title: iPKO 4

city: Los Angeles

first: Juehua

last: Yu

state: CA

address: 615 Charles E. Young South BSRB 457

institute: UCLA

data_processing:
Sequenced reads were trimmed for adaptor sequence using Trimmomatic Bolger, A. M. (2014 Bioinformatics)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C (2012 Nature Protocol)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: 2i ground state embryonic stem cells

growth_protocol: ESCs were derived as previously described on MEFs in the presence of 0.5μM PD0325901 inhibitor plus LIF (Markoulaki et al, 2008). The male ESC lines PC1 (iPHet) and PC4 (iPKO) were used for the majority of experiments. ESCs were transitioned to ground state conditions and maintained as previously described (Hayashi et al, 2011; Hayashi & Saitou, 2013). To induce a deletion at the Prmt5 locus we used 4-OHT (T176, Sigma) at a final concentration of 2μM for 48 hours.

extract_protocol:
Total RNA extractions from iPHet and iPKO ESCs were performed with Qiagen RNeasy Mini kit using 1-2 million cells. The RNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation kit and 100bp paired-end sequencing was performed on the Illumina HighSeq 2500.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All cells were treated with 2uM 4-hydroxytamoxifen for 48 hrs followed by replacement with fresh 2i media.

tag: cell types

value: ESCs derived from E3.5 mouse blastocysts

tag: passage

tag: genotype/variation

value: iPKO


title: iPKO 2

status: Public on Dec 05 2014

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain


title: iPKO 1


title: iPKO 3


title: iPHet 4

value: iPHet


title: iPHet 3


title: Extracted RNA from Cdx2null small intestine organoids Cdx2null_SI_3

city: Utrecht

first: Lennart

last: Kester

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired end reads were aligned to the transcriptome using bwaPaired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
Genome_build: mm10
Supplementary_files_format_and_content: data_counts_ORG.txt: Processed data for Organoid1. Tab separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicates the sample type, SI for intestine and Sto for stomach, Cdx2null for Cdx2 knock out and Cdx2+ for Cdx2 overexpression. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

growth_protocol: Cdx2null, Control SI and Control Sto clonal organoids were generated and expanded in Matrigel from FACS sorted Lgr5-EGFPhi single cells in stomach specific culture medium (ENRWfg). Cdx2+ Stomach (Sto) organoids were generated by infection of the wild type stomach organoids with lentiviral stock expressing Cdx2 and were cultured in stomach medium (ENRWfg). Medium was refreshed every 2 days. Organoids were passaged about once per week by mechanical disruption in split ratios of 1:4.

extract_protocol:
Organoids were freed from Matrigel and resuspended in RTL buffer (Qiagen). RNA was extracted from Cdx2null SI, Control SI, Control Sto and Cdx2+ Sto organoids using the RNeasy Mini RNA Extraction Kit (Qiagen).
10ng of total RNA per sample was processed using the previously described CEL-seq technique. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: genotype

value: Cdx2 null

tag: tissue

value: small intestine organoids


title: Paired-end_CERM_rep2

status: Public on Dec 04 2014

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc), and contaminated adaptor portions of sequenced reads were trimmed using the Trim Galore program (http://www.bioinformatics.babraham.ac.uk/project/trim_galore).
Single- and paired-end reads of each biological replicate (single-end: two replicates of WT, Esr1, CYP19A1 and Brca1 KO; paired-end: one WT, two replicates of Brca1 KO and three replicates of Esr1 and CYP19A1) were aligned to the mouse reference genome (mm9 assembly) using TopHat.
Cufflinks was used to assemble transcriptomes, estimate the abundance of transcripts (FPKM, Fragments Per Kilobase of transcript per Million mapped reads) and identify differentially expressed genes (DEGs).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited file reports FPKMs

source_name: mammary glands

extract_protocol:
Total RNA was extracted from homogenized mammary glands using Trizol (Invitrogen) and 300μl chloroform (Thermo Fisher Scientific, Waltham, MA) for phase separation, precipitated with 650μl isopropanol (Thermo Fisher Scientific) and purified using an RNeasy Plus Mini Kit (Qiagen, Valencia, CA).
Polyadenylated (polyA) RNA was isolated from 1ug total RNA and converted to cDNA using SuperScript II (Invitrogen). A TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA) was used to generate sequencing libraries according to the manufacturer’s instructions. Libraries were independently sequenced by both single- and paired-end methods using HiSeq 2000 (Illumina).

