title: C2_H10

description: Htseq-counts-all

data_processing:
QC: Qualities of de-barcoded raw sequence reads were checked by fastqc.
Mapping: Mapping to the merged genome of mm10, ERCC, and E.coli K12 was performed with Tophat2 (2.1.0) using default settings. Cells with low ratiois of % of counts mapped to mm10 : % of counts mapped to spikein were excluded for further analysis.
Counting: Gene expression was counted with Htseq-count (0.6.1p1) using the union mode.
Normalization: The raw counts were normalized in three steps. First, they were normalized to a technical factor based on spike-in reads/cell and a biological factor based on mouse reads/cell in R with the DEseq package. Then they were normalized to an expt size factor based on mouse reads/experiment. Lastly the nonimmune cells were normalized using Combat to remove residual batch effects.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file containing the normalized counts for each gene in each cell.

source_name: Cardiac fibroblasts

growth_protocol: P1.5 neonatal hearts were isolated from CD1 mice and cardiac fibroblasts were isolated with the enzyme digestion method followed by MACS purification of Thy1+ cells. Purified cells were seeded onto 0.1% gelatin-coated plates at 2 x 104/cm2 in fibroblast media (IMDM + 20% FBS). After overnight culturing, media was replaced before retroviral transduction to remove unattached cells.

extract_protocol:
On day 3 post transduction, cells were collected by trypsinization, stained with 7AAD live/dead dye (Thermo Fisher Scientific), and FACS-sorted for live cells (negative for 7AAD). The sorted single cell suspension was loaded on a medium-sized (10-17 µm) microfluidic RNA-seq chip and single cells were captured with the C1 system. Bright field images were taken for each well of captured cells for later assessment of cell number and quality in each well. Next, RNA spike-in was added and cDNAs were prepared on chip using the SMARTer Ultra Low RNA kit from Illumina (Clontech).  Judged by cell number and morphology in the microscopic images, only cDNA libraries from single healthy cells were selected for Illumina library preparation.
Illumina libraries were prepared for sequencing using standard Illumina protocols (the Nextera XT Kit).

treatment_protocol: Retroviruses encoding M/ G/ T/ DsRed/ puro were packaged by transfecting platE cells (Cell Biolabs) with lipofectamine 2000 (Life Technology). Viruses collected from one 10 cm2 dish were resuspended in 100 µl iCM media. For cells under reprogramming, cardiac fibroblasts in one well of a 24 well plate were transduced with 10 µl of each of M, G, T viruses. For control cells, cardiac fibroblasts were either untransduced or transduced with 10 µl of pMXs-DsRed and 20 µl of pMXs-puro. Twenty-four hours post infection, viral medium was replaced with regular iCM medium.

tag: sample type

value: control


title: C2_H11

status: Public on Oct 25 2017

type: SRA

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

department: Biology

country: USA

institute: Medical College of Wisconsin

description: Htseq-counts-all

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: strain


title: Control cells for Tgfb receptors1/2 -deficient fibroblasts (HK7_run2110)

city: Cincinnati

first: Vikram

last: Prasad

state: OH

address: 240, Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description:
Fibroblasts are CRE+ and GFP+
Run_2110TGFbr1_2_DKO_vs_Tcf21_Cre_control_ALLGENES_rawvalues.txt
run2110_lane12_indexN704-S504=HK_7

data_processing:
Sequence reads were aligned using Strand NGS Software (Ver. 2.6) against Mouse mm10 (UCSC) using Ensembl transcript annotations ((2013.04.03)
Quantification using known annotation with Normalization Type: RPKM; Threshold for normalization =1;
Fold Change Analysis was carried out using Strand NGS Software and identifies genes with ratio between experimental and control conditions, above an assigned threshold. Both our analyses had two conditions; therefore, in each case, control cells were chosen as the reference condition against which the fold change for the DKO cells (experimental condition) was computed. As per Strand NGS manual, the exact fold change is computed as follows:
1. For each gene and condition, the average of the normalized signal values (in log-scale) is calculated.
2. Log Fold Change (Log FC) for a given gene, between the two conditions, is then the difference between their respective averages.
3. Fold change (FC) is then computed as (sign of Log FC) x 2ǀlogFCǀ; absolute FC is ǀFCǀ.
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: RPKMs and fold-change

molecule: total RNA

growth_protocol: All genetically-modified mouse lines utilized in this study have been previously described in the literature: these include lines containing a knock-in of a MerCreMer cDNA into either the Postn or Tcf21 genomic loci (1, 2), the Rosa26 reporter mice (R26eGFP) purchased from Jackson laboratories (Stock# 012429), LoxP-targeted Smad2/3 mice (3), and the Tgfbr1/2-loxP-targeted mice (4). Mice received i.p. injections with pharmaceutical grade tamoxifen (100 mg/kg body weight) dissolved in 95% peanut oil/ 5% ethanol for 2 consecutive days followed by continuous tamoxifen-citrate chow (40 mg/kg body weight, Envigo - TD.130860) until the experiment was terminated. Eight to ten week-old mice of the relevant genotypes were subjected to pressure overload by TAC surgery. Interstitial cells were isolated from cardiac ventricles, as described previously (1), 4 weeks after TAC injury. Flow cytometry analysis was performed on these cells using a Becton Dickinson FACSCanto II running FACSDiva software. For analysis and sorting of fibroblasts from either Tcf21 or Postn expressing lineages, we utilized endogenous eGFP fluorescence expressed by the recombined reporter allele. The count of GFP+ cells was normalized to the number of CD31+ cells to assure similar digestion of samples and to eliminate differences in total counts due to sample preparation variability.  1. Kanisicak O, et al. Genetic lineage tracing defines myofibroblast origin and function in the injured heart. Nat Commun. 2016;7:12260.  2. Acharya A, et al. Efficient inducible Cre-mediated recombination in Tcf21 cell lineages in the heart and kidney. Genesis. 2011;49:870-7.  3. Park BV, et al. TGFbeta1-Mediated SMAD3 Enhances PD-1 Expression on Antigen-Specific T Cells in Cancer. Cancer Discov. 2016;6:1366-81.  4. Koitabashi N, et al. Pivotal role of cardiomyocyte TGF-beta signaling in the murine pathological response to sustained pressure overload. J Clin Invest. 2011;121:2301-12.

extract_protocol:
Total RNA was extracted from fibroblasts. RNA quality and yield were determined using Agilent Bioanalyzer and submitted for RNA-seq analysis.
Total RNA was amplified using the Ovation RNA-Seq System v2 (NuGEN) according to the manufacturer’s protocol. The libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). 1 ng of cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Amplicon Tagment Mix), incubating at 55C for 10 min. NT Buffer was then added to neutralize the samples. Libraries were prepared by PCR with the Nextera PCR Master Mix, and 2 Nextera Indexes (N7XX, and N5XX) according to the following program: one cycle of 72C for 3min, one cycle of 98C for 30s, 12 cycles of 95C for 10s, 55C for 30s, and 72C for 1min, and one cycle of 72C for 5min.  The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocol.

treatment_protocol:
Upon tamoxifen administration, expression of Cre-recombinase under control of the endogenous Tcf21 promoter is turned on, and and eGFP reporter allele is recombined.
GFP+ fibroblasts were flow-sorted directly into Qiazol for lysis and RNA isolation.

tag: genetic modifications

value: MerCreMer cDNA in Tcf21 genomic locus; enhanced green fluorescent protein (eGFP) Cre-dependent reporter transgene in Rosa locus

tag: cell type

value: Cardiac fibroblasts

tag: genotype

value: Control for TGFbreceptors1/2 deficient mutant


title: Control cells for Smad2/3 deficient fibroblasts (HK3_run1739)

description:
Fibroblasts are CRE+ and GFP+
Run_1739Smad2_3_DKO_vs_Postn_Cre_control_ALLGENES_rawvalues.txt
run1739_lane1_indexN712-S508=Con_HK3_16112

treatment_protocol:
Upon induction of Postn gene expression, and tamoxifen administration, expression of Cre-recombinase is turned on, and eGFP reporter allele is recombined.
GFP+ fibroblasts were flow-sorted directly into Qiazol for lysis and RNA isolation.

value: MerCreMer cDNA in periostin (Postn) genomic locus; enhanced green fluorescent protein (eGFP) Cre-dependent reporter transgene in Rosa locus

value: Control for Smad2/3 DKO mutant


title: Mutant Smad2/3 DKO fibroblasts (HK16_run1739)

description:
Fibroblasts are CRE+, GFP+, SMAD2-deficient, and SMAD3-deficient
Run_1739Smad2_3_DKO_vs_Postn_Cre_control_ALLGENES_rawvalues.txt
run1739_lane1_indexN703-S503=DKO_Mut_HK16_16115

source_name: Mutant Smad2/3 DKO fibroblasts

treatment_protocol:
Upon induction of Postn gene expression, and tamoxifen administration, expression of Cre-recombinase is turned on, Cre/LoxP-dependent recombination of Smad2 and Smad3 genes occurs, and and eGFP reporter allele is recombined.
GFP+ fibroblasts were flow-sorted directly into Qiazol for lysis and RNA isolation.

value: MerCreMer cDNA in periostin (Postn) genomic locus; enhanced green fluorescent protein (eGFP) Cre-dependent reporter transgene in Rosa locus; Smad2 flox/flox; Smad3 flox/flox

value: Smad2/3 DKO mutant


title: Control cells for Tgfb receptors1/2 -deficient fibroblasts (HK6_run2110)

description:
Fibroblasts are CRE+ and GFP+
Run_2110TGFbr1_2_DKO_vs_Tcf21_Cre_control_ALLGENES_rawvalues.txt
run2110_lane12_indexN703-S503=HK_6

treatment_protocol:
Upon tamoxifen administration, expression of Cre-recombinase under control of the endogenous Tcf21 promoter is turned on, andand eGFP reporter allele is recombined.
GFP+ fibroblasts were flow-sorted directly into Qiazol for lysis and RNA isolation.


title: CF1

data_processing:
QC: Qualities of de-barcoded raw sequence reads were checked by fastqc.
Mapping: Mapping to the merged genome of mm10 was performed with Tophat2 (2.1.0) using default settings.
Counting: Gene expression was counted with Htseq-count (0.6.1p1) using the union mode and counts per million were calculated for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing CPM for each gene in each sample.

source_name: neonatal cardiac fibroblasts

growth_protocol: P1.5 neonatal hearts were isolated from CD1 mice and cardiac fibroblasts were isolated with the enzyme digestion method followed by MACS purification of Thy1+ cells. P1.5 cardiomyocytes were isolated using the neonatal cardiomyocytes isolation system (Worthington Biochemical Corporation). For reprogramming, CF cells were seeded onto 0.1% gelatin-coated plates at 2 x 104/cm2 in fibroblast media (IMDM + 20% FBS). After overnight culturing, media was replaced before retroviral transduction to remove unattached cells.

extract_protocol:
After three days, cells were collected and lysed in TRIzol.
Illumina libraries were prepared for sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Retroviruses encoding MGT were packaged by transfecting platE cells (Cell Biolabs) with lipofectamine 2000 (Life Technology) and lentiviruses encoding non-targeting shRNA control (shRNA) or shPtbp1 were packaged by transfecting 293T cells. Viruses collected from one 10 cm2 dish were resuspended in 100 µl iCM media. For RNA-seq of Ptbp1-silencing experiments, 2.5 x 105 CF were seeded into one well in a 6-well plate. On the following day, 50 µl of pMXs-puro/ pMXs-puro-MGT or 50 µl each of pMXs-puro-MGT and shNT/ shPtbp1-271 were added to the cells.

tag: age


title: Mutant TGFbreceptors1/2 deficient fibroblasts (HK2_run2110)

description:
Fibroblasts are CRE+, GFP+, TGFbreceptor1-deficient, and TGFbreceptor2-deficient
Run_2110TGFbr1_2_DKO_vs_Tcf21_Cre_control_ALLGENES_rawvalues.txt
run2110_lane12_indexN701-S517=HK_2

treatment_protocol:
Upon tamoxifen administration, expression of Cre-recombinase under control of the endogenous Tcf21 promoter is turned on, Cre/LoxP-dependent recombination of Tgfbr1 and Tgfbr2 genes occurs, and and eGFP reporter allele is recombined.
GFP+ fibroblasts were flow-sorted directly into Qiazol for lysis and RNA isolation.

value: MerCreMer cDNA in Tcf21 genomic locus; enhanced green fluorescent protein (eGFP) Cre-dependent reporter transgene in Rosa locus; Tgfbreceptor1flox/flox; Tgfbreceptor2flox/flox

value: TGFbreceptors1/2 deficient mutant


title: dCLIP hCBX7 rep 1

city: Boston

first: Michael

last: Rosenberg

state: MA - Massachusetts

address: 185 Cambridge street

department: Molecular Biology

institute: Massachusetts General Hospital, Harvard Medical School

description:
RNA extracted from membrane
dCLIP-seq Library.
dCLIP-seq

data_processing:
Base-calling was performed with Illumina real time analysis (RTA) basecaller v1.17.21.3
Adaptor sequences were trimmed from libraries with either Trim Galore! v0.3.3 (for CLIP-seq and RNA-seq; stringency 15 and allowed error rate 0.2) or Cutadapt v1.0 (for ChIP-seq; allowed error rate 0.2). PCR duplicates were removed by custom programs prior to alignment. Reads were aligned to the reference hg19 genome. RNA was aligned with Tophat (v2.0.8 or greater), while DNA was aligned using Novoalign (3.00.03). Post-processing of mm9 alignments was performed with custom C and Perl programs and bash shell scripts, SAMtools v0.1.18, and BEDtools v2.17.0. These included accounting, alignment file-type conversion, extracting and sorting uniquely/paired-end reads (SAMtools), and obtaining wig coverage files (DNA: BEDtools genomecov; RNA: SAMtools depth).
For dCLIP, Fragment per million (fpm) wig files were then created by scaling uniquely aligned wig files to total number of fragments per million in each library (determined by SAMtools flagstat combining reads “with itself and mate mapped” and “singletons”).
dCLIP-seq enriched tag density wig files were viewed in UCSC genome browser (7) or Integrated Genome Browser (IGB) (8). Then consecutive wig entries of equal coverage were merged forming bed files that were used for peak calling. The peak caller software PeakRanger (v.16)  was used. The software requires an even distribution of watson/crick entries, thus, prior to peak calling, strand specific bed file entries were randomized per each strand. PeakRanger was called with arguments ranger –p 0.01 –-format bed –gene_annot_file (hg19), –d experiment and –c mock-transfected control, to identify narrow peaks with p-value 0.01 or less. Peaks were called once over parental control (3.1 and 4.1) and once over GFP control (3.2 and 4.2).
Genome_build: hg19

organism: Homo sapiens

source_name: HEK293 cells

growth_protocol: HEK293 cells were routinely maintained in DME + 10% FBS.

extract_protocol:
UV-cross-linked cells, expressing BirA biotinylase and Biotin-tagged Cbx7 or mock vector, were isolated and lysed. Lysates were DNase-treated and RNAse-treated. Cleared lysates were incubated 2hrs with Streptavidin beads. After stringent washing and 2nd DNase treatment, CLIP-tags on beads were radiolabelled with [γ-32P]ATP, run on Bis-Tris SDS-PAGE in MOPS buffer, and transferred to nitrocellulose membrane. Membrane fragments containing CLIP signal and corresponding positions on control lanes were excised, and RNA was eluted by proteinase K, followed by Trizol extraction and ethanol precipitation.
Multiplex Compatible NEBNext Small RNA Library Prep Set for Illumina (NEB). Illumina barcode #6,GCCAAT. Paired-end 50bp reads
none provided by the submitter

treatment_protocol: UV cross-linking

tag: cells

value: Human Embryonic Kidney cells with stable expression of BirA biotinylase and Avi-GFP-hCBX7, clone 4G

tag: Sex

value: Female


title: PUM knockdown 3

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

description: PUMKD.txt

data_processing:
Base calls using CASAVA
Spliced reads were aligned to the genome using tophat 2.0.9 (calling bowtie 2.1.0)
cufflinks 2.1.0 was used to quantify expression based on the reference transcriptome
cuffdiff 2.1.1  was used to normalize counts and obtain abundance estimates for each sample and differential expression calls beween the PUMKD and NTC conditions
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Text files contain FPKM estimates for each gene from the genes.fpkm_tracking cuffdiff output file; results are pooled across replicates for each condition

growth_protocol: HEK293 cells were cultured at 37°C under 5% CO2 in DMEM with glucose and 1 x Penicillin/Streptomycin/Glutamine and 10% FBS (Gibco)

extract_protocol:
RNA was isolated using the Maxwell simplyRNA cells kit (Promega) and a MaxWell16 instrument, and subsequently poly-A purified
Prepared using a TruSeq RNA kit following the manufacturer's instructions

treatment_protocol: PUMs were knocked down in HEK293 cells using On-target Plus Smartpool siRNAs for PUM1 (L-014179-00), PUM2 (L-014031-02), or non-targeting control siRNAs (GE Dharmacon). HEK293 cells (2 x 10^5 cells per well) were plated into a 12-well culture plate. Three replicates were performed for each condition. After 24 hours, 500 μL culture medium was removed and cells were transfected with 100 fmoles of siRNAs using Dharmafect-I (Dharmacon). After 4-8 hours of siRNA treatment, 500 μL culture medium was refreshed. After 24 hours, 500 μL culture medium was removed and cells were transfected again with 100 fmoles of siRNAs using Dharmafect-I. After 4-8 hours of siRNA treatment, 650 μL culture medium was refreshed. Cells were harvested 48 hours after last transfection for RNA purification and RNA Seq experiments

value: immortalized human cell line HEK293

tag: shRNA


title: Non-targeting control 1

description: NTC.txt

value: Non-target control


title: dCLIP hCBX7 rep 2

extract_protocol:
UV-cross-linked cells, expressing BirA biotinylase and Biotin-tagged Cbx7 or mock vector, were isolated and lysed. Lysates were DNase-treated and RNAse-treated. Cleared lysates were incubated 2hrs with Streptavidin beads. After stringent washing and 2nd DNase treatment, CLIP-tags on beads were radiolabelled with [γ-32P]ATP, run on Bis-Tris SDS-PAGE in MOPS buffer, and transferred to nitrocellulose membrane. Membrane fragments containing CLIP signal and corresponding positions on control lanes were excised, and RNA was eluted by proteinase K, followed by Trizol extraction and ethanol precipitation.
Multiplex Compatible NEBNext Small RNA Library Prep Set for Illumina (NEB). Illumina barcode #8,ACTTGA. Paired-end 50bp reads
none provided by the submitter

value: Human Embryonic Kidney cells with stable expression of BirA biotinylase and Avi-GFP-hCBX7, clone 5G


title: C2_H09

description: Htseq-counts-all


title: Control cells for Smad2/3 deficient fibroblasts (HK4_run1739)

description:
Fibroblasts are CRE+ and GFP+
Run_1739Smad2_3_DKO_vs_Postn_Cre_control_ALLGENES_rawvalues.txt
run1739_lane1_indexN701-S517=Con_HK4_16113


title: Mutant Smad2/3 DKO fibroblasts (HK15_run1739)

description:
Fibroblasts are CRE+, GFP+, SMAD2-deficient, and SMAD3-deficient
Run_1739Smad2_3_DKO_vs_Postn_Cre_control_ALLGENES_rawvalues.txt
run1739_lane1_indexN702-S502=DKO_Mut_HK15_16114


title: C2_H07

description: Htseq-counts-all


title: C2_H06

description: Htseq-counts-all


title: Lib1_Rods_Rep1

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
RNA Barcodes in Rods
processed data file: Lib1Results.tab

data_processing:
Library strategy: Parallel Reporter Assay
A custom pipeline was created to assign barcodes to each tested sequences. Then sequence activity was calculated as the ratio of barcode abundance in the RNA sample compare to its abundance in the AAV pool.
Barcode sequences were extracted from 50bp reads by taking only reads starting with the expected backbone sequence: “TCCTGCTGGAGTTCGTGACCTGCATGCGCCGAA”. From these reads the sequence at position 34-48 was extracted. The frequency of each barcode sequence was calculated to get counts for each sample. Counts of barcodes were normalized to library size. Enrichment of barcodes in the RNA sample was calculated over their representation in the AAV input. Barcodes not sufficiently covered in the AAV sequencing were discarded (depending on sequencing depth 2-16 reads). The median activity of all barcodes per CRE was calculated. Only CREs that were covered in at least 2 out of 3 biological replicates with at least three barcodes were used for downstream analysis.
processed data: Tab delimited, summary table of the expression values for each tested seqeunce in the tested cell types
Genome_build: mm9

source_name: Rods

extract_protocol:
RNA was isolated from sorted cells using Qiagen RNeasy® Mini Kit with on-column DNase digestion followed by reverse transcription using Takara PrimeScript RT Reagent Kit (#RR047A).
barcodes were amplified with KAPA HIFI Hotstart using Primer #1 and indexing primers (Primers #3-11)

tag: tissue

value: Rods

tag: mouse strain

value: b2-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007913


title: C2_H04

description: Htseq-counts-all

value: control


title: ARD_pUTX_3d_Rep1

city: Pamplona

first: Teresa

last: Ezponda

state: Navarra

address: Pio XII 55

department: Hematology/Oncology

country: Spain

institute: Center for Applied Medical Research

description:
ARD cells were transduced with a plasmid to express UTX in a doxycyline inducible manner. Cells were grown in the absence (pUTX) or presence (pUTXDox) of doxycycline for 3 days.
ARP-UTX-Dox-FPKMs.csv

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw files were QC_processed to remove any reads which failed Illumina's purity filer, and were then trimmed using the Sickle tool
Reads were alinged using STAR (v 2.3.0e_r291)
Read counts per gene were calculated using HTSeq (v0.6.0).
The R (v3.1.1) Bioconductor package, edgeR (v3.8.5) was used to identify statistically significant differentially expressed genes
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited files containing FPKMs for all genes.

source_name: ARD

extract_protocol:
Cell pellets were frozen at -80 C and total RNA was extracted using the Rneasy mini kit (Qiagen), including the on column Dnase step. Libraries were prepared using the TruSeq RNA sample kit (Illumina) and multiplexed samples were sequenced on a Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: multiple myeloma

tag: utx status

tag: culture condition

value: Advanced RPMI + 4% Fetal Bovine Serum + glutamax


title: C2_H05

description: Htseq-counts-all


title: C2_H03

description: Htseq-counts-all


title: Mutant TGFbreceptors1/2 deficient fibroblasts (HK4_run2110)

description:
Fibroblasts are CRE+, GFP+, TGFbreceptor1-deficient, and TGFbreceptor2-deficient
Run_2110TGFbr1_2_DKO_vs_Tcf21_Cre_control_ALLGENES_rawvalues.txt
run2110_lane12_indexN702-S502=HK_4

value: Cardiac fibroblasts


title: C2_H01

description: Htseq-counts-all


title: C2_G10

description: Htseq-counts-all


title: C2_G09

description: Htseq-counts-all


title: C2_G07

description: Htseq-counts-all


title: C2_G11

description: Htseq-counts-all


title: C2_G06

description: Htseq-counts-all


title: C2_H02

description: Htseq-counts-all


title: C2_G05

description: Htseq-counts-all


title: C2_F11

description: Htseq-counts-all


title: C2_G03

description: Htseq-counts-all


title: C2_G08

description: Htseq-counts-all


title: C2_G04

description: Htseq-counts-all


title: C2_G01

description: Htseq-counts-all


title: C2_F10

description: Htseq-counts-all


title: C2_F07

description: Htseq-counts-all


title: C2_H08

description: Htseq-counts-all


title: C2_F09

description: Htseq-counts-all


title: C2_F08

description: Htseq-counts-all


title: C2_F06

description: Htseq-counts-all


title: C2_F05

description: Htseq-counts-all


title: C2_F03

description: Htseq-counts-all


title: C2_F04

description: Htseq-counts-all


title: C2_E11

description: Htseq-counts-all


title: C2_E10

description: Htseq-counts-all


title: C2_F01

description: Htseq-counts-all


title: C2_E09

description: Htseq-counts-all


title: C2_E08

description: Htseq-counts-all


title: C2_E07

description: Htseq-counts-all


title: C2_G02

description: Htseq-counts-all


title: C2_E05

description: Htseq-counts-all


title: C2_E06

description: Htseq-counts-all


title: C2_E04

description: Htseq-counts-all


title: C2_E03

description: Htseq-counts-all


title: C2_E01

description: Htseq-counts-all


title: C2_E02

description: Htseq-counts-all


title: C2_D08

description: Htseq-counts-all


title: C2_D11

description: Htseq-counts-all


title: C2_D09

description: Htseq-counts-all


title: C2_D06

description: Htseq-counts-all


title: C2_F02

description: Htseq-counts-all


title: C2_D05

description: Htseq-counts-all


title: C2_D07

description: Htseq-counts-all


title: C2_D02

description: Htseq-counts-all


title: C2_D04

description: Htseq-counts-all


title: C2_D01

description: Htseq-counts-all


title: C2_D03

description: Htseq-counts-all


title: C2_C12

description: Htseq-counts-all


title: C2_C11

description: Htseq-counts-all


title: C2_C07

description: Htseq-counts-all


title: C2_C06

description: Htseq-counts-all


title: C2_C10

description: Htseq-counts-all


title: C2_C08

description: Htseq-counts-all


title: C2_C04

description: Htseq-counts-all


title: C2_C03

description: Htseq-counts-all


title: C2_C01

description: Htseq-counts-all


title: C2_C05

description: Htseq-counts-all


title: C2_C02

description: Htseq-counts-all


title: C2_B12

description: Htseq-counts-all


title: C2_B10

description: Htseq-counts-all


title: C2_B11

description: Htseq-counts-all


title: C2_B09

description: Htseq-counts-all


title: C2_B08

description: Htseq-counts-all


title: C2_C09

description: Htseq-counts-all


title: C2_B04

description: Htseq-counts-all


title: C2_B07

description: Htseq-counts-all


title: C2_B05

description: Htseq-counts-all


title: C2_B06

description: Htseq-counts-all


title: C2_B02

description: Htseq-counts-all


title: C2_A10

description: Htseq-counts-all


title: C2_B03

description: Htseq-counts-all


title: C2_A09

description: Htseq-counts-all


title: C2_A11

description: Htseq-counts-all


title: C2_A12

description: Htseq-counts-all


title: C2_A08

description: Htseq-counts-all


title: C2_A06

description: Htseq-counts-all


title: C2_A04

description: Htseq-counts-all


title: C2_A07

description: Htseq-counts-all


title: C2_A03

description: Htseq-counts-all


title: C2_A02

description: Htseq-counts-all


title: C2_A01

description: Htseq-counts-all


title: M5_H08

description: Htseq-counts-all

value: reprogramming cells and retroviral-infected control cells


title: M5_H07

description: Htseq-counts-all


title: M5_H06

description: Htseq-counts-all


title: M5_H05

description: Htseq-counts-all


title: M5_H03

description: Htseq-counts-all


title: M5_H04

description: Htseq-counts-all


title: M5_H02

description: Htseq-counts-all


title: C2_B01

description: Htseq-counts-all


title: M5_H01

description: Htseq-counts-all


title: C2_A05

description: Htseq-counts-all


title: M5_G07

description: Htseq-counts-all


title: M5_G06

description: Htseq-counts-all


title: M5_G04

description: Htseq-counts-all


title: M5_G05

description: Htseq-counts-all


title: M5_G03

description: Htseq-counts-all


title: M5_G08

description: Htseq-counts-all


title: C2_D10

description: Htseq-counts-all


title: M5_G02

description: Htseq-counts-all


title: M5_F05

description: Htseq-counts-all


title: M5_F02

description: Htseq-counts-all


title: M5_F06

description: Htseq-counts-all


title: M5_F07

description: Htseq-counts-all


title: M5_F04

description: Htseq-counts-all


title: M5_F03

description: Htseq-counts-all


title: M5_E06

description: Htseq-counts-all


title: M5_E07

description: Htseq-counts-all


title: M5_F01

description: Htseq-counts-all


title: M5_E05

description: Htseq-counts-all


title: M5_E04

description: Htseq-counts-all


title: M5_E08

description: Htseq-counts-all


title: M5_E03

description: Htseq-counts-all


title: M5_E02

description: Htseq-counts-all


title: M5_E01

description: Htseq-counts-all


title: M5_D06

description: Htseq-counts-all


title: M5_D08

description: Htseq-counts-all


title: M5_D05

description: Htseq-counts-all


title: M5_G01

description: Htseq-counts-all


title: M5_F08

description: Htseq-counts-all


title: M5_D04

description: Htseq-counts-all


title: M5_D01

description: Htseq-counts-all


title: M5_D02

description: Htseq-counts-all


title: M5_C06

description: Htseq-counts-all


title: M5_C07

description: Htseq-counts-all


title: M5_C08

description: Htseq-counts-all


title: M5_D03

description: Htseq-counts-all


title: M5_C05

description: Htseq-counts-all


title: M5_C01

description: Htseq-counts-all


title: M5_B09

description: Htseq-counts-all


title: M5_B08

description: Htseq-counts-all


title: M5_C04

description: Htseq-counts-all


title: M5_B02

description: Htseq-counts-all


title: M5_B06

description: Htseq-counts-all


title: M5_D07

description: Htseq-counts-all


title: M5_B04

description: Htseq-counts-all


title: M5_A09

description: Htseq-counts-all


title: M5_C02

description: Htseq-counts-all


title: M5_A08

description: Htseq-counts-all


title: M5_B03

description: Htseq-counts-all


title: M5_B05

description: Htseq-counts-all


title: M5_B07

description: Htseq-counts-all


title: M5_B01

description: Htseq-counts-all


title: M5_A07

description: Htseq-counts-all


title: M5_A05

description: Htseq-counts-all


title: M5_A04

description: Htseq-counts-all


title: M5_A06

description: Htseq-counts-all


title: M5_A02

description: Htseq-counts-all


title: M5_A01

description: Htseq-counts-all


title: M4_H05

description: Htseq-counts-all


title: M4_H04

description: Htseq-counts-all


title: M4_H08

description: Htseq-counts-all


title: M4_H09

description: Htseq-counts-all


title: M4_H06

description: Htseq-counts-all


title: M4_H03

description: Htseq-counts-all


title: M4_G10

description: Htseq-counts-all


title: M4_H01

description: Htseq-counts-all


title: M4_H02

description: Htseq-counts-all


title: M4_G08

description: Htseq-counts-all


title: M4_G06

description: Htseq-counts-all


title: M4_G02

description: Htseq-counts-all


title: M4_G07

description: Htseq-counts-all


title: M4_F10

description: Htseq-counts-all


title: M4_G05

description: Htseq-counts-all


title: M4_G04

description: Htseq-counts-all


title: M4_F08

description: Htseq-counts-all


title: M4_G01

description: Htseq-counts-all


title: M4_G03

description: Htseq-counts-all


title: M4_F06

description: Htseq-counts-all


title: M4_F05

description: Htseq-counts-all


title: M4_F07

description: Htseq-counts-all


title: M4_F04

description: Htseq-counts-all


title: M5_A03

description: Htseq-counts-all


title: M4_F03

description: Htseq-counts-all


title: M4_F02

description: Htseq-counts-all


title: M4_E09

description: Htseq-counts-all


title: M4_E10

description: Htseq-counts-all


title: M4_F01

description: Htseq-counts-all


title: M5_C03

description: Htseq-counts-all


title: M4_E07

description: Htseq-counts-all


title: M4_E08

description: Htseq-counts-all


title: M4_F09

description: Htseq-counts-all


title: M4_H07

description: Htseq-counts-all


title: M4_E06

description: Htseq-counts-all


title: M4_E03

description: Htseq-counts-all


title: M4_E05

description: Htseq-counts-all


title: M4_E04

description: Htseq-counts-all


title: M4_D05

description: Htseq-counts-all


title: M4_D06

description: Htseq-counts-all


title: M4_D10

description: Htseq-counts-all


title: M4_D08

description: Htseq-counts-all


title: M4_D04

description: Htseq-counts-all


title: M4_E02

description: Htseq-counts-all


title: M4_D07

description: Htseq-counts-all


title: M4_D02

description: Htseq-counts-all


title: M4_D03

description: Htseq-counts-all


title: M4_C11

description: Htseq-counts-all


title: M4_C10

description: Htseq-counts-all


title: M4_C09

description: Htseq-counts-all


title: M4_C08

description: Htseq-counts-all


title: M4_C06

description: Htseq-counts-all


title: M4_C05

description: Htseq-counts-all


title: M4_C03

description: Htseq-counts-all


title: M4_C02

description: Htseq-counts-all


title: M4_B11

description: Htseq-counts-all


title: M4_C04

description: Htseq-counts-all


title: M4_C01

description: Htseq-counts-all


title: M4_B10

description: Htseq-counts-all


title: M4_E01

description: Htseq-counts-all


title: M4_B07

description: Htseq-counts-all


title: M4_B08

description: Htseq-counts-all


title: M4_D09

description: Htseq-counts-all


title: M4_B09

description: Htseq-counts-all


title: M4_D01

description: Htseq-counts-all


title: M4_B05

description: Htseq-counts-all


title: M4_B04

description: Htseq-counts-all


title: M4_B02

description: Htseq-counts-all


title: M4_B03

description: Htseq-counts-all


title: M4_B01

description: Htseq-counts-all


title: M4_A11

description: Htseq-counts-all


title: M4_A10

description: Htseq-counts-all


title: M4_C07

description: Htseq-counts-all


title: M4_A09

description: Htseq-counts-all


title: M4_A08

description: Htseq-counts-all


title: M4_A06

description: Htseq-counts-all


title: M4_A07

description: Htseq-counts-all


title: M4_A03

description: Htseq-counts-all


title: M4_A05

description: Htseq-counts-all


title: M4_A02

description: Htseq-counts-all


title: M4_B06

description: Htseq-counts-all


title: M3_H09

description: Htseq-counts-all

value: reprogramming cells


title: M4_A01

description: Htseq-counts-all


title: M3_H08

description: Htseq-counts-all


title: M3_H07

description: Htseq-counts-all


title: M3_H05

description: Htseq-counts-all


title: M3_H04

description: Htseq-counts-all


title: M3_H06

description: Htseq-counts-all


title: M3_H01

description: Htseq-counts-all


title: M3_G10

description: Htseq-counts-all


title: M3_H03

description: Htseq-counts-all


title: M3_G09

description: Htseq-counts-all


title: M3_G07

description: Htseq-counts-all


title: M3_G05

description: Htseq-counts-all


title: M3_G06

description: Htseq-counts-all


title: M3_G08

description: Htseq-counts-all


title: M3_G02

description: Htseq-counts-all


title: M3_G01

description: Htseq-counts-all


title: M3_G04

description: Htseq-counts-all


title: M3_F11

description: Htseq-counts-all


title: M4_A04

description: Htseq-counts-all


title: M3_H10

description: Htseq-counts-all


title: M3_F10

description: Htseq-counts-all


title: M3_F07

description: Htseq-counts-all


title: M3_F08

description: Htseq-counts-all


title: M3_F09

description: Htseq-counts-all


title: M3_H02

description: Htseq-counts-all


title: M3_G11

description: Htseq-counts-all


title: M3_F06

description: Htseq-counts-all


title: M3_F04

description: Htseq-counts-all


title: M3_F03

description: Htseq-counts-all


title: M3_F01

description: Htseq-counts-all


title: M3_F02

description: Htseq-counts-all


title: M3_E11

description: Htseq-counts-all


title: M3_E09

description: Htseq-counts-all


title: M3_E10

description: Htseq-counts-all


title: M3_E08

description: Htseq-counts-all


title: M3_G03

description: Htseq-counts-all


title: M3_E07

description: Htseq-counts-all


title: M3_E05

description: Htseq-counts-all


title: M3_E02

description: Htseq-counts-all


title: M3_E03

description: Htseq-counts-all


title: M4_H10

description: Htseq-counts-all


title: M3_E06

description: Htseq-counts-all


title: M3_E01

description: Htseq-counts-all


title: M3_D09

description: Htseq-counts-all


title: M3_D11

description: Htseq-counts-all


title: M3_D10

description: Htseq-counts-all


title: M3_D08

description: Htseq-counts-all


title: M3_F05

description: Htseq-counts-all


title: M3_D01

description: Htseq-counts-all


title: M3_D05

description: Htseq-counts-all


title: M3_D04

description: Htseq-counts-all


title: M3_D03

description: Htseq-counts-all


title: M3_C11

description: Htseq-counts-all


title: M3_D02

description: Htseq-counts-all


title: M3_C10

description: Htseq-counts-all


title: M3_E04

description: Htseq-counts-all


title: M3_C05

description: Htseq-counts-all


title: M3_C04

description: Htseq-counts-all


title: M3_C06

description: Htseq-counts-all


title: M3_C03

description: Htseq-counts-all


title: M3_C07

description: Htseq-counts-all


title: M3_C01

description: Htseq-counts-all


title: M3_B07

description: Htseq-counts-all


title: M3_B09

description: Htseq-counts-all


title: M3_D07

description: Htseq-counts-all


title: M3_B11

description: Htseq-counts-all


title: M3_B06

description: Htseq-counts-all


title: M3_B03

description: Htseq-counts-all


title: M3_B02

description: Htseq-counts-all


title: M3_C09

description: Htseq-counts-all


title: M3_C08

description: Htseq-counts-all


title: M3_B05

description: Htseq-counts-all


title: M3_B04

description: Htseq-counts-all


title: M3_A09

description: Htseq-counts-all


title: M3_A06

description: Htseq-counts-all


title: M3_A10

description: Htseq-counts-all


title: M3_B01

description: Htseq-counts-all


title: M3_A05

description: Htseq-counts-all


title: M3_C02

description: Htseq-counts-all


title: M3_A07

description: Htseq-counts-all


title: M3_B08

description: Htseq-counts-all


title: M3_B10

description: Htseq-counts-all


title: M3_A08

description: Htseq-counts-all


title: M3_A11

description: Htseq-counts-all


title: M3_A03

description: Htseq-counts-all


title: C1_H09

description: Htseq-counts-all


title: C1_H10

description: Htseq-counts-all


title: M3_A01

description: Htseq-counts-all


title: M3_A02

description: Htseq-counts-all


title: C1_H07

description: Htseq-counts-all


title: M3_A04

description: Htseq-counts-all


title: C1_H06

description: Htseq-counts-all


title: M4_G09

description: Htseq-counts-all


title: C1_H08

description: Htseq-counts-all


title: M3_D06

description: Htseq-counts-all


title: Poly I:C + Pten-1 (2W)

city: La Jolla

first: Jin

last: Lee

state: California

address: 9500 Gilman Drive BRF II

department: Pathology Department

institute: University California, San Diego

description:
Sample 22
Processed data file: Pten vs Poly I-C + Pten (2W).txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Data expression genes level generated from Cuffdiff.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text files include expression level of genes (log value) for each Sample. D1, D2, PKO_1, and PKO_2 represent samples that were not treated with poly I:C, and DP1, DP2, PKO_P1, and PKO_P2 represent samples that were treated with poly I:C.

source_name: Liver, Pten KO, Poly I:C, 2wk

extract_protocol:
RNA was harvested 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: Poly I:C (15 ug/kg, BW) injected intraperitoneally into DEN-induced Shp2∆H (Shp2F/F:Alb-cre) and Pten∆H (PtenF/F:Alb-cre) mice and then liver tissue collected 7 days and 14 days after poly I:C treatment.

tag: strain/background

tag: genotype/variation

value: Pten KO in hepatocytes

value: Liver

tag: treatment

value: Poly I:C

tag: time point


title: Pten-2 (1W)

description:
Sample 14
Processed data file: Pten vs Poly I-C + Pten (1W).txt

source_name: Liver, Pten KO, untreated, 1wk


title: Pten-3 (2W)

description:
Sample 21
Processed data file: Pten vs Poly I-C + Pten (2W).txt

source_name: Liver, Pten KO, untreated, 2wk


title: Pten-1 (2W)

description:
Sample 19
Processed data file: Pten vs Poly I-C + Pten (2W).txt


title: Poly I:C + Pten-1 (1W)

description:
Sample 16
Processed data file: Pten vs Poly I-C + Pten (1W).txt

source_name: Liver, Pten KO, Poly I:C, 1wk


title: C1_H04

description: Htseq-counts-all

tag: sample type


title: Poly I:C + Pten-2 (1W)

description:
Sample 17
Processed data file: Pten vs Poly I-C + Pten (1W).txt


title: Pten-3 (1W)

description:
Sample 15
Processed data file: Pten vs Poly I-C + Pten (1W).txt


title: Pten-2 (2W)

description:
Sample 20
Processed data file: Pten vs Poly I-C + Pten (2W).txt


title: C1_H05

description: Htseq-counts-all

tag: strain


title: C1_H03

description: Htseq-counts-all


title: Poly I:C + Pten-2 (2W)

description:
Sample 23
Processed data file: Pten vs Poly I-C + Pten (2W).txt


title: Poly I:C + Pten-3 (2W)

description:
Sample 24
Processed data file: Pten vs Poly I-C + Pten (2W).txt


title: C1_G09

description: Htseq-counts-all


title: C1_G10

description: Htseq-counts-all


title: C1_H02

description: Htseq-counts-all


title: C1_H01

description: Htseq-counts-all


title: Poly I:C + Pten-3 (1W)

description:
Sample 18
Processed data file: Pten vs Poly I-C + Pten (1W).txt


title: Pten-1 (1W)

description:
Sample 13
Processed data file: Pten vs Poly I-C + Pten (1W).txt


title: Poly I:C + DEN-Shp2-3 (2W)

description:
Sample 12
Processed data file: DEN-Shp2 vs Poly I-C + DEN-Shp2 (2W).txt

source_name: Liver, Shp2 KO, Poly I:C + DEN, 2wk

value: Shp2 KO in hepatocytes

value: Poly I:C + DEN


title: C1_G06

description: Htseq-counts-all


title: C1_G05

description: Htseq-counts-all


title: C1_G07

description: Htseq-counts-all


title: C1_G08

description: Htseq-counts-all


title: Poly I:C + DEN-Shp2-2 (2W)

description:
Sample 11
Processed data file: DEN-Shp2 vs Poly I-C + DEN-Shp2 (2W).txt


title: Poly I:C + DEN-Shp2-1 (2W)

description:
Sample 10
Processed data file: DEN-Shp2 vs Poly I-C + DEN-Shp2 (2W).txt


title: C1_G04

description: Htseq-counts-all


title: DEN-Shp2-3 (2W)

description:
Sample 9
Processed data file: DEN-Shp2 vs Poly I-C + DEN-Shp2 (2W).txt

source_name: Liver, Shp2 KO, DEN, 2wk

value: DEN


title: C1_G03

description: Htseq-counts-all


title: DEN-Shp2-2 (2W)

description:
Sample 8
Processed data file: DEN-Shp2 vs Poly I-C + DEN-Shp2 (2W).txt


title: DEN-Shp2-3 (1W)

description:
Sample 3
Processed data file: DEN-Shp2 vs Poly I-C + DEN-Shp2 (1W).txt

source_name: Liver, Shp2 KO, DEN, 1wk


title: Poly I:C + DEN-Shp2-3 (1W)

description:
Sample 6
Processed data file: DEN-Shp2 vs Poly I-C + DEN-Shp2 (1W).txt

source_name: Liver, Shp2 KO, Poly I:C + DEN, 1wk


title: Poly I:C + DEN-Shp2-2 (1W)

description:
Sample 5
Processed data file: DEN-Shp2 vs Poly I-C + DEN-Shp2 (1W).txt


title: C1_G02

description: Htseq-counts-all


title: Poly I:C + DEN-Shp2-1 (1W)

description:
Sample 4
Processed data file: DEN-Shp2 vs Poly I-C + DEN-Shp2 (1W).txt


title: DEN-Shp2-1 (1W)

description:
Sample 1
Processed data file: DEN-Shp2 vs Poly I-C + DEN-Shp2 (1W).txt


title: C1_G01

description: Htseq-counts-all


title: DEN-Shp2-2 (1W)

description:
Sample 2
Processed data file: DEN-Shp2 vs Poly I-C + DEN-Shp2 (1W).txt


title: DEN-Shp2-1 (2W)

description:
Sample 7
Processed data file: DEN-Shp2 vs Poly I-C + DEN-Shp2 (2W).txt


title: C1_F06

description: Htseq-counts-all


title: C1_F07

description: Htseq-counts-all


title: C1_F08

description: Htseq-counts-all


title: C1_F09

description: Htseq-counts-all


title: C1_F05

description: Htseq-counts-all


title: C1_F11

description: Htseq-counts-all


title: C1_F10

description: Htseq-counts-all


title: 11-6-15-WT_S113.1

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

data_processing:
Raw reads were mapped to reference genome mm9 using BWA MEM (Li and Durbin, 2010), and apparent PCR duplicates were removed using Picard MarkDuplicates (Wysoker, et al., 2013). Read alignment positions were adjusted to account for the transposase binding motif: alignments to the + strand were adjusted by +4 bp, and reads on the – strand by -5bp. Open chromatin peak calls were called using Macs2 (Zhang, et al., 2008) with a q-value threshold of 1e-5 and --nomodel selected. Bedgraph tracks quantifying open chromatin were created using bedtools genomecov (Quinlan and Hall, 2010) on the adjusted alignments, followed by conversion to bigWig using UCSC tool bedGraphToBigWig (Kent, et al., 2010). Open chromatin enrichment tracks were normalized to counts per billion bases, based on the sum of read lengths in the library. To quantify ATAC enrichment, a union of peak calls from all ATAC-seq samples was created using bedtools merge (Quinlan and Hall, 2010). Enrichment was quantified as raw counts against this annotation of merged peak calls using featureCounts (Liao, et al., 2014). We computed differential expression statistics in the same manner as for RNA-seq with one exception: using principle component analysis,, we noticed a batch effect among the ATAC samples that separated the samples into three batches, correlated with their processing dates (batches: batch 1 – 11-16-15-KO_S56, 11-16-15-WT_S39; batch 2 – 7-22-16-DOX_S41, 10-30-15-KO_S34, 10-30-15-WT_S32, 12-11-15-WT_S31, 7-22-16-No-Dox_S40; batch 3 – 1-12-16-Dox_S37, 12-18-15-Dox_S38, 12-11-15-KO_S33, 10-23-15-KO_S55, 10-23-15-WT_S38, 1-12-16-No-Dox_S35, 12-18-15-No-Dox_S36).  We controlled for the batch effect in the edgeR processing by including the batch as a factor in the differential enrichment analysis and using removeBatchEffect to subtract it from the log-scaled normalized enrichment levels.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig: Open chromatin enrichment tracks for ATAC-seq data. Units are reads per billion bases.
Supplementary_files_format_and_content: bed: Peak calls for ATAC-seq data. Scores are -log10 q-value from Macs2.
Supplementary_files_format_and_content: normalized expression/enrichment: Normalized expression levels (RNA-seq) or open chromatin enrichment levels (ATAC-seq). RNA expression are in counts per million (CPM). ATAC enrichment are in log2 CPM, and have been corrected for batch effect observed among ATAC samples using edgeR; batches are: batch 1 – 11-16-15-KO_S56, 11-16-15-WT_S39; batch 2 – 7-22-16-DOX_S41, 10-30-15-KO_S34, 10-30-15-WT_S32, 12-11-15-WT_S31, 7-22-16-No-Dox_S40; batch 3 – 1-12-16-Dox_S37, 12-18-15-Dox_S38, 12-11-15-KO_S33, 10-23-15-KO_S55, 10-23-15-WT_S38, 1-12-16-No-Dox_S35, 12-18-15-No-Dox_S36.
Supplementary_files_format_and_content: raw expression/enrichment: Raw counts for RNA-seq and ATAC seq samples. Regions in merged.bed were used for quantification of ATAC-seq samples.

source_name: OT-II, day 3 post immunization

growth_protocol: OT-II CD4+ (Rag1-/-) TCR transgenic cells from lymph nodes of Irf4-/-, Irf4+/+, or Irf4-inducible donor mice were quantitated by measuring the frequency of CD4+Vβ5+ cells and 5x105  OT-II cells were adoptively transferred into CD45.1 congenic recipients. For all transfers involving Irf4-inducible OT-II cells, donor cells were enriched by negative selection involving a cocktail of biotinylated antibodies (CD8, CD11b, GR-1, DX5, B220, CD19, IgM, CD25, CD44) followed by anti-biotin magnetic beads (Miltenyi) and magnetic separation; cells were typically ≥90% CD4+ after the procedure. The next day, transplanted mice were immunized with RFR-OVA emulsified in CFA. Three days after immunization, responding cells OT-II cells were sorted (CD45.1-B220-MHCII-CD45.2+CD4+) on a FACSAria and cells were processed for RNA-seq and ATAC-seq. Each replicate sample was derived by pooling responding OT-II cells from multiple immunized mice.

extract_protocol: For RNA-seq, total RNA was prepared using RNEasy micro kit (Qiagen) and analyzed on RNA pico bioanalyzer chips (Agilent) prior to library construction. Strand-specific RNA-seq libraries were generated for each sample from 100 ng of total RNA using the Kapa Stranded RNA-seq kit (Kapa Biosystems, Cape Town, South Africa) after poly-A enrichment according to the instructions of the manufacturer.  The consistent fragment lengths of the sequencing libraries were ascertained using a Bioanalyzer 2100 micro-capillary gel electrophoresis instrument (Agilent, Santa Clara, CA).  The barcoded libraries were quantified by fluorometry on a Qubit instrument (LifeTechnologies, Carlsbad, CA), and pooled in equimolar ratios. The pool was quantified by qPCR with a Kapa Library Quant kit (Kapa Biosystems) and sequenced on one lane of an Illumina HiSeq 4000 sequencer (Illumina, San Diego, CA) run with single-end 90 bp reads.

treatment_protocol: Each OT-II group represented a different genotype of Irf4. For the Irf4-inducible group, such mice were administered DOX in the drinking water for the first two days of the response and switch to normal water thereafter.

tag: condition


title: 12-10-15-NoDox_S117.1

tag: cell type

value: OT-II CD4+ (Rag1-/-) TCR transgenic cells


title: C1_F04

description: Htseq-counts-all


title: 12-18-15-No-Dox_S121.1


title: C1_F03

description: Htseq-counts-all


title: 1-12-16-No-Dox_S126.1


title: C1_F01

description: Htseq-counts-all


title: 11-16-15-WT_S115.1


title: C1_E11

description: Htseq-counts-all


title: C1_E10

description: Htseq-counts-all


title: 12-23-15-KO_S125.1


title: 12-23-15-No-Dox_S123.1


title: 11-6-15-KO_S114.1


title: 12-11-15-KO_S120.1


title: C1_E09

description: Htseq-counts-all


title: C1_E07

description: Htseq-counts-all


title: 11-16-15-KO_S116.1


title: C1_F02

description: Htseq-counts-all


title: C1_E06

description: Htseq-counts-all


title: 12-23-15-Dox_S124.1

value: Irf4-inducible (Irf4+/+) + DOX


title: 12-18-15-Dox_S122.1


title: C1_E08

description: Htseq-counts-all


title: C1_E03

description: Htseq-counts-all


title: C1_E05

description: Htseq-counts-all


title: 12-10-15-Dox_S118.1


title: 1-12-16-Dox_S127.1


title: 10-23-15-KO_S112.1


title: C1_D10

description: Htseq-counts-all


title: 7.22.16.No.Dox_S40

library_source: genomic

molecule: genomic DNA

extract_protocol: ATAC-seq libraries were constructed using the Nexterra kit (Illumina) and then subjected to 8 rounds of amplification with index-specific primers. The ATAC-seq libraries were quantified by both Bioanalyzer and Qubit measurements and pooled in equimolar ratios. They were sequenced on an Illumina HiSeq 4000 sequencer with paired-end 100bp reads on 6 lanes.


title: C1_D11

description: Htseq-counts-all


title: 12.11.15.WT_S31


title: C1_E02

description: Htseq-counts-all


title: 12.18.15.No.Dox_S36


title: C1_D08

description: Htseq-counts-all


title: 10.30.15.WT_S32


title: 1.12.16.No.Dox_S35


title: C1_D07

description: Htseq-counts-all


title: 11.16.15.WT_S39


title: 10.23.15.WT_S38


title: C1_E04

description: Htseq-counts-all


title: C1_D09

description: Htseq-counts-all


title: C1_D06

description: Htseq-counts-all


title: 11.16.15.KO_S56


title: C1_D05

description: Htseq-counts-all


title: 10.23.15.KO_S55


title: C1_D04

description: Htseq-counts-all


title: C1_D03

description: Htseq-counts-all


title: 12.11.15.KO_S33


title: C1_E01

description: Htseq-counts-all


title: C1_D02

description: Htseq-counts-all


title: 7.22.16.DOX_S41


title: C1_D01

description: Htseq-counts-all


title: 10.30.15.KO_S34


title: 12.18.15.Dox_S38


title: 1.12.16.Dox_S37


title: C1_C07

description: Htseq-counts-all


title: C1_C09

description: Htseq-counts-all


title: C1_C06

description: Htseq-counts-all


title: C1_C05

description: Htseq-counts-all


title: C1_C10

description: Htseq-counts-all


title: C1_C02

description: Htseq-counts-all


title: C1_C03

description: Htseq-counts-all


title: C1_C08

description: Htseq-counts-all


title: C1_C11

description: Htseq-counts-all


title: C1_C04

description: Htseq-counts-all


title: C1_B11

description: Htseq-counts-all


title: C1_B10

description: Htseq-counts-all


title: C1_C01

description: Htseq-counts-all


title: C1_B09

description: Htseq-counts-all


title: C1_B08

description: Htseq-counts-all


title: C1_B05

description: Htseq-counts-all


title: C1_B04

description: Htseq-counts-all


title: C1_B03

description: Htseq-counts-all


title: C1_B02

description: Htseq-counts-all


title: C1_B01

description: Htseq-counts-all


title: C1_A11

description: Htseq-counts-all


title: C1_A10

description: Htseq-counts-all


title: C1_A09

description: Htseq-counts-all


title: C1_A07

description: Htseq-counts-all


title: C1_A08

description: Htseq-counts-all


title: C1_A06

description: Htseq-counts-all


title: C1_A04

description: Htseq-counts-all


title: C1_A05

description: Htseq-counts-all


title: C1_A03

description: Htseq-counts-all


title: C1_A01

description: Htseq-counts-all


title: C1_A02

description: Htseq-counts-all


title: M2_H09

description: Htseq-counts-all


title: M2_H08

description: Htseq-counts-all


title: M2_H05

description: Htseq-counts-all


title: M2_H06

description: Htseq-counts-all


title: M2_H10

description: Htseq-counts-all


title: M2_H07

description: Htseq-counts-all


title: M2_H02

description: Htseq-counts-all


title: M2_H01

description: Htseq-counts-all


title: M2_H03

description: Htseq-counts-all


title: C1_B07

description: Htseq-counts-all


title: M2_G10

description: Htseq-counts-all


title: M2_H04

description: Htseq-counts-all


title: M2_G09

description: Htseq-counts-all


title: C1_B06

description: Htseq-counts-all


title: M2_G06

description: Htseq-counts-all


title: M2_G04

description: Htseq-counts-all


title: M2_G05

description: Htseq-counts-all


title: M2_G07

description: Htseq-counts-all


title: M2_G03

description: Htseq-counts-all


title: M2_G02

description: Htseq-counts-all


title: M2_F11

description: Htseq-counts-all


title: M2_F10

description: Htseq-counts-all


title: M2_G01

description: Htseq-counts-all


title: M2_F09

description: Htseq-counts-all


title: M2_F06

description: Htseq-counts-all


title: M2_F04

description: Htseq-counts-all


title: M2_E09

description: Htseq-counts-all


title: M2_F01

description: Htseq-counts-all


title: M2_F02

description: Htseq-counts-all


title: M2_F05

description: Htseq-counts-all


title: M2_F08

description: Htseq-counts-all


title: M2_E10

description: Htseq-counts-all


title: M2_E08

description: Htseq-counts-all


title: M2_F03

description: Htseq-counts-all


title: M2_E07

description: Htseq-counts-all


title: M2_E02

description: Htseq-counts-all


title: M2_G08

description: Htseq-counts-all


title: M2_E03

description: Htseq-counts-all


title: M2_E01

description: Htseq-counts-all


title: M2_E05

description: Htseq-counts-all


title: M2_D11

description: Htseq-counts-all


title: M2_D10

description: Htseq-counts-all


title: M2_D09

description: Htseq-counts-all


title: M2_D08

description: Htseq-counts-all


title: M2_F07

description: Htseq-counts-all


title: M2_D06

description: Htseq-counts-all


title: M2_D07

description: Htseq-counts-all


title: M2_E11

description: Htseq-counts-all


title: M2_D05

description: Htseq-counts-all


title: 17_Pc_B108T17

city: Orsay

first: Anne-Helene

last: Monsoro-Burq

address: Bat 110

department: Université Paris Sud

country: France

institute: Institut Curie

data_processing:
Reads were mapped on the X. laevis genome (9.1), using tophat 2.0.14 with the following parameters (--rg-library Illumina --rg-platform Illumina --keep-fasta-order -N 6 --read-gap-length 6 --read-edit-dist 6 --segment-mismatches 3 -i 5 -I 500000 -r 155 --mate-std-dev 80 --no-coverage-search -p 6 --library-type fr-firststrand -g 2).
Read counts were computed using HTSeq with the gene models v1.8.0 of the Xenopus laevis 9.1 genome annotation.
Genome_build: Xenopus laevis 9.1
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample.

organism: Xenopus laevis

source_name: Placode

growth_protocol: Xenopus laevis embryos were obtained by in vitro fertilization using standard procedures and grown until the desired stage (12.5, 14, or 17) according to Nieuwkoop and Faber developmental table.

extract_protocol:
Ectodermal explant were microdissected, RNA was harvested using Trizol Reagent, RNA-seq libraries were prepared using the TruSeq Stranded mRNA library preparation kit (Illumina) starting with 40-300 ng of total RNA, and sequenced on a HiSeq 2000 (Illumina) with a target of 15-20 million 100 bp paired reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Placode

tag: genotype

value: wild type


title: 17_Pc_B108T16


title: M2_E06

description: Htseq-counts-all


title: M2_D03

description: Htseq-counts-all


title: 14_NB_B108T12

source_name: Neural Border

value: Neural Border


title: M2_D04

description: Htseq-counts-all

source_name: Cardiac fibroblasts


title: 17_NC_B108T9

source_name: Neural Crest

value: Neural Crest


title: 18-19_WE_B108T48

source_name: Whole Embryo

value: Whole Embryo


title: 16-17_WE_B108T47


title: M2_C11

description: Htseq-counts-all


title: M2_C10

description: Htseq-counts-all


title: M2_D01

description: Htseq-counts-all


title: M2_C09

description: Htseq-counts-all


title: 12.5_WE_B108T44


title: M2_C07

description: Htseq-counts-all


title: 13_WE_B108T45


title: 11-11.5_WE_B108T42


title: M2_C08

description: Htseq-counts-all


title: 12_WE_B108T43


title: M2_E04

description: Htseq-counts-all


title: 16-17_WE_B108T40


title: M2_C06

description: Htseq-counts-all


title: 18-19_WE_B108T41


title: M2_C04

description: Htseq-counts-all


title: 17_NC_B108T14


title: M2_C03

description: Htseq-counts-all


title: 14-15_WE_B108T39


title: M2_D02

description: Htseq-counts-all


title: 13_WE_B108T38


title: M2_C02

description: Htseq-counts-all


title: 12.5_WE_B108T37


title: 12_WE_B108T36


title: M2_B11

description: Htseq-counts-all


title: M2_B10

description: Htseq-counts-all


title: 11-11.5_WE_B108T35


title: 14-15_WE_B108T46


title: 14_NB(p)_B100T20

source_name: Neural Border(posterior)

value: Neural Border(posterior)


title: 14_NB(a)_B108T84

source_name: Neural Border(anterior)

value: Neural Border(anterior)

tag: dissected embryo id number


title: 14_NB(a)_B108T28


title: M2_B09

description: Htseq-counts-all


title: 14_WE_B108T27


title: M2_C05

description: Htseq-counts-all


title: M2_B08

description: Htseq-counts-all


title: M2_B07

description: Htseq-counts-all


title: M2_B05

description: Htseq-counts-all


title: 14_NB_B108T18


title: 14_WE_B108T26


title: M2_B04

description: Htseq-counts-all


title: M2_B03

description: Htseq-counts-all


title: 14_ANF/PPE_B108T59

source_name: Anterior Neural Fold/Pre-Placodal Ectoderm


title: 14_NP(p)_B108T58

source_name: Neural Plate(posterior)

value: Neural Plate(posterior)


title: M2_B02

description: Htseq-counts-all

value: reprogramming cells


title: M2_C01

description: Htseq-counts-all


title: 14_NNE(a)_B108T82

source_name: Non-Neural Ectoderm(anterior)

value: Non-Neural Ectoderm(anterior)


title: 14_ANF/PPE_B108T57

value: Anterior Neural Fold/Pre-Placodal Ectoderm


title: M2_B01

description: Htseq-counts-all


title: M2_A09

description: Htseq-counts-all


title: 14_NNE(a)_B108T96


title: M2_A08

description: Htseq-counts-all


title: 14_NP(p)_B108T79


title: M2_A07

description: Htseq-counts-all


title: 14_NB(p)_B100T17


title: 14_NB(p)_B108T81


title: 14_ANF/PPE_B108T8


title: M2_A06

description: Htseq-counts-all


title: M2_B06

description: Htseq-counts-all


title: 14_ANF/PPE_B100T9


title: 14_NNE(p)_B108T95

source_name: Non-Neural Ectoderm(posterior)

value: Non-Neural Ectoderm(posterior)


title: M2_A05

description: Htseq-counts-all


title: M2_A04

description: Htseq-counts-all


title: M2_A03

description: Htseq-counts-all


title: M2_A02

description: Htseq-counts-all


title: 14_NP(p)_B108T77


title: M2_A11

description: Htseq-counts-all


title: M2_A01

description: Htseq-counts-all


title: M1_H09

description: Htseq-counts-all


title: M2_A10

description: Htseq-counts-all


title: 14_NB(a)_B108T80


title: M1_H07

description: Htseq-counts-all


title: M1_H08

description: Htseq-counts-all


title: 14_ANF/PPE_B108T56


title: 14_NP(a)_B108T7

source_name: Neural Plate(anterior)

value: Neural Plate(anterior)


title: 14_NP(a)_B108T76


title: 14_NNE(p)_B108T93


title: 14_NNE(a)_B108T92


title: M1_H06

description: Htseq-counts-all


title: 14_NB(p)_B108T91


title: C3638: XY d39 DSD littermate gonad

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.5 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 was used to map reads to the Dog CanFam3 reference genome, guided by the CanFam3 annotated transcriptome (Ensembl).
Novel transcripts were analyzed with cufflinks v2.2.1 (cufflinks, cuffmerge) guided by the CanFam3 annotated transcriptome (Ensembl). File: GuidedDiscovery_genes.gtf.gz
Transcripts were quantified with cuffquant v2.2.1 (-max-bundle-frags 5000000 to handle intervals with high read counts). Analyses included annotated genes only (CanFam3 gtf file with Amh added; --no-novel-juncs) and 'discovery' guided by annotated genes (cuffmerge output: GuidedDiscovery_genes.gtf.gz).
FPKM values were generated with cufflinks v2.2.1: cuffnorm was used for analysis of all samples in parallel for both annotated genes only (+Amh) and for the set of novel genes in GuidedDiscovery_genes.gtf.gz (guided by CanFam3 annotated genes); cuffdiff was used to call differentially expressed annotated genes for age-matched XX cohorts at d37 and d43.
Genome_build: CanFam3 (Ensembl)
Supplementary_files_format_and_content: Tab delimited text files generated with Cufflinks including FPKM values for all samples (Annotated_genes_FPKM.txt, GuidedDiscovery_genes_FPKM.txt) and differential gene expression analysis, including q-values reflecting multiple hypothesis testing correction, for age-matched XX cohorts at d37 and d43 (XX_d37_gene_exp.diff, XX_d43_gene_exp.diff).

organism: Canis lupus familiaris

source_name: embryonic gonad

extract_protocol:
Total RNA was isolated with the RNeasy Plus Mini Kit (Qiagen)
Standard polyA+ RNAseq libraries were prepared with the TruSeq RNA Library Prep Kit v2 (Illumina) by the Cornell Biotechnology Resource Center Genomics Facility

treatment_protocol: gonadal tissue was dissected from embryos and then flash frozen and stored in liquid nitrogen

value: embryonic gonad

tag: developmental age

tag: sex chromosomes

value: XY

tag: pedigree

value: DSD


title: 14_NB(a)_B108T90

tag: tissue


title: 14_NP(p)_B108T55


title: 14_NNE(p)_B108T94


title: C3637: XY d39 DSD littermate gonad


title: 14_NB(a)_B108T78


title: M1_H02

description: Htseq-counts-all


title: C3626: XY d39 DSD littermate gonad


title: M1_H03

description: Htseq-counts-all


title: M1_H04

description: Htseq-counts-all


title: C3633: XX d39 DSD gonad

value: XX


title: 12.5_ANB/PPE_B108T54

source_name: Anterior Neural Border/Pre-Placodal Ectoderm


title: C3632: XX d39 DSD gonad


title: C3627: XY d39 DSD littermate gonad


title: C3642: XX d39 DSD gonad


title: M1_G09

description: Htseq-counts-all


title: M1_H05

description: Htseq-counts-all


title: C3630: XX d39 DSD gonad


title: C3636: XX d39 DSD gonad


title: M1_G07

description: Htseq-counts-all


title: 12.5_NB(a)_B108T89


title: 12.5_NNE_B108T6

source_name: Non-Neural Ectoderm

value: Non-Neural Ectoderm


title: C3619: XY d35 DSD littermate gonad


title: 12.5_NP(a)_B108T74

value: wild type


title: C3618: XY d35 DSD littermate gonad


title: 14_NP(a)_B108T75


title: M1_H01

description: Htseq-counts-all


title: C3574: XY d35 DSD littermate gonad


title: C3575: XX d35 DSD gonad


title: C3616: XX d35 DSD gonad


title: 12.5_NB(p)_B108T73


title: M1_G05

description: Htseq-counts-all


title: C3573: XX d35 DSD gonad


title: C3572: XX d35 DSD gonad


title: M1_G03

description: Htseq-counts-all


title: M1_G08

description: Htseq-counts-all


title: 12.5_NB(a)_B108T72


title: C3571: XX d35 DSD gonad


title: C3525: XX d35 DSD gonad


title: M1_G02

description: Htseq-counts-all


title: C3617: XY d35 DSD littermate gonad


title: 12.5_ANB/PPE_B108T5

value: Anterior Neural Border/Pre-Placodal Ectoderm


title: C3510: XX d35 DSD gonad


title: C3624: XX d39 DSD gonad


title: C3511: XX d35 DSD gonad


title: M1_G01

description: Htseq-counts-all


title: C3509: XX d35 DSD gonad


title: 12.5_NB(a)_B108T71


title: M1_G06

description: Htseq-counts-all


title: M1_F09

description: Htseq-counts-all


title: 12.5_NP(a)_B108T52


title: M1_G04

description: Htseq-counts-all


title: BCtoPr_Lib4_Rep2

description:
Barcode to promoter assignment
processed data file: BCtoPr_Lib4.tab

data_processing:
Library strategy: Parallel Reporter Assay
A custom pipeline was created to assign barcodes to each tested sequences. Then sequence activity was calculated as the ratio of barcode abundance in the RNA sample compare to its abundance in the AAV pool.
Sequences from Read1 starting with "TCCACTGGGAGAAGAGGAAGTCAAA" were linked to mutant sequences using a custom script. Sequences from Read2 between “CGTTTAAACTGTCGACCGAGCT” and 'TTCGGCGCATG” were extracted as barcodes and the reverse complement was generated. barcodes and aligned reads were matched by read ID. Barcodes that were associated with one CRE or with a CRE that represents >90% of all reads of a barcode were used for the analysis, the rest was discarded.
processed data: Tab delimited, correspondance between the tested element and its barcode in each library
Genome_build: mm9

molecule: other

organism: synthetic construct

source_name: Plasmid

extract_protocol:
Qiagen-Midi
CRE-barcode sequences were amplified using Primer #2 and one of the Indexing primers (Primers #3-11) containing the Illumina flow cell annealing sequences. PCR products were purified using AmPure XP beads (Beckman Coulter, #A63880).

value: Plasmid


title: XX d34 control gonads, pool of 6

value: Control


title: 12.5_NB(l)_B108T53

source_name: Neural Border(lateral)

value: Neural Border(lateral)


title: M1_F08

description: Htseq-counts-all


title: 12.5_NP(p)_B100T16


title: BCtoPr_Lib4_Rep1


title: BCtoPr_Lib3

description:
Barcode to promoter assignment
processed data file: BCtoPr_Lib3.tab

data_processing:
Library strategy: Parallel Reporter Assay
A custom pipeline was created to assign barcodes to each tested sequences. Then sequence activity was calculated as the ratio of barcode abundance in the RNA sample compare to its abundance in the AAV pool.
Sequences from Read1 starting with "TCCACTGGGAGAAGAGGAAGTCAAA" were aligned from position 55 on to the Mus Musculus genome (BSgenome.Mmusculus.UCSC.mm9) using Bowtie. Sequences from Read2 between “CGTTTAAACTGTCGACCGAGCT” and 'TTCGGCGCATG” were extracted as barcodes and the reverse complement was generated. barcodes and aligned reads were matched by read ID. Barcodes that were associated with one CRE or with a CRE that represents >90% of all reads of a barcode were used for the analysis, the rest was discarded.
processed data: Tab delimited, correspondance between the tested element and its barcode in each library
Genome_build: mm9


title: BCtoPr_Lib2

description:
Barcode to promoter assignment
processed data file: BCtoPr_Lib2.tab


title: M1_F07

description: Htseq-counts-all


title: BCtoPr_Lib1_Rep2

description:
Barcode to promoter assignment
processed data file: BCtoPr_Lib1.tab


title: 12.5_NB(l)_B108T51


title: M1_F06

description: Htseq-counts-all


title: 12.5_NNE_B108T70


title: BCtoPr_Lib1_Rep1


title: M1_F04

description: Htseq-counts-all


title: 12.5_NB(p)_B108T69

value: Neural Border(posterior)


title: 12.5_NP(p)_B108T50

value: Neural Plate(posterior)


title: M1_F05

description: Htseq-counts-all

value: reprogramming cells


title: fb_L3_PGAM5'_-

city: Novato

first: Martin

last: Borch Jensen

address: 8001 Redwood Blvd.

institute: Buck Institute for Research on Aging

data_processing:
Basecalls performed by Illumina MiSeq v2.5.0.5
Sequenced reads were mapped and aligned using Bowtie/Tophat.
Mapped reads were quantified using Cufflinks
Genome_build: Dm genome release 5.75
Supplementary_files_format_and_content: Excel table containing fragments per kilobase million

organism: Drosophila melanogaster

source_name: Fat body

extract_protocol:
Tissue dissected into Trizol, RNA isolated per manufacturer's protocol.
RNA libraries were prepared using the Illumina TruSeq RNA Library Prep Kit, with standard protocols

value: PGAM5 null, DaGeneSwitch x PGAM5 null, UAS-dOTC

value: L3 larvae


title: fb_L3_WT_-

value: DaGeneSwitch x UAS-dOTC


title: fb_L3_PGAM5'_RU


title: 12.5_ANB/PPE_B108T4


title: XY d34 control gonads, pool of 7


title: fb_L3_WT_RU


title: fb_adult_PGAM5'_-

value: Adult


title: 12.5_NB(a)_B108T68

value: Neural Border(anterior)


title: fb_adult_PGAM5'_RU


title: M1_F03

description: Htseq-counts-all


title: M1_F02

description: Htseq-counts-all


title: thorax_dOTC

source_name: Thorax

value: tubulinGeneSwitch x UAS-dOTC


title: fb_adult_WT_-


title: thorax_ND75

value: tubulinGeneSwitch x ND75 RNAi


title: 12.5_NNE_B108T3


title: M1_F01

description: Htseq-counts-all

source_name: Cardiac fibroblasts


title: 12.5_NP(a)_B108T67

value: Neural Plate(anterior)


title: thorax_control

value: tubulinGeneSwitch x w1118


title: M1_E08

description: Htseq-counts-all


title: M1_E09

description: Htseq-counts-all


title: 12.5_NB(p)_B108T66

value: wild type


title: M1_E07

description: Htseq-counts-all


title: MEL18_ChIP-seq_in_NTERA2-D1_cells_replicate1

city: Umeå

first: Yuri

middle: B

last: Schwartz

address: Byggnad 6L, NUS

country: Sweden

institute: Umeå University

data_processing:
Base calling and quality score assignment were done with built in Real-time analysis (RTA) software (Illumina)
ChIP-seq reads were aligned to the Hg19 genome assembly using bowtie2 using the default parameters
The SAM files were filtered with samtools to remove all reads with q-scores less than 10
The filtered SAM files were converted to wig format using pyicos. During conversion the reads were extended to 180bp
Genome_build: Hg19
Supplementary_files_format_and_content: wig files were generated using pyicos; Scores represent the number of reads overlapping each genomic position.

source_name: Cultured cells

growth_protocol: Cells were cultured in high-glucose DMEM (Gibco) supplemented with 10% Fetal Bovine Serum (Sigma), Penicillin/Streptomycin (Gibco) and 1.5g/L Sodium Bicarbonate (Sigma) at 37C in atmosphere of 5% CO2

extract_protocol:
Live cells were crosslinked with 1% formaldehyde for 10 min at 37C and soluble chromatin prepared as described in Schwartz et al., 2006. ChIP was done as described in Schwartz et al., 2006.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina and Multiplex Oligos for Illumina (New England BioLabs) following the manufacturer instructions.

tag: cell line

tag: mutation

tag: antibody

value: anti-MEL18 Abcam #ab77255


title: 14_NP_B100T19

source_name: Neural Plate

value: Neural Plate


title: 14_NB_B108T83

source_name: Neural Border

value: Neural Border


title: SUZ12_ChIP-seq_in_NTERA2-D1_cells_replicate1

value: anti-SUZ12 Cell Signalling #3737


title: 14_NP_B100T18


title: 12.5_NB(l)_B108T49

value: Neural Border(lateral)


title: M1_E04

description: Htseq-counts-all


title: M1_E06

description: Htseq-counts-all


title: M1_E03

description: Htseq-counts-all


title: M1_E05

description: Htseq-counts-all


title: fb_adult_WT_RU


title: 17_NC_B100T3

source_name: Neural Crest

value: Neural Crest


title: 17_NC_B108T1


title: M1_D09

description: Htseq-counts-all

value: reprogramming cells


title: M1_E01

description: Htseq-counts-all


title: 12.5_NP(p)_B108T65

value: Neural Plate(posterior)


title: M1_E02

description: Htseq-counts-all


title: M1_D08

description: Htseq-counts-all


title: 14_NB_B108T22


title: M1_D07

description: Htseq-counts-all


title: M1_D05

description: Htseq-counts-all


title: 14_NB(p)_B100T2

source_name: Neural Border(posterior)

value: Neural Border(posterior)


title: M1_D04

description: Htseq-counts-all


title: M1_D03

description: Htseq-counts-all


title: M1_D02

description: Htseq-counts-all


title: M1_C10

description: Htseq-counts-all


title: M1_D01

description: Htseq-counts-all


title: M1_C09

description: Htseq-counts-all


title: M1_C08

description: Htseq-counts-all


title: M1_C05

description: Htseq-counts-all


title: M1_C04

description: Htseq-counts-all


title: M1_C07

description: Htseq-counts-all


title: M1_C06

description: Htseq-counts-all


title: M1_C01

description: Htseq-counts-all


title: M1_C02

description: Htseq-counts-all


title: M1_B09

description: Htseq-counts-all


title: M1_B08

description: Htseq-counts-all


title: M1_B07

description: Htseq-counts-all


title: M1_B05

description: Htseq-counts-all


title: M1_B06

description: Htseq-counts-all


title: M1_B04

description: Htseq-counts-all


title: M1_D06

description: Htseq-counts-all


title: M1_B03

description: Htseq-counts-all


title: 14_NB(a)_B100T1

source_name: Neural Border(anterior)


title: M1_B02

description: Htseq-counts-all


title: M1_A08

description: Htseq-counts-all


title: M1_A09

description: Htseq-counts-all


title: M1_A10

description: Htseq-counts-all


title: M1_B01

description: Htseq-counts-all


title: M1_A05

description: Htseq-counts-all


title: M1_A07

description: Htseq-counts-all


title: M1_A04

description: Htseq-counts-all


title: M1_A06

description: Htseq-counts-all


title: Input for ChIP-seq, lin-35(n745) extract rep 1

city: Santa Cruz

first: Paul

last: Goetsch

state: CA

address: 1156 High Street

department: MCD Biology

institute: UCSC

data_processing:
bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10
SPP v1.10.1 peak caller (from phantompeakqualtools) was run on the bowtie output for each subunit for each replicate (rep 1-3), pseudoreplicates (rep1.pr1,rep1.pr2,etc), pooled replicates (rep 0), and pooled psuedoreplicates (rep0.pr1,rep0.pr2) against pooled input with the following parameters: -npeak=40000, -savn, -savp, -rf
IDR v2.0.2 was run on SPP peak outputs for each subunit on replicates (rep1v2, rep1v3, rep2v3) defining N1-2, N1-3, and N2-3 (threshold IDR < 0.01), selfPseudoReplicates (rep1.pr1vpr2) defining N1, N2, and N3 (threshold IDR < 0.02), and pooledPseudoReplicates (rep0.pr1vpr2) defining Np (threshold IDR  < 0.005). N1-2, N1-3, and N2-3 were averaged to define Nt for each factor, which was selected as the final number of peaks passing the 1% IDR threshold. The Rescue Ratio (Np/Nt) and Self-consistency ratio (Max(N1,N2,N3)/Min(N1,N2,N3)) were calculated to check for low consistency between replicates (low consistency is defined as ratio >> 2).
The deepTools v2.0 tool bamCompare was used to normalize to input and create bigwig signal track files for visualization. Pooled replicates were normalized to pooled input using the Signal Extraction Scaling (SES) method using the following parameters: --scaleFactorsMethod SES--numberOfSamples=100000 --ratio ratio  --binSize 10 --pseudocount=1 --extendReads x (x was calculated from SPP analysis for each factor)
Genome_build: ws220 (ce10)
Supplementary_files_format_and_content: bigwig signal track files of combined replicates (rep0) for each ChIP normalized to pooled input using the SES method (Diaz et al. 2012) and narrowPeak files containing peak regions for each ChIP (IDR < 0.01)

organism: Caenorhabditis elegans

growth_protocol: Synchronized N2 or lin-35(n745) L1s were grown in standard S-basal media liquid culture for 72 or 96 hours, respectively. Adult worms were treated with standard bleaching solution to collect embryos, and embryos were incubated for up to 3.5 hours then frozen in liquid nitrogen

extract_protocol:
Crosslinked samples were resuspended in FA buffer, and sonicated in a Diagenode Bioruptor (60 pulses of 30 seconds at full power with 1 minute rest in between). Extracts were clarified, protein concentrations determined using a Qubit fluorometer, and precleared with Protein A Dynabeads before proceeding to ChIP. DRM subunits were individually IPed using 1-5 μg appropriate antibodies on prepared lysates. ChIPs were performed with 1-2 mg of extract, and 2% of the extract was set aside for an input reference control. ChIPs were incubated overnight at 4°C with 1% sarkosyl. Protein A Dynabeads equilibrated in 20 μL FA buffer were added and incubated for 2 hours at 4°C. ChIPs were washed with the following buffers: once with FA buffer containing 1 M NaCl, once with FA buffer containing 0.5 M NaCl, once with TEL buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). 2 elutions of 50 μL elution buffer containing TE plus 1% SDS and 250 mM NaCl were incubated at 55°C. Eluted ChIP and input samples were incubated with proteinase K for 1 hour at 55°C. Crosslinks were reversed overnight at 65°C. DNA was purified by phenol-chloroform extraction and ethanol precipitation using glycogen as a carrier.
Libraries from wild-type late embryos, extracts rep 1a, 1b, 2a, and 2b: Both ChIP and input DNA samples have their ends blunted and phosphorylated with KlenowDNAP, T4 DNAP, and T4 PNK. 3?-dA overhangs are then added with Klenow Fragment (3? to 5?exo minus), and Illumina adapters are subsequently ligated to the ends. Next, PCRamplification is performed using Illumina 1.1 and 2.1 primers, for a total of 18 cycles. AmplifiedDNA libraries are size-selected on a 2% agarose gel so that fragments sized between 250-350bp are obtained; gel extraction is carried out at room temperature. Libaries from wild-type late embryo extract rep 3 and lin-35(n745) late embryo extracts rep 1-3 were prepared using the TruSeq ChIP Sample Prep Kit (Illumina). Amplifed libraries were size selected to obtain 200-500 base pair fragments using Agencourt AMPure XP beads (Beckman Coulter).

treatment_protocol: Frozen late embryos were ground using a mortar and pestle and crosslinked for 10 minutes in 1% formaldehyde.

value: late embryo


title: M1_C03

description: Htseq-counts-all

extract_protocol:
On day 3 post transduction, cells were collected by trypsinization, stained with 7AAD live/dead dye (Thermo Fisher Scientific), and FACS-sorted for live cells (negative for 7AAD). The sorted single cell suspension was loaded on a medium-sized (10-17 µm) microfluidic RNA-seq chip and single cells were captured with the C1 system. Bright field images were taken for each well of captured cells for later assessment of cell number and quality in each well. Next, RNA spike-in was added and cDNAs were prepared on chip using the SMARTer Ultra Low RNA kit from Illumina (Clontech).  Judged by cell number and morphology in the microscopic images, only cDNA libraries from single healthy cells were selected for Illumina library preparation.
Illumina libraries were prepared for sequencing using standard Illumina protocols (the Nextera XT Kit).


title: Input for ChIP-seq, lin-35(n745) extract rep 2


title: M1_A03

description: Htseq-counts-all


title: M1_B10

description: Htseq-counts-all


title: M1_A02

description: Htseq-counts-all


title: Input for ChIP-seq, wildtype extract rep 2a

source_name: Input for ChIP-seq, wildtype extract

value: wild-type


title: M1_A01

description: Htseq-counts-all


title: LIN-54 ChIP-seq in lin-35(n745) late embryos, rep 1

description:
processed data file:
LIN-54.BH00004.lin-35.n745.rep0.vsInputRep0.SES.bw
LIN-54.BH00004.lin-35.n745.IDR.0.01.narrowPeak

tag: chip-antibody

value: Horvitz lab BH0004 (Harrison et al. 2006)

tag: input control

value: lin-35(n745) extract rep 1


title: LIN-54 ChIP-seq in lin-35(n745) late embryos, rep 2

value: lin-35(n745) extract rep 2


title: WGBS_SBAC_4

data_processing:
Raw sequence files were pre-processed using Trimmomatic1 to remove Illumina adaptor sequences, discard low quality reads and trim low quality bases. The trimmed reads were then aligned using QuasR (using Bowtie as an aligner) against a bisulfite index of the Mus Musculus genome (BSgenome.Mmusculus.UCSC.mm9). CpG methylation call was performed using QuasR. Conversion rates were determined (and controlled to be >98%) by calling methylation of mitochondrial DNA and non-CG context Cs. Methylation was called genome wide for CpGs covered at least 8 times. Since most datasets arise from female mice, sex chromosomes were excluded from the methylation analysis. Curves represent smoothed data obtained by averaging data using a sliding window over 10 Cs.
processed data: Tab delimited, average methylation values for single CpG across four cell types (coverage>7); Tab delimited, average methylation values for hypomethylated regions (LMRs) across four cell types. Only LMRs sufficiently covered in all cell types were considered.
Genome_build: mm9

source_name: Starbust amacrine cells

extract_protocol:
DNA was extracted from cells sorted from single retinas. 50-100ng of DNA was used as an input for bisulfite conversion (Zymo Gold Kit).
The converted DNA was used to prepare whole genome bisulfite libraries using Illumina Truseq DNA methylation preparation kit (EGMK81312) following manufacturer recommendation. PCR product was purified using AMPureXP beads (Beckman Coulter - A63880)

value: Starbust amacrine cells

tag: mouse strain

value: 129S6-Chat_tm1(cre)Lowl/J x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007922


title: WGBS_SBAC_3

value: 129S6-Chat_tm1(cre)Lowl/J x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007921


title: WGBS_SBAC_2

value: 129S6-Chat_tm1(cre)Lowl/J x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007920


title: LIN-54 ChIP-seq in wild-type late embryos, rep 2a

description:
processed data file:
LIN-54.BH00004.N2.rep0.vsInputRep0.SES.bw
LIN-54.BH00004.N2.IDR.0.01.narrowPeak

value: wild-type extract rep 2a


title: LIN-52 ChIP-seq in lin-35(n745) late embryos, rep 1

description:
processed data file:
LIN-52.BH00001.lin-35.n745.rep0.vsInputRep0.SES.bw
LIN-52.BH00001.lin-35.n745.IDR.0.01.narrowPeak

value: Horvitz lab BH0001 (Harrison et al. 2006)


title: LIN-37 ChIP-seq in lin-35(n745) late embryos, rep 1

description:
processed data file:
LIN-37.SDQ3166.lin-35.n745.rep0.vsInputRep0.SES.bw
LIN-37.SDQ3166.lin-35.n745.IDR.0.01.narrowPeak

value: SDIX/Novus Biologicals Q3166


title: LIN-37 ChIP-seq in lin-35(n745) late embryos, rep 2


title: WGBS_HC_8

source_name: Horizontal Cells

value: Horizontal Cells

value: B6Cf1-Tg(Gja10-Cre, #14)BR x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007919


title: WGBS_SBAC_1


title: LIN-9 ChIP-seq in lin-35(n745) late embryos, rep 2

description:
processed data file:
LIN-9.BH00005.lin-35.n745.rep0.vsInputRep0.SES.bw
LIN-9.BH00005.lin-35.n745.IDR.0.01.narrowPeak

value: Horvitz lab BH0005 (Harrison et al. 2006)


title: LIN-52 ChIP-seq in lin-35(n745) late embryos, rep 2


title: WGBS_HC_7

value: B6Cf1-Tg(Gja10-Cre, #14)BR x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007918


title: WGBS_HC_4

value: B6Cf1-Tg(Gja10-Cre, #14)BR x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007917


title: WGBS_HC_6


title: WGBS_HC_5


title: WGBS_HC_3


title: LIN-35 ChIP-seq in wild-type late embryos, rep 2a

description:
processed data file:
LIN-35.SDQ2003.N2.rep0.vsInputRep0.SES.bw
LIN-35.SDQ2003.N2.IDR.0.01.narrowPeak

value: late embryo

value: SDIX/Novus Biologicals Q2003


title: LIN-35 ChIP-seq in lin-35(n745) late embryos, rep 1

description:
processed data file:
LIN-35.SDQ2003.lin-35.n745.rep0.vsInputRep0.SES.bw


title: LIN-35 ChIP-seq in lin-35(n745) late embryos, rep 2


title: WGBS_HC_2


title: WGBS_HC_1


title: WGBS_rods_2

source_name: Rods

value: Rods

value: b2-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007915


title: Input for ChIP-seq, wildtype extract rep 1a

value: wild-type


title: Input for ChIP-seq, wildtype extract rep 1b


title: EFL-1 ChIP-seq in lin-35(n745) late embryos, rep 1

description:
processed data file:
EFL-1.SDQ3590.lin-35.n745.rep0.vsInputRep0.SES.bw
EFL-1.SDQ3590.lin-35.n745.IDR.0.01.narrowPeak

value: SDIX/Novus Biologicals Q3590

value: lin-35(n745) extract rep 1


title: LIN-54 ChIP-seq in wild-type late embryos, rep 1a

value: Horvitz lab BH0004 (Harrison et al. 2006)

value: wild-type extract rep 1a


title: DPL-1 ChIP-seq in lin-35(n745) late embryos, rep 2

description:
processed data file:
DPL-1.SDQ3599.lin-35.n745.rep0.vsInputRep0.SES.bw
DPL-1.SDQ3599.lin-35.n745.IDR.0.01.narrowPeak

value: SDIX/Novus Biologicals Q3599

value: lin-35(n745) extract rep 2


title: WGBS_rods_1

value: b2-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007913


title: WGBS_cones_2

source_name: Cones

value: Cones

value: d4-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007911


title: LIN-52 ChIP-seq in wild-type late embryos, rep 2b

description:
processed data file:
LIN-52.BH00001.N2.rep0.vsInputRep0.SES.bw
LIN-52.BH00001.N2.IDR.0.01.narrowPeak

value: Horvitz lab BH0001 (Harrison et al. 2006)

value: wild-type extract rep 2b


title: DPL-1 ChIP-seq in lin-35(n745) late embryos, rep 1


title: WGBS_cones_1

value: d4-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007909


title: LIN-52 ChIP-seq in wild-type late embryos, rep 1b

value: late embryo

value: wild-type extract rep 1b


title: DPL-1 ChIP-seq in wild-type late embryos, rep 2a

description:
processed data file:
DPL-1.SDQ3599.N2.rep0.vsInputRep0.SES.bw
DPL-1.SDQ3599.N2.IDR.0.01.narrowPeak

value: wild-type extract rep 2a


title: LIN-9 ChIP-seq in lin-35(n745) late embryos, rep 1

value: Horvitz lab BH0005 (Harrison et al. 2006)


title: HPSC G2Vh 03

city: Edinburgh

first: Elaine

last: Dzierzak

address: 47 Little France Crescent

department: MRC Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

data_processing:
Reads were aligned to the mouse genome (GRCm38/mm10), using Tophat/Bowtie v1.1.2
Counts were computed with HTSeq python script version 0.6.1
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: flat text read counts per gene

source_name: aorta gonad mesonephros

extract_protocol:
RNA was prepared with the mirVana miRNA Kit (Ambion) and SMARTER protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cell sorting based on expression of CD31, ckit, Gata2Venus reporter

tag: age

value: embryonic day 10.5

value: aorta

value: hematopoietic progenitor/stem cells (HP/SC)

tag: population


title: LIN-9 ChIP-seq in wild-type late embryos, rep 1a

description:
processed data file:
LIN-9.BH00005.N2.rep0.vsInputRep0.SES.bw
LIN-9.BH00005.N2.IDR.0.01.narrowPeak

value: wild-type


title: RNAseq_SBAC_Rep3

data_processing:
Raw sequence files were aligned using QuasR (using Bowtie as an aligner against the Mus Musculus genome (BSgenome.Mmusculus.UCSC.mm9).Reads in genes were collected using QuasR based on UCSC transcript annotation for mm9 and RPKM per gene were calculated.
processed data: Tab delimited, average RPKM for UCSC transcripts across four cell types
Genome_build: mm9

extract_protocol: After retina dissection and dissociation, cells were FACS-sorted directly in lysis buffer of the RNA-easy mini kit (Qiagen) that was used for RNA extraction. RNA-seq libraries for were prepared using the Norgen single cell RNA-seq preparation kit (51800).

value: Starbust amacrine cells

value: 129S6-Chat_tm1(cre)Lowl/J x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007922


title: HPSC G2Vh 02

tag: strain


title: LIN-9 ChIP-seq in wild-type late embryos, rep 2a


title: EFL-1 ChIP-seq in lin-35(n745) late embryos, rep 2

value: SDIX/Novus Biologicals Q3590

value: lin-35(n745) extract rep 2


title: Input for ChIP-seq, wildtype extract rep 2b


title: RNAseq_SBAC_Rep1

value: 129S6-Chat_tm1(cre)Lowl/J x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007920


title: RNAseq_SBAC_Rep2

value: 129S6-Chat_tm1(cre)Lowl/J x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007921


title: EFL-1 ChIP-seq in wild-type late embryos, rep 2b

description:
processed data file:
EFL-1.SDQ3590.N2.rep0.vsInputRep0.SES.bw
EFL-1.SDQ3590.N2.IDR.0.01.narrowPeak


title: EFL-1 ChIP-seq in wild-type late embryos, rep 1b


title: HPSC G2Vi 02

tag: cell type


title: HPSC G2Vi 03


title: HPSC G2Vh 01


title: LIN-35 ChIP-seq in wild-type late embryos, rep 1a

value: SDIX/Novus Biologicals Q2003

value: wild-type extract rep 1a


title: HPSC G2Vi 01


title: DPL-1 ChIP-seq in wild-type late embryos, rep 1b

value: SDIX/Novus Biologicals Q3599


title: RNAseq_HC_Rep1

value: Horizontal Cells

value: B6Cf1-Tg(Gja10-Cre, #14)BR x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007917


title: RNAseq_HC_Rep3

value: B6Cf1-Tg(Gja10-Cre, #14)BR x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007919


title: RNAseq_HC_Rep2

value: B6Cf1-Tg(Gja10-Cre, #14)BR x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007918


title: RNAseq_Rods_Rep4

value: Rods

value: b2-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007916


title: delayedbisulfitesample

city: New York City

first: Jason

middle: Gardiner

last: Dumelie

address: 1300 York Ave

department: Phamacology

institute: Weill Cornell Medicine

data_processing:
Base calling was perfomed using CASAVA version 1.8.2
Data filtering was performed using Flexbar version 2.5 with the following settings: quality format i1.8, phred minimum of 30, 10 nt removed from 5' end of reads
Alignment was performed using Bismark version 0.14.3 with the following settings: paired-end reads were analysed with the distance between reads limited to 1000 nt, alignments steps used Bowtie2 alignment tool version 2.2.5, post-bisulfite adapter tagging was selected, no mismatched nucleotides were allowed.
Alignment was repeated on reads that were not successfully aligned in the first alignment. This second round of alignment used Bismark version 0.14.3 with the following settings: single-end reads were analysed, alignments steps used Bowtie2 alignment tool version 2.2.5, post-bisulfite adapter tagging was selected, no mismatched nucleotides were allowed.
Data filtering was performed on reads that did not align in the first two alignment steps using Flexbar version 2.5 with the following settings: all nucleotides 55 nt or further 3' of the start of the read were removed
Alignment was repeated on trimmed reads that were not successfully aligned in the first two alignments. This third round of alignment used Bismark version 0.14.3 with the following settings: trimmed single-end reads were analysed, alignments steps used Bowtie2 alignment tool version 2.2.5, post-bisulfite adapter tagging was selected, no mismatched nucleotides were allowed.
Duplicate reads were removed using the deduplicate_bismark tool from the Bismark version 0.14.3 library
The cytosine conversion status of each cytosine in each read was determined using the bismark_methylation_extractor from Bismark version 0.14.3
BisDRIP-seq scores were calculated for each read using custom scripts.  To do this, we first created an estimate of the frequency at which conversions would be seen in a read by chance using a sample-specific estimate of the stochastic rate of conversion.  This frequency was then used to calculate the expected number of reads with a given number of conversions assuming conversions are stochastic and assuming a binomial distribution.  A read bisDRIP-seq score was then calculated based on the ratio of the observed number of reads with a specific cytosine-conversion frequency to the expected number of reads with that cytosine-conversion frequency.  Thus a pair of reads that contained the same number of cytosines and the same number of conversions would be given the same bisDRIP-seq score.
BisDRIP-seq scores for each ten nucleotide region in the genome were calculated by multiplying the bisDRIP-seq score of any reads that aligned to that ten nucleotide region with the fraction of the read that interesected with the ten nucleotide region.
For *bed.txt files: 'bisDRIP-seq scores' were calculated for each read. bisDRIP-seq scores were calculated based on the number of cytosines converted in the read, relative to the likelihood of observing that number of conversions by stochastic noise using a binomial distribution (see Methods from Dumelie and Jaffrey, 2017 for full details).
bisDRIP-seq score were normalized so that the sum of bisDRIP-seq scores within each sample was 1,000,000.
Genome_build: GRCh38
Supplementary_files_format_and_content:
Tab-delimitted files containing the: chromosome, position of a cytosine, number of conversions observed at that cytosine, fraction of reads where that cytosine was converted, number of reads that aligned to that cytosine.
bedGraph files containing: chromosome, start and stop of ten nucleotide region, bisDRIP-seq score of that region
*bed.txt files contain the chromosome, start, stop, read name, bisDRIP-seq score and strand in tab-seperated columns for each read with a bisDRIP-seq score above zero

source_name: MCF-7 cells

growth_protocol: MCF-7 cells (10 million per 15 cm plate) were cultured for three days at 37oC in 50 ml of Gibco's phenol red-free Dulbecco's Modified Eagle's Medium (Thermo Fisher Scientific, Waltham, Massachusetts) containing 5% charcoal-stripped fetal bovine serum (Thermo Fisher Scientific, Waltham, Massachusetts).  Media was replaced after two days.

extract_protocol:
Cells were lysed using SDS in the presense of bisulfite. Bisulfite was dialysed out of the sample. Samples were treated with SDS and proteinase K to remove proteins. Nucleic acids were then extracted with phenol/chloroform. DNA was then digested with restriction enzymes and RNA-DNA hybrids were immunoprecipitated using S9.6 enzymes.
DNA was sonicated using a covaris S-2 into 300 bp fragments. A Pico-Methyl Seq Library Prep Kit (Zymo Research, Irvine, California) was used to create the DNA sequencing library.  This kit is primarily designed for mapping 5-methylcytosine in small quantities of genomic DNA.  We omitted the bisulfite-treatment steps included in this kit.  Instead, only the library preparation steps were followed. These steps were followed for each sample as instructed by the manufacturer.  These steps amplified the DNA and used random priming to add indexes to the DNA library that are compatible with Illumina's TruSeq technology. As described in the Pico-Methyl Seq Library Prep Kit instructions, these indexes contain one of six barcodes that we used to differentiate samples added to the same lane during sequencing.

treatment_protocol: In these experiments, we included MCF-7 cells that were treated with 100 µM estrogen (Sigma-Aldrich, Saint Louis, Missouri) prior to lysis to ensure transcriptional activation at a broad set of genes. In this sample, no 100 µM estrogen was added prior to cell lysis.

value: MCF-7 cells

tag: treatment

value: Delayed bisulfite bisDRIP-seq. No bisulfite was added during cell lysis. Instead, bisulfite was added immediately prior to fragment the DNA with restriction enzymes.


title: KO 12hr IL6SB  3

city: Chapel Hill

first: Yisong

last: Wan

state: NC

address: 125 Mason Farm Road

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill

description: Smad4_Featurecount_STAR_DESeq_exp_log2_normalized.xlsx

data_processing:
Raw reads were first cleaned for adapter sequences using Trim Galore with default parameters;
RNA-SEQ reads (~40M per sample) were aligned to the UCSC mm10 reference genome using STAR
The quantification results from featureCounts  were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Genome_build: mm10
Supplementary_files_format_and_content: excel table; log2 transformed and normalized abundance measurements by DESeq2

source_name: peripheral lymph-nodes and spleens

extract_protocol:
Cells were collected after treatment and RNA extracted with Trizol and purified with with Qiagen Rneasy Kit
Libraries were constructed with the use of the Illumina TruSeq library construction kit V2 (Cat #RS-122-2001) according to manufacturer's protocol. Libaries were pooled and sequenced on the Illumina HiSeq 2000 sequencer

treatment_protocol: CD4+ T cells were activated and cultured under Th0 or IL6+TGFbR inhibitor condition

tag: background

tag: gender

value: Female

value: Spleen+Lymph nodes

value: CD4+T cell

tag: timepoint

value: 12 hour post treatment

value: IL6+TGFbR inhibitor

tag: genotype


title: KO 12hr IL6SB  1


title: RNAseq_Rods_Rep3

value: b2-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007915


title: WT 12hr IL6SB  3

value: WT


title: inputsample2

value: Input treatment. No S9.6 antibody immunoprecipitation step was performed.


title: KO 12hr IL6SB  2


title: RNaseHmatchedcontrol

value: RNase H matched-control. Using the same sample that was used for the RNase H experiment. 0.1U/ul RNase I was added to both samples and two additional washes were performed to the immunoprecipitation. 0.1mM DTT was added as vehicle instead of RNase H.


title: inputsample1


title: WT 12hr IL6SB  1


title: RNAseq_Rods_Rep2

value: b2-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007914


title: RNAseq_Cones_Rep3

value: Cones

value: d4-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007911


title: WT 12hr IL6SB  2


title: RNAseq_Cones_Rep4

value: d4-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007912


title: KO 3hr IL6SB  3

value: 3 hour post treatment


title: RNAseq_Cones_Rep1

value: d4-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007909


title: RNAseq_Cones_Rep2

value: d4-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007910