMeLC, non-sorted


title: Ctrl_MIXL1, iMeLC, MS089Y08

description:
Sample 91
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at iMeLC, non-sorted


title: Ctrl_TFAP2C/T, iMeLC, MS081Y90

description:
Sample 76
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at iMeLC, non-sorted


title: Ctrl_TFAP2C/T, iMeLC, MS081Y61

description:
Sample 75
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at iMeLC, non-sorted


title: MIXL1 KO, iMeLC, MS089Y21

description:
Sample 96
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at iMeLC, non-sorted


title: Ctrl_TFAP2C/T, iMeLC, MS081Y68

description:
Sample 79
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at iMeLC, non-sorted


title: Ctrl_MIXL1, iMeLC, MS089Y38

description:
Sample 93
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at iMeLC, non-sorted


title: T KO, iPSC, MS081Y47

description:
Sample 33
Transcriptome of amplified cDNA from PGCLC induction of T-/-#19 line, harvested at iPSC, non-sorted


title: MIXL1 KO, iPSC, MS089Y48

description:
Sample 46
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at iPSC, non-sorted


title: Ctrl_MIXL1, iPSC, MS089Y50

description:
Sample 42
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at iPSC, non-sorted


title: MIXL1 KO, iPSC, MS089Y33

description:
Sample 45
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at iPSC, non-sorted


title: T KO, iPSC, MS081Y48

description:
Sample 34
Transcriptome of amplified cDNA from PGCLC induction of T-/-#19 line, harvested at iPSC, non-sorted


title: MIXL1 KO, iPSC, MS089Y18

description:
Sample 44
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at iPSC, non-sorted


title: TFAP2C KO, iPSC, MS081Y87

description:
Sample 32
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#7 line, harvested at iPSC, non-sorted


title: MIXL1 KO, iPSC, MS089Y03

description:
Sample 43
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at iPSC, non-sorted


title: TFAP2C KO, iPSC, MS081Y73

description:
Sample 30
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#2 line, harvested at iPSC, non-sorted


title: TFAP2C KO, iPSC, MS081Y58

description:
Sample 29
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#2 line, harvested at iPSC, non-sorted


title: Ctrl_MIXL1, iPSC, MS089Y35

description:
Sample 41
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at iPSC, non-sorted


title: Ctrl_MIXL1, iPSC, MS089Y20

description:
Sample 40
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at iPSC, non-sorted


title: Ctrl_TFAP2C/T, iPSC, MS081Y50

description:
Sample 26
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at iPSC, non-sorted


title: TFAP2C KO, iMeLC, MS082Y35

description:
Sample 83
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#7 line, harvested at iMeLC, non-sorted


title: Ctrl_TFAP2C/T, iPSC, MS081Y74

description:
Sample 24
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at iPSC, non-sorted


title: TFAP2C KO, iPSC, MS082Y33

description:
Sample 28
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#2 line, harvested at iPSC, non-sorted


title: SOX17 KO, day2, MS081Y83

description:
Sample 144
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at day2, non-sorted

value: Series 1, SOX17 KO and EOMES KO


title: Ctrl_TFAP2C/T, iPSC, MS081Y65

description:
Sample 27
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at iPSC, non-sorted

value: WT control


title: Ctrl_TFAP2C/T, iPSC, MS081Y30

description:
Sample 25
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at iPSC, non-sorted


title: Ctrl_MIXL1, iPSC, MS089Y05

description:
Sample 39
Transcriptome of amplified cDNA from PGCLC induction of control for MIXL1 KO line, harvested at iPSC, non-sorted

value: Control BTAG


title: T KO, day4, MS082Y01

description:
Sample 210
Transcriptome of amplified cDNA from PGCLC induction of T-/-#27 line, harvested at day4, BT-sorted


title: SOX17 KO, day2, MS081Y84

description:
Sample 148
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at day2, non-sorted

value: day2 PGCLC


title: MIXL1 KO, day1, MS089Y09

description:
Sample 130
Transcriptome of amplified cDNA from PGCLC induction of MIXL1-/-#3 line, harvested at day1, non-sorted


title: SOX17 KO, day1, MS081Y81

description:
Sample 114
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at day1, non-sorted


title: Ctrl_SOX17/EOMES, day2, MS081Y85

description:
Sample 139
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at day2, non-sorted


title: T KO, iPSC, MS081Y49

description:
Sample 37
Transcriptome of amplified cDNA from PGCLC induction of T-/-#27 line, harvested at iPSC, non-sorted

value: iPSC


title: EOMES KO, day2, MS102Y96

description:
Sample 154
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#18 line, harvested at day2, non-sorted

value: EOMES-/-


title: Ctrl_TFAP2C/T, iPSC, MS081Y59

description:
Sample 23
Transcriptome of amplified cDNA from PGCLC induction of control for TFAP2C KO and T KO lines, harvested at iPSC, non-sorted


title: EOMES KO, day2, MS102Y48

description:
Sample 153
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 line, harvested at day2, non-sorted


title: SOX17 KO, day2, MS082Y31

description:
Sample 151
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at day2, non-sorted


title: Ctrl_SOX17/EOMES, day1, MS081Y82

description:
Sample 109
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at day1, non-sorted


title: SOX17 KO, iMeLC, MS081Y78

description:
Sample 63
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at iMeLC, non-sorted


title: SOX17 KO, day2, MS082Y25

description:
Sample 150
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at day2, non-sorted


title: EOMES KO, day2, MS102Y47

description:
Sample 152
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 line, harvested at day2, non-sorted


title: SOX17 KO, day2, MS082Y12

description:
Sample 149
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at day2, non-sorted


title: SOX17 KO, iMeLC, MS081Y79

description:
Sample 67
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at iMeLC, non-sorted


title: TFAP2C KO, day2, MS082Y36

description:
Sample 161
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#2 line, harvested at day2, BT-sorted


title: EOMES KO, day2, MS102Y97

description:
Sample 155
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#26 line, harvested at day2, non-sorted


title: SOX17 KO, iPSC, MS081Y76

description:
Sample 15
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at iPSC, non-sorted


title: Ctrl_SOX17/EOMES, iMeLC, MS081Y80

description:
Sample 58
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at iMeLC, non-sorted


title: SOX17 KO, day2, MS082Y24

description:
Sample 146
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at day2, non-sorted


title: Ctrl_SOX17/EOMES, iPSC, MS081Y77

description:
Sample 6
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at iPSC, non-sorted


title: SOX17 KO, day2, MS082Y14

description:
Sample 145
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at day2, non-sorted


title: TFAP2C KO, iPSC, MS082Y34

description:
Sample 31
Transcriptome of amplified cDNA from PGCLC induction of TFAP2C-/-#7 line, harvested at iPSC, non-sorted


title: SOX17 KO, day2, MS082Y42

description:
Sample 147
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at day2, non-sorted


title: Ctrl_SOX17/EOMES, day2, MS082Y32

description:
Sample 142
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at day2, non-sorted


title: Ctrl_SOX17/EOMES, day2, MS102Y49

description:
Sample 143
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at day2, non-sorted


title: EOMES KO, day1, MS102Y82

description:
Sample 124
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#18 line, harvested at day1, non-sorted


title: Ctrl_SOX17/EOMES, day2, MS082Y26

description:
Sample 141
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at day2, non-sorted


title: Ctrl_SOX17/EOMES, day2, MS082Y15

description:
Sample 140
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at day2, non-sorted


title: EOMES KO, day1, MS102Y44

description:
Sample 122
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 line, harvested at day1, non-sorted


title: SOX17 KO, day1, MS082Y41

description:
Sample 121
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at day1, non-sorted


title: EOMES KO, day1, MS102Y45

description:
Sample 123
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 line, harvested at day1, non-sorted


title: SOX17 KO, day1, MS082Y03

description:
Sample 119
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at day1, non-sorted


title: SOX17 KO, day1, MS082Y22

description:
Sample 120
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at day1, non-sorted


title: SOX17 KO, day1, MS082Y29

description:
Sample 117
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at day1, non-sorted


title: SOX17 KO, day1, MS082Y21

description:
Sample 116
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at day1, non-sorted


title: SOX17 KO, day1, MS082Y04

description:
Sample 115
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at day1, non-sorted


title: SOX17 KO, iPSC, MS081Y75

description:
Sample 11
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at iPSC, non-sorted


title: Ctrl_SOX17/EOMES, day1, MS082Y30

description:
Sample 112
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at day1, non-sorted


title: Ctrl_SOX17/EOMES, day1, MS082Y11

description:
Sample 110
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at day1, non-sorted


title: tt2KO_st34_cross9

city: London

first: George

middle: E.

last: Gentsch

state: Greater London

address: 1 Midland Road

department: Developmental Biology Laboratory

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Bases were called using Casava version 1.8.2
Paired-end reads were aligned to a revised version of X. tropicalis gene models 7.2 and known off-genome EST assemblies including ribosomal and mitochondrial RNA by running Bowtie2 (version 2.1.0) with the following constraints: -k 200 -X 800 --rdg 6,5 --rfg 6,5 --score-main L,-.6,-.4 --no-discordant --no-mixed.
Only read pairs that uniquely align to one gene were counted. Differential expression analysis was performed with raw fragment counts excluding those belonging to ribosomal and mitochondrial RNA using DESeq2 (Love et al., 2014)
For genome browser visualisation, paired-end reads were mapped to the X. tropicalis genome assembly 7.1 and known off-genome EST assemblies using Tophat (version 2.0.10) with the following parameters: -r 77 --mate-std-dev 110 -G v7.2 (gene models of version 7.2 as used above) -g 200 --report-secondary-alignments. genome_v71.gff3.gz (genome annotation file in GFF3 format) and GO_terms_v71.txt.gz (GO term annotation file) are linked on the Series record.
Genome_build: X. tropicalis v7.1

organism: Xenopus tropicalis

source_name: embryo

growth_protocol: Embryos were grown to the indicated developmental stage in 5% MMR at 25ºC.

extract_protocol:
Single embryos were homogenised in 200 µl TRIzol (Thermo Fisher Scientific) by vortexing. For phase separation, 40 µl of chloroform was added to the homogenate, shaken vigorously for 15 secs before spinning for 5 mins at 16,000 g at 4ºC. The aqueous phase containing total RNA was snap-frozen in liquid nitrogen and stored at -80ºC while the interphase-organic layer was processed to extract genomic DNA for genotyping. The aqueous phases from 5 to 10 sibling embryos of shared genotype or treatment were then combined. Total RNA was precipitated with one volume of 100% ethanol and cleaned using the RNA Clean and Concentrator 5 or 25 (Zymo Research) with in-column 3 U Turbo DNase (Thermo Fisher Scientific) treatment according to the manufacturer’s instructions.
Libraries were made from ~1 µg total RNA by following version 2 of the TruSeq RNA low sample protocol (Illumina) with the following modifications. After second strand synthesis 1 µl of the remaining eluate was used to measure the cDNA concentration using the Qubit fluorometer and Qubit dsDNA high sensitivity reagents (Thermo Fisher Scientific). The resultant cDNA yield was used to estimate the number of requisite PCR cycles to generate high complexity libraries without chimera fragments. We routinely used ten PCR cycles for 10 ng cDNA and adjusted the number of PCR cycles accordingly.

treatment_protocol: Embryos were injected as indicated at 1-cell stage with 18 ng morpholino antisense oligonucleotide.

value: te1.2D/e1.2D t2e3.7D/e3.7D (out-bred Nigerian)

tag: developmental stage

value: mid-tailbud (stage 34)

tag: origin

value: t/t2 null mutants (t/t2 KO) from natural pairing of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 9)


title: EOMES KO, iMeLC, MS102Y73

description:
Sample 74
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#26 line, harvested at iMeLC, non-sorted

value: iMeLC

tag: cell line


title: Ctrl_SOX17/EOMES, day1, MS082Y23

description:
Sample 111
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at day1, non-sorted

value: Blimp1-tdTomato, TFAP2C-EGFP


title: EOMES KO, iMeLC, MS102Y72

description:
Sample 73
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#18 line, harvested at iMeLC, non-sorted


title: EOMES KO, day1, MS102Y83

description:
Sample 125
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#26 line, harvested at day1, non-sorted


title: EOMES KO, iMeLC, MS102Y41

description:
Sample 71
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 line, harvested at iMeLC, non-sorted


title: tt2KO_st34_cross2

value: t/t2 null mutants (t/t2 KO) from natural pairing of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 2)


title: tt2_het_st34_cross9

value: te1.2D/+ t2e3.7D/+ (out-bred Nigerian)

value: t/t2 heterozygotes (t/t2 het) from natural pairing of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 9)


title: tt2_het_st34_cross1

value: t/t2 heterozygotes (t/t2 het) from natural pairing of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 1)


title: tt2KO_st34_cross1

value: t/t2 null mutants (t/t2 KO) from natural pairing of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 1)


title: SOX17 KO, iMeLC, MS082Y19

description:
Sample 69
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at iMeLC, non-sorted


title: wt_st34_cross2

value: wild-type (out-bred Nigerian)

value: wild-type (wt) from cross of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 2)


title: wt_st34_cross9

value: wild-type (wt) from cross of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 9)


title: EOMES KO, iMeLC, MS102Y42

description:
Sample 72
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 line, harvested at iMeLC, non-sorted

value: Series 1, SOX17 KO and EOMES KO


title: SOX17 KO, day1, MS082Y02

description:
Sample 118
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at day1, non-sorted

value: day1 PGCLC


title: tt2_het_st34_cross2

value: t/t2 heterozygotes (t/t2 het) from natural pairing of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 2)


title: wt_st34_cross1

value: wild-type (wt) from cross of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 1)


title: SOX17 KO, iMeLC, MS082Y06

description:
Sample 68
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at iMeLC, non-sorted


title: tt2KO_st26_cross9

value: te1.2D/e1.2D t2e3.7D/e3.7D (out-bred Nigerian)

value: mid-tailbud (stage 26)


title: Ctrl_SOX17/EOMES, day1, MS102Y46

description:
Sample 113
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at day1, non-sorted

value: WT control


title: SOX17 KO, iMeLC, MS082Y18

description:
Sample 65
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at iMeLC, non-sorted

value: iMeLC


title: d06900GX1

city: Utrecht

first: Robin

last: Ohm

address: Padualaan 8

country: Netherlands

institute: Utrecht University

description:
gene_exp.diff: d06900GX
Barcode: CGATGT

data_processing:
Illumina Casava pipeline version 1.8.3 was used for base calling
The RNA-Seq pipeline used the TRIMMOMATIC read trimmer version 0.32 (Bolger et al., 2014) to remove low quality regions and the Illumina adapters from the reads
Tophat version 2.1.13 (Trapnell et al., 2009) was used to align sequence reads to the A. niger ATCC 1015 genome assembly
The program Cuffdiff (version 2.2.1), which is part of Cufflinks (Trapnell et al., 2010), was used to identify reads mapping to predicted genes and to identify differentially expressed genes.
Genome_build: Aspergillus niger ATCC 1015 v4.0 (http://genome.jgi.doe.gov/Aspni7/Aspni7.home.html)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Aspergillus niger

growth_protocol: Conidia of Aspergillus niger strains MA234.1 and ΔfusR were grown as liquid shaken cultures at 200 rpm and 30 °C in 300 ml Transformation Medium + 1% glucose for 16 hours. Subsequently, the mycelium was transferred to 150 ml Minimal Medium + 25 mM xylose and grown for another 4 hours at 250 rpm and 30 °C.

extract_protocol:
Mycelium was flash-frozen in liquid nitrogen and ground using the TissueLyzer II (Qiagen, Venlo, The Netherlands). RNA was isolated using a standard TRIzol isolation procedure, followed by purification using the Nucleospin® RNA kit (Macherey-Nagel, Düren, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mycelium


title: tt2KO_st26_cross2

value: t/t2 null mutants (t/t2 KO) from natural pairing of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 2)


title: wtGX2

description:
gene_exp.diff: MA234.1XX
Barcode: GCCAAT

source_name: wtGX


title: SOX17 KO, iMeLC, MS082Y07

description:
Sample 64
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at iMeLC, non-sorted

value: Blimp1-tdTomato, TFAP2C-EGFP


title: tt2KO_st26_cross1


title: SOX17 KO, iMeLC, MS082Y27

description:
Sample 70
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at iMeLC, non-sorted


title: Ctrl_SOX17/EOMES, iMeLC, MS082Y28

description:
Sample 61
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at iMeLC, non-sorted


title: tt2_het_st26_cross2

value: te1.2D/+ t2e3.7D/+ (out-bred Nigerian)


title: tt2_het_st26_cross9

value: t/t2 heterozygotes (t/t2 het) from natural pairing of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 9)


title: wtGX1

description:
gene_exp.diff: MA234.1GX
Barcode: TGACCA


title: ∆ribN RF- rep3

city: Cuernavaca

first: Luis

middle: Fernando

last: Lozano

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México

description: RF- riboflavin absent

data_processing:
Quality control visualization and analysis (adapter and quality trimming) was performed using FastQC version 0.11.2 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) and Trim_galore version 0.4.1 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), respectively.
Reads were mapped to the genome of Vibrio cholerae 01 biovar El Tor str. N16961 (RefSeq, NCBI) using Bowtie2 version 2.1.0 (Langmead and Salzberg, 2012). In all the samples the alignment percentage of reads were above 98%.
Differential expression analysis between samples was performed with the Bioconductor package edgeR version 3.18.1 (Robinson et al., 2010) using negative binomial model and exact test based on quantile-adjusted conditional maximum likelihood method (qCML). Genes with a statistically significant change in expression (P<0.05) were selected for further analysis.
Analyses of enrichment of Gene Ontology (GO) terms of biological processes in the indicated subsets of genes were performed on the online platform of the Gene Ontology Consortium (www.geneontology.org), and statistically significant (P<0.05) functional terms were retrieved.
Genome_build: Vibrio cholerae 01 biovar El Tor str. N16961 (RefSeq, NCBI)
Supplementary_files_format_and_content: tab-delimited text files include read counts of every gene for each Sample

organism: Vibrio cholerae

source_name: Bacteria Strain

growth_protocol: V. cholerae N16961 strain and its ∆ribD and ∆ribN derivatives were grown overnight in LB plates at 37 °C. 5 ml of LB broth were inoculated with a colony of the plate cultures and incubated at 37 °C in an orbital shaker at 150 rpm until they reached an OD600 nm of 1.0.

extract_protocol:
RNA extraction was performed with the Thermo Scientific Genejet RNA purification kit according to manufacturer´s instructions. RNA extracts were digested with Turbo DNA-free DNAase at 37 °C for 1 hour.
rRNA removal, cDNA libraries generation and RNAseq were performed at Genoma Mayor (Santiago, Chile)

tag: genotype

value: RF- (riboflavin absent)


title: Ctrl_SOX17/EOMES, iMeLC, MS082Y05

description:
Sample 59
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at iMeLC, non-sorted


title: SOX17 KO, iMeLC, MS082Y40

description:
Sample 66
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at iMeLC, non-sorted


title: d06900GX2

description:
gene_exp.diff: d06900XX
Barcode: ACTTGA


title: EOMES KO, iPSC, MS102Y61

description:
Sample 22
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#26 line, harvested at iPSC, non-sorted

value: iPSC

value: EOMES-/-


title: wt_st26_cross2

value: wild-type (out-bred Nigerian)

tag: treatment

value: wild-type (wt) from cross of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 2)


title: ∆ribN RF- rep2

description: RF- riboflavin absent

tag: strain


title: wt_st26_cross9

value: wild-type (wt) from cross of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 9)


title: Bone marrow, Epo-stimulated

city: Worcester

first: Merav

last: Socolovsky

state: MA

address: 364 Plantation St

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

description:
eBM
The barcode reads are: SRR5010987 SRR5010989
The cDNA reads are: SRR5010988 SRR5010990

data_processing:
The barcode read was first filtered based on presence of two sample barcode components separated by the W1 adaptor sequence (GAGTGATTGCTTGTGACGCCTT), as previously described (Klein et al., Cell 2015).
The cDNA read was then trimmed using Trimomatic (5) (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
Barcodes for each read were matched against a list of the pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.  All files were submitted to SRA.
The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 100 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes).
A custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene, as previously described (Zilionis et al., Nature Protocols in press)
Genome_build: GRCm38
Supplementary_files_format_and_content: The raw_umifm_counts files include raw unique molecular identifier (UMI)-filtered counts for all transcriptomes (prior to filtering). The filtered_normalized_counts files have normalized counts for transcriptomes passing all filtering steps. In both cases, columns = genes (with exception of first 5 columns), rows = cells. Column 1 contains cell identifier. Column 2 contains matching cell barcode. Column 3 contains library ID. Column 4 contains sequencing run ID (cells with same run ID were run on same flow cell). Column 5 contains flag for cell pass filtering (0=fail, 1=pass). Columns 6+ contain counts for each gene.

source_name: Bone marrow Kit+ cells, Epo-stimulated

extract_protocol:
Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 4nL microfluidic droplets using a final concentration of 0.4% NP-40. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Libraries were prepared as in Zilionis et al., Nature Protocols (in press), with the exception of the first round of libraries, for which the final PCR step was carried out as in Klein et al., Cell 2015.

treatment_protocol: For bone-marrow preparation, femurs and tibiae were harvested immediately following euthanasia and placed in cold (4°C) ‘staining buffer’ (phosphate- buffered saline (PBS) containing 0.2% Bovine Serum Albumin (BSA) and 0.08% Glucose). Bones were flushed using a 2 mL syringe with a 26-gauge needle and then crushed with a pestle and mortar to obtain all cells. Harvested bone marrow cells were filtered through a 40 μm strainer and washed in cold ‘Easy Sep’ buffer (PBS; 2% fetal bovine serum (FBS); 1mM EDTA). Fetal livers were prepared by mechanical dissociation in staining buffer and a wash in ‘Easy-Sep’ buffer. Bone marrow and fetal liver cell samples were each enriched for Kit expressing cells using magnetic beads, with the Mouse Biotin Selection Kit (STEMCELL technologies [Cat # 18556]) and Biotin Rat Anti-Mouse CD117 antibody (clone 2B8 , BD Bioscience), following the manufacturer’s protocol. Dead cells and debris were removed from the bone marrow and fetal liver samples using density centrifugation in OptiPrep (Sigma, Cat # D1556). Briefly, cells were re-suspended in 0.5ml staining buffer, mixed with 1mL of 40% of Optiprep in PBS, and placed in a 5 mL tube. The cell suspension was carefully over-layered with 2 mL of 20% OptiPrep solution, and 1mL of 5% OptiPrep solution, and centrifuged at 800g for 15 min (Centrifuge break OFF). The top visible cell band that formed during centrifugation contained the live, Kit+ single cells, confirmed by flow cytometric analysis. This layer was carefully aspirated and used directly in the inDrops platform.

value: BALB/cJ

value: 8-week old adult

value: bone marrow

value: Kit+ hematopoietic progenitors

value: Epo-stimulated


title: ∆ribN RF- rep1

description: RF- riboflavin absent


title: WT RF- rep1

description: RF- riboflavin absent

value: Wild Type


title: WT RF- rep2

description: RF- riboflavin absent


title: wt_st26_cross1

value: mid-tailbud (stage 26)

value: wild-type (wt) from cross of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 1)


title: EOMES KO, iPSC, MS102Y39

description:
Sample 20
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#14 line, harvested at iPSC, non-sorted

value: Blimp1-tdTomato, TFAP2C-EGFP

value: Series 1, SOX17 KO and EOMES KO


title: WT RF- rep3

description: RF- riboflavin absent


title: tt2MO_st34_frogF

description: injected 18 ng t/t2 donor splice- and translation-blocking morpholino (t/t2 MO) into 1-cell stage embryos from frog F

value: mid-tailbud (stage 34)

value: morpholino


title: Ctrl_SOX17/EOMES, iMeLC, MS102Y43

description:
Sample 62
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at iMeLC, non-sorted

value: iMeLC

value: WT control