tag: gender

value: female

tag: parity

value: nulliparous

value: mammary glands


title: iPHet 2


title: iPHet 1


title: Paired-end_BRCA_rep1


title: Paired-end_CERM_rep1


title: Paired-end_BRCA_rep2


title: Paired-end_AROM_rep2


title: Paired-end_WT

value: wild type


title: Single-end_CERM_rep1


title: Paired-end_AROM_rep3


title: MA_g04_ATAC_Microglia2

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

library_source: genomic

data_processing:
HISEQ split using cassava Y60,I10
alignment using bowtie 1.0.0. command (bowtie -a -m 1 --sam --best --strata -v 2 mm9)
makeTagDirectory -tbp
makeUCSCfile  -bigWig -fsize 1e20
Genome_build: mm9

molecule: genomic DNA

source_name: Brain microglia

extract_protocol:
Cells were sorted into MACS buffer, washed and lysed in 10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% or 0.5% Igepal CA-630. Nuclei were pelleted by centrifugation for 30min at 500g, 4°C.
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol developed by (Buenrostro et al., 2013); single end protocol (some samples used read2 to read molecule barcodes only)

value: Brain

tag: cell type

value: Brain microglia


title: Single-end_AROM_rep2


title: Single-end_BRCA_rep2


title: MA_g07_ATAC_SI1

source_name: Small intestine macrophages

value: Small intestine

value: Small intestine macrophages


title: Single-end_WT_rep2


title: Paired-end_CERM_rep3


title: MPEC (Mm)

city: New York

first: Der-I

last: Kao

state: NY

address: 1300 York Ave

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed  low-quality sequence, then mapped to hg19 for human and mm9 for mouse whole genome using Tophat v2.0.0.7 with default settings.
Fragments Per Kilobase of Transcript per Million mapped fragments  (RPKM) were calculated using a protocol from Trapnell et al., Nature Protocol, 2012. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: [FPKM_matrix_Hs.txt] This file includes FPKM values for BJ and AKT-HUVEC.
Supplementary_files_format_and_content: [FPKM_matrix_Mm.txt] This file includes FPKM values for MPEC and BJ (negative control).

extract_protocol:
RNA was extracted with Qiagen Rneasy mine followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Endothelial Cells

value: pancreas/islet of Langerhans; endothelium

tag: sources

value: ATCC CRL-2279


title: H3K27Ac_Il4ra_UU

city: Bethesda

first: Marei

last: Dose

state: MD

address: 9000 Rockville Pk

institute: National Institutes of Health

data_processing:
base-calling: Illumina CASAVA 1.8.0 to 1.8.2
ChIP-Seq_density: alignment: bowtie-0.12.8/bowtie -S -m 1 -p 20 -a --best --strata -n 2
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.18/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
ChIP-Seq_SE: alignment: bowtie-0.12.8/bowtie -S -m 1 -p 20 -a --best --strata -n 2
ChIP-Seq_SE: peak calling: MACS 1.4.2 with the flag ‘-p 1e9’
ChIP-Seq_SE: Super-enhancer calling:    ROSE (https://bitbucket.org/young_computation/rose.git) with ‘TSS_EXCLUSION_ZONE_SIZE=2000’
ChIP-Seq_mutations: align and fix read group: bwa  0.6.2-r126 ‘bwa aln –B 3 –n 2’ and ‘bwa samse –r <new_read_group_string>’
ChIP-Seq_mutations: flag and sort bam files: ‘samtools view –S –b –F4’ and 'samtools sort'
ChIP-Seq_mutations: deduplicate: picard 1.7.9 MarkDuplicates with ‘REMOVE_DUPLICATES=true
ChIP-Seq_mutations: GATK, version 2.5-2 RealignerTargetCreator (default settings)
ChIP-Seq_mutations: GATK, version 2.5-2 IndelRealigner with the flag ‘--consensusDeterminationModel KNOWNS_ONLY’
ChIP-Seq_mutations: GATK, version 2.5-2 BaseRecalibrator  (default settings)
ChIP-Seq_mutations: GATK, version 2.5-2 PrintReads  (default settings)
ChIP-Seq_mutations: GATK, version 2.5-2 UnifiedGenotyper with the flags ‘-stand_call_conf 4 -stand_emit_conf 4’
ChIP-Seq_mutations: hard filtering : custom software (python, bash) > 5bp from known indels; QUAL >= 20; GQ >= 20; DP >=3; callable in both WT replicates >=1 mutant sample
ChIP-Seq_mutations:  SNP counts:  custom software (R version 3.1.1 (2014-07-10)) remove AIDmm positions, count SNPs and callable bases per peak, obtain p-values using binomial distribution, BH correction
RNA-Seq: alignment: gsnap v. 2013-05-09
RNA-Seq: alignment:  normalized coverage: custom software
4C:  bowtie-1.0; create bowtie index of all mm9 DpnII restriction fragment ends (40 bp from cut site)
4C: custom software; analyzed read pairs for presence of  correct bait sequence
4C: bowtie 1.0; if bait sequence present, align second read to DpnII fragment ends
4C: custom software, count number of hits to the left and right  end of each DpnII fragment
4C: For the analysis of local data, fragment densities were normalized  and displayed as described in [Van de Werken et al., PMID:      22961246]
ChIA-PET: Chia-PET tool :  collapse redundant reads into non-redundant PET sequence
ChIA-PET:  Chia-PET tool : analyze linker barcode composition to estimate error rate
ChIA-PET:  Chia-PET tool :  trim linkers
ChIA-PET:  BatMis 3.0 :  align to mm9 reference, only perfectly and uniquely aligned reads are retained
ChIA-PET:  Chia-PET tool :  remove PCR duplicate (merge tags mapping within +/-2bp into one PET)
ChIA-PET:  Chia-PET tool :  categorize reads as either a self-ligation PET (two ends of the same DNA fragment) or and inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex)
ChIA-PET:  Chia-PET tool : classify inter-ligation PETs as intrachromosomal or interchromosomal PETs
ChIA-PET:  Chia-PET tool : intrachromosomal PET connections supported by at least 2 independent PETs are provided in bed12 format with the thick ends representing the PET clusters on either end of the connection
ChIA-PET: Chia-PET processing pipeline is described in greater detail in Li et al., 2010 (PMCID: PMC2872882)
Genome_build: mm9 (if mouse) or hg19 (if human)
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: ChIP-Seq: .SuperEnhancers.bed files contain super-enhancer intervals called based on H3K27Ac ChIP-Seq
Supplementary_files_format_and_content: ChIP-Seq: .SNPs.bed files contain the positions of mutations
Supplementary_files_format_and_content: ChIP-Seq:  the file k4me3.1kbmerge.pool.bed contains the peak calls from pooled and downsampled RAMOS IP's used to identify hotspots
Supplementary_files_format_and_content: ChIP-Seq:   the file me1.Nipbl.pos.bed contains regulatory elements in RAMOS cells, called based on H3K4me1 and Nipbl ChIP-Seq
Supplementary_files_format_and_content: RNA-seq: .bigWig files contain extenden tag coverage in 100 nt windows divided by library size in millions to obtain normalized read coverage (rpm)
Supplementary_files_format_and_content: 4C: *.tab files contain counts per fragment for DpnII fragments. Columns: chrom, start, end, counts_left_end, counts_right_end, norm_total_counts
Supplementary_files_format_and_content: ChIA-PET: .bed files show the significant connections that are supported by 2 or more independent PETs in a bed12 format

source_name: activated B cell

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at  37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.                RNA-Seq: Total RNA from 1e6  activated B cells was isolated by Trizol extraction.                                                                                4C-Seq: Ten million mouse B cells were crosslinked in 2% formaldehyde at room temperature for 10 min. The reaction was quenched by the addition of glycine (final concentration of 0.125 M). Cells were then washed with cold PBS and lysed (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40, 1× complete protease inhibitors (Roche)) at 4 °C for 1 h. Nuclei were incubated at 65 °C for 30 min, 37 °C for 30 min in 500 μl of restriction buffer (New England Biolabs DpnII buffer) containing 0.3% SDS. To sequester SDS, Triton X-100 was then added to a final concentration of 1.8%. DNA digestion was performed with 400 U of DpnII (New England Biolabs) at 37 °C overnight. After heat inactivation (65 °C for 30 min), the reaction was diluted to a final volume of 7 ml with ligation buffer containing 100 U T4 DNA Ligase (Roche) and incubated at 16 °C overnight. Samples were then treated with 500 μg Proteinase K (Ambion) and incubated overnight at 65 °C to reverse formaldehyde crosslinking. DNA was then purified by phenol extraction and ethanol precipitation. For circularization, the ligation junctions were digested with Csp6I (Fermentas) at 37 °C overnight. After enzyme inactivation and phenol extraction, the DNA was religated in a 7-ml volume (1,000 U T4 DNA Ligase, Roche). Three micrograms of 4C library DNA was amplified with Expand Long template PCR System (Roche). Thermal cycle conditions were DNA denaturing for 2 min at 94 °C, followed by 30 cycles of 15 s at 94 °C, 1 min at 58 °C, 3 min at 68 °C, and a final step of 7 min at 68 °C. Baits were amplified with inverse PCR primers as follows: Il4ra with DpnII_4C 5′-TCAGGTAGTTCCATGGGATC-3′, Il4ra_Csp6i 5′-ATCTCTGCACCAGACATCAG-3, IL21r_DpnII: CCAGACCTACTTAGCAGATC, and IL21r_Csp6i: ACTTAGACACTGCTCAGCTG.                                                                   ChIA-PET: RNA PolII ChIA-PET was performed as previously described (Fullwood et al., 2009, Goh et al., 2012 and Li et al., 2012). Briefly, RAMOS cells (up to 3e9 cells) were treated with 1% formaldehyde at room temperature for 10 min and then neutralized using 0.2 M glycine. The crosslinked chromatin was subjected to fragmentation with an average length of 300 bp by sonication. The anti-PolII monoclonal antibody 8WG16 (Covance, MMS-126R) was used to enrich PolII-bound chromatin fragments. A portion of ChIP DNA was eluted off from antibody-coated beads for concentration quantification using Picogreen fluorimetry and for enrichment analysis using quantitative PCR.
ChIP-Seq and 4C: DNA was blunt-ended with End-It DNA end repair kit (Epicenter) and A-tailed with Taq DNA polymerase (Invitrogen) in the presence of 200mM of dATP for 40 min at 70°C. Samples were purified by phenol-chloroform extraction after each reaction. Illumina compatible adaptors (Bioo Scientific) were then ligated with T4 DNA ligase (Enzymatics), and the reaction was purified once with AMpure XP magnetic beads (Beckman Coulter). Samples were PCR amplified for 12~15 cycles with KAPA HiFi DNA polymerase mix (KAPA Biosystems) and run on a 2% agarose gel and size-selected at 250–350 bp. 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                                                                RNA-Seq: Standard RNA-Seq library preparation was performed following Illumina’s RNA-Seq protocol v2.                                                   ChIA-PET: For ChIA-PET library construction ChIP DNA fragments from two biological replicates were end-repaired using T4 DNA polymerase (NEB) and ligated to either linker A or linker B. Other than four nucleotides in the middle of the linkers that were used as nucleotide barcode, the two linkers share the same nucleotide sequences. After linker ligation, the two samples were combined for proximity ligation in diluted conditions. During the proximity ligation, DNA fragments within the same ChIP complex with the same linker were ligated, which generated the ligation products with homodimer linker composition. However, chimeric ligations between ChIP fragments that are bound in different chromatin complexes could also occur, thus producing ligation products with heterodimer linker composition. Following proximity ligation, the Paired-End-Tag (PET) constructs were extracted from the ligation products and the PET templates were subjected to paired-end sequencing using Illumina HiSeq.

value: spleen

tag: chip antibody

value: Abcam, ab4729


title: Single-end_WT_rep1


title: Single-end_AROM_rep1


title: H3K27Ac_Il4ra_WT

value: WT


title: LPM Input DNA for C57BL6/J 4ng/ml Mcsf 7d, 2um ATAR 7d

city: Québec

first: David

last: Gosselin

state: Quebec

address: CRCHUL - 2705 Boulevard Laurier, Bloc T - 2-34

department: Molecular Medicine

country: Canada

institute: Université Laval

description: formaldehyde cross-linked

data_processing:
For ChIP-Seq and RNA-Seq samples, reads were aligned to the mm10 genome (C57BL6) or the corresponding genome of the inbred strain using default parameter for bowtie (RNA-Star, respectively). Non-reference alignments were shifted back to reference coordinates. Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif-  and  other analyses in the study. Genetic variation analyses were performed using custom R scripts.
Genome_build: mm10, NOD/ShiLtJ and SPRET/EiJ from mm10 using published variants (Keane, T. M. et al., Nature 477, 289-294 (2011))
Supplementary_files_format_and_content: Processed files include BED-like files (ChIP-Seq peak positions), expression text files (RNA-Seq expression data, using default HOMER parameters).  All genomic coordinates are relative to mm10 (NCBI 38) mouse assembly.

source_name: large peritoneal macrophages

extract_protocol:
Microglia, LPMs, SPMs: After cell surface staining with antibodies required for cell sorting, pre-sorted cells samples containing microglia, or LPMs, and SPMs were fixed at room temperature with 1% paraformaldehyde/PBS containing 1mM butyric acid (Sigma) for 10 minutes. Reaction was then quenched by adding glycine to 0.125 M. Cells were then washed twice and sorted on BD Influx cell sorter, pelleted and snap-frozen in liquid nitrogen and stored at -80°C until ready for ChIP-Seq protocol preparation. RNA-Seq samples were immediately sorted after staining and not cross-linked. Cultured LPMs, TGEMs and BMDMs: Culture media was removed and cells were washed once in PBS at room temperature containing 1mM butyric acid (Sigma). Cells were then fixed at room temperature with 1% paraformaldehyde/PBS with 1mM butyric acid for 10 minutes. Reaction was then quenched by adding glycine to 0.125 M, and washed twice in PBS at room temperature. Cells were then scraped into the supernatant using a rubber policeman, pelleted, and snap-frozen in liquid nitrogen. RNA-Seq samples were not cross-linked. ChIPs for PU.1, H3K4me2, and H3K27Ac were performed as follow. 0.2e6-1.0e6 cells were incubated for 10 min in 1 ml (L1) 1.0% IGEPAL CA-630-containing 10 mM HEPES pH 7.9/85 mM KCl/1 mM EDTA on ice, centrifuged, sonicated on wet ice with a Bioruptor Standard Sonicator in 200ml 10mM Tris/HCl pH 7.5, 100mM NaCl/0.5mM EGTA/0.1% Deoxcycholate/0.5% Sarkosyl for two cycles of 15min of 30sec on/60sec off each, on high settings. Triton-X to final concentration of 1% was then added, and lysates were cleared by centrifugation for 5min at 18,000 x g at 4°C. Supernatant was then immunoprecipitated for two hours at 4°C with antibody pre-bound to 20ml Protein A Dynabeads (Life Technologies)  (PU.1: 3mg/sample, H3k4me2: 2ul from stock/sample, H3k27Ac: 1ul from stock/sample) Immunoprecipitates were washed three times each on ice with ice-cold wash buffer I (150 mM NaCl/1% Triton X-100/0.1% SDS/2mM EDTA), wash buffer III (10mM Tris/HCl/250 mM LiCl/1% IGEPAL CA-630/0.7% Deoxycholate/1mM EDTA) and TET (10mM Tris/HCl pH7.5/1mM EDTA/0.1% Tween-20), and eluted with 1% SDS/TE at room temperature in a final volume of 100ul. After addition of NaCl to 300 mM final Na+ concentration, crosslinks were reversed overnight at 65°C in a hot air oven, RNA digested for 1 h at 37°C with 0.33 mg/ml RNase A, proteins digested for 1 h at 55°C with 0.5 mg/ml proteinase K, and DNA extracted using Sera-Mag SpeedBeads (Thermo Scientific, cat no 6515205050250). To control for open chromatin and library biases, 1% input chromatin libraries after sonication were sequenced for each ChIP samples. These were also sampled before incubation with antibodies, reversed cross-linked and DNA collected as above. RNA-Seq: RNA was isolated by Trizol, precipitated with ethanol, treated with TurboDNASSE (Ambion/Life technologies cat. no.1907), precipitated with ethanol, and treated to either PolyA-selected RNA (MicroPoly(A)Purist kit (Ambion/Life Technologies cat. no. 1919)) or RiboZero rRNA removel kit (Epicentre cat. no. MRZH11124).
ChIP-Seq: Sequencing libraries were prepared from collected DNA by blunting, A-tailing, adapter ligation as previously described (Heinz, S. et al. Molecular Cell 38, 576-589 (2010)) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 12-15 cycles, size selected by gel extraction and sequenced on a Hi-Seq 2000 (Illumina) for 51 cycles.
RNA-Seq: Enriched mRNA was hydrolyzed with Fragmentation Buffer (Ambion) for 10 min at 70°C and re-buffered to 10 mM Tris pH 7.4 using P-30 size exclusion columns (Bio-Rad). RNA was then de-capped for 2 h at 37°C with 0.5 µl (10 U/µl) TAP (Epicentre) in 20 µl TAP buffer containing 1 U/µl SUPERase-IN. Samples were 3’ dephosphorylated for 50’ at 37°C with 1 µl PNK (Enzymatics), 0.5 µl 10x TAP buffer, 1.5 µl water, 0.5 μl 0.25 M MgCl2 (3 mM free Mg2+ final), 0.5 μl 10 mM ATP (0.2 μM final to protect PNK). Subsequently, RNA was 5’-phosphorylated for 60 min at 37°C by adding 2 μl (10 U/µl) PNK, 10 μl 10x T4 DNA ligase buffer and 63 μl water. RNA was extracted with Trizol LS, precipitated in the presence of Glycoblue (Ambion), and dissolved in 4.5 µl water. 0.5 µl 9 µM of a 5’-adenylated sRNA3'MPX adapter /5Phos/AG ATC GGA AGA GCA CAC GTC TGA /3AmMO/ (IDT, desalted;  adenylated with Mth ligase (NEB) according to the manufacturer’s instructions, phenol-chloroform/chloroform-extracted, ethanol-precipitated with glycogen and dissolved in water at 9 µM) were heat-denatured together with the RNA for 2 minutes at 70°C, and ligated with 100 U truncated T4RNA ligase 2 K227Q (NEB) in 10 µl 1x T4 RNA ligase buffer without ATP, containing 10 U SUPERase-In and 15% PEG8000 for 2 hours at 16°C. To reduce adapter dimer formation, 0.5 μl 10 μM MPX_ RT primer    5’-GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T-3’ (IDT, desalted) was added and annealed to the ligation product by incubating at 75°C for 2 minutes, then 37°C for 30 minutes, then 25°C for 15 minutes. Finally, 0.5 µl 5 µM hybrid DNA/RNA sRNA5'h adapter 5’-GTT CAG AGT TCT ACA rGrUrC rCrGrA rCrGrA rUrC-3’ (IDT) were ligated to previously capped RNA 5’ ends by adding 2 µl T4 RNA ligase buffer, 6 µl 50% PEG8000 (15% final), 1 µl 10 mM ATP, 9.5 µl water and 0.5 µl (5 U) T4 RNA ligase 1 for 90 minutes at 20°C. To 15 μl ligation reaction, an additional 0.5 μl 10 μM MPX_ RT primer were added, reactions were denatured at to 70°C for 1 minute, then placed on ice. RNA was reverse-transcribed by adding 3 µl 10x first strand buffer, 4.5 µl water, 1.5 µl 10 mM dNTP, 3 µl 0.1 M DTT, 1.5 µl RNaseOUT and 1 µl Superscript III reverse transcriptase (Invitrogen), and incubating for 30 minutes at at 50°C. Complementary DNA was isolated by adding 35 µl AMPure XL beads (Beckman), binding and washing according to manufacturer’s instructions and dissolved in 40 µl TET. Libraries were PCR-amplified for 13 cycles with 0.75 µM primers oNTI201 (5'-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GAC G-3' and TruSeq-compatible indexed primers (e.g. 5’-CAA GCA GAA GAC GGC ATA CGA GAT iii iii GTG ACT GGA GTT CAG ACG TGT GCT CTT-3’ (desalted, IDT, i signifies index nucleotides) using Phusion Hot Start II (Thermo Scientific) in HF buffer containing 0.5 M betaine (98°C, 30s/12x(98°C, 10s/57°C, 25s/72°C, 20s)/ 72°C, 1min/4°C, ∞), 175-225 bp fragments were size-selected on 10% PAGE gels and sequenced for 51 cycles on a HiSeq 2000 sequencer (Illumina) with small RNA sequencing primer 5’-CGA CAG GTT CAG AGT TCT ACA GTC CGA CGA TC-3’ and TruSeq Index sequencing primer (Illumina).

treatment_protocol: BMDMs: Mouse bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI-1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.

tag: treatment

value: 4ng/ml Mcsf 7d, 2um ATRA 7d


title: LPM Input DNA for C57BL6/J 4ng/ml Mcsf 7d, 1ng/ml TGFB1 7d

description: formaldehyde cross-linked

value: 4ng/ml Mcsf 7d, 1ng/ml TGFB1 7d


title: Paired-end_AROM_rep1


title: LPM Input DNA for C57BL6/J 4ng/ml Mcsf 7d, 1ng/ml VehTGFB1 7d

description: formaldehyde cross-linked

value: 4ng/ml Mcsf 7d, 1ng/ml VehTGFB1 7d


title: MA_g11_ATAC_Neut1

source_name: Neutrophils

value: Bone marrow

value: Neutrophils


title: LPM PU.1 ChIP-Seq C57BL6/J 4ng/ml Mcsf 7d, 1ng/ml TGFB1 7d

description: formaldehyde cross-linked

tag: chip (antibody)

value: PU.1 (Vendor:Santa Cruz, cat# sc-352, lot# B0314)


title: LPM PU.1 ChIP-Seq C57BL6/J 4ng/ml Mcsf 7d, 2um ATAR 7d

description: formaldehyde cross-linked


title: LPM PU.1 ChIP-Seq C57BL6/J 4ng/ml Mcsf 7d, 2um DMSO 7d

description: formaldehyde cross-linked

value: 4ng/ml Mcsf 7d, 2um DMSO 7d


title: LPM PU.1 ChIP-Seq C57BL6/J 4ng/ml Mcsf 7d, 1ng/ml VehTGFB1 7d

description: formaldehyde cross-linked


title: LPM Input DNA for C57BL6/J 4ng/ml Mcsf 7d, 2um DMSO 7d

description: formaldehyde cross-linked


title: LPM H3K4me2 ChIP-Seq C57BL6/J 4ng/ml Mcsf 7d, 1ng/ml VehTGFB1 7d

description: formaldehyde cross-linked

value: H3K4me2 (Vendor:Millipore, cat# 07030, lot#2309072)


title: LPM H3K4me2 ChIP-Seq C57BL6/J 4ng/ml Mcsf 7d, 2um ATAR 7d

description: formaldehyde cross-linked


title: LPM H3K27Ac ChIP-Seq C57BL6/J 4ng/ml Mcsf 7d, 1ng/ml VehTGFB1 7d

description: formaldehyde cross-linked

value: H3K27Ac (Vendor:Active Motif, cat# 39135, lot#39135)


title: LPM H3K27Ac ChIP-Seq C57BL6/J 4ng/ml Mcsf 7d, 2um ATAR 7d

description: formaldehyde cross-linked


title: LPM H3K27Ac ChIP-Seq C57BL6/J 4ng/ml Mcsf 7d, 1ng/ml TGFB1 7d

description: formaldehyde cross-linked


title: SPM Ribozero RNA-Seq C57BL6/J no treatment

description:
RiboZero RNA
results file: GeneExpressionReplicates.txt.gz

source_name: small peritoneal macrophages

value: no treatment


title: LPM H3K4me2 ChIP-Seq C57BL6/J 4ng/ml Mcsf 7d, 2um DMSO 7d

description: formaldehyde cross-linked


title: Microglia Ribozero RNA-Seq C57BL6/J no treatment

source_name: Microglia


title: LPM H3K27Ac ChIP-Seq C57BL6J 4ng/ml Mcsf 7d, 2um DMSO 7d

description: formaldehyde cross-linked


title: Single-end_BRCA_rep1

value: female

value: nulliparous

value: mammary glands


title: TGEM RNA-Seq C57BL6/J no treatment rep2


title: Microglia RNA-Seq SPRET/EiJ no treatment

description:
RiboZero RNA
results file: GeneExpressionStrains.txt.gz

value: SPRET/EiJ


title: LPM H3K4me2 ChIP-Seq C57BL6/J 4ng/ml Mcsf 7d, 1ng/ml TGFB1 7d

description: formaldehyde cross-linked


title: Microglia Input DNA for SPRET/EiJ no treatment

description: formaldehyde cross-linked


title: LPM Ribozero RNA-Seq C57BL6/J no treatment


title: BMDM RNA-Seq C57BL6/J no treatment rep2

description: results file: GeneExpressionReplicates.txt.gz

source_name: bone marrow derived macrophages


title: LPM RNA-Seq SPRET/EiJ no treatment


title: LPM RNA-Seq NOD/ShiLtJ no treatment

value: NOD/ShiLtJ


title: Microglia H3K4me2 ChIP-Seq SPRET/EiJ no treatment

description: formaldehyde cross-linked


title: Microglia H3K27Ac ChIP-Seq SPRET/EiJ no treatment

description: formaldehyde cross-linked


title: Microglia PU.1 Chip-Seq NOD/ShiLtJ no treatment

description: formaldehyde cross-linked


title: LPM Input DNA for SPRET/EiJ no treatment

description: formaldehyde cross-linked


title: LPM H3K27Ac ChIP-Seq SPRET/EiJ no treatment

description: formaldehyde cross-linked


title: LPM H3K4me2 ChIP-Seq SPRET/EiJ no treatment

description: formaldehyde cross-linked


title: LPM Input DNA for NOD/ShiLtJ no treatment

description: formaldehyde cross-linked


title: LPM PU.1 Chip-Seq NOD/ShiLtJ no treatment

description: formaldehyde cross-linked


title: Single-end_CERM_rep2


title: Microglia RNA-Seq NOD/ShiLtJ no treatment


title: Microglia RNA-Seq C57BL6/J 4ng/ml Mcsf 7d

description:
RiboZero RNA
results file: GeneExpressionRiboZero.txt.gz

value: 4ng/ml Mcsf 7d


title: Microglia RNA-Seq C57BL6/J no treatment


title: LPM RNA-Seq C57BL6/J 4ng/ml MCsf 7d, 1ng/ml VehTGFB1 7d


title: LPM RNA-Seq C57BL6/J 4ng/ml Mcsf 7d, 1ng/ml TGFB1 7d


title: LPM H3K4me2 ChIP-Seq NOD/ShiLtJ no treatment

description: formaldehyde cross-linked


title: Microglia RNA-Seq C57BL6/J 4ng/ml GMcsf 7d


title: LPM RNA-Seq C57BL6/J 4ng/ml Mcsf 7d, 2um ATRA 7d


title: LPM H3K27Ac ChIP-Seq NOD/ShiLtJ no treatment

description: formaldehyde cross-linked


title: Microglia RNA-Seq C57BL6/J 4ng/ml IL34 7d

value: 4ng/ml IL34 7d


title: Microglia H3K27Ac ChIP-Seq NOD/ShiLtJ no treatment

description: formaldehyde cross-linked


title: LPM PU.1 ChIP-Seq SPRET/EiJ no treatment

description: formaldehyde cross-linked


title: LPM RNA-Seq C57BL6/J 4ng/ml Mcsf 7d, 2um DMSO 7d


title: LPM RNA-Seq C57BL6/J 4ng/ml IL34 7d, 1ng/ml VehTGFB1 7d

value: 4ng/ml IL34 7d, 1ng/ml VehTGFB1 7d


title: LPM RNA-Seq C57BL6/J 4ng/ml IL34 7d, 1ng/ml TGFB1 7d

value: 4ng/ml IL34 7d, 1ng/ml TGFB1 7d


title: SPM polyA RNA-Seq C57BL6/J no treatment

description: results file: GeneExpressionPolyA.txt.gz


title: LPM RNA-Seq C57BL6/J 4ng/ml IL34 7d, 2um ATRA 7d

value: 4ng/ml IL34 7d, 2um ATRA 7d


title: TGEM polyA RNA-Seq C57BL6/J no treatment


title: LPM polyA RNA-Seq C57BL6/J no treatment


title: Microglia polyA RNA-Seq C57BL6/J no treatment


title: LPM RNA-Seq C57BL6/J 4ng/ml IL34 7d, 2um DMSO 7d

value: 4ng/ml IL34 7d, 2um DMSO 7d


title: TGEM Input DNA for PU.1 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: TGEM PU.1 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked

value: PU.1 (Vendor:Santa Cruz, cat# sc-352, lot# F1808)


title: TGEM Input DNA for H3K4me2 ChIP-Seq C57BL6/J no treatment

description: Mnase-treated genomic DNA


title: TGEM H3K4me2 ChIP-Seq C57BL6/J no treatment

description: Mnase-treated genomic DNA

value: H3K4me2 (Vendor:Millipore, cat# 07030, lot#DAM1570816)


title: TGEM Input DNA for H3K27Ac ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: TGEM H3K27Ac ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked

value: H3K27Ac (Vendor:Abcam, cat# ab4729, lot# GR45787-1)


title: Microglia Input DNA for PU.1 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: Microglia PU.1 ChIP-Seq SPRET/EiJ no treatment

description: formaldehyde cross-linked

value: PU.1 (Vendor:Santa Cruz, cat# sc-352, lot# B0314)


title: Microglia Input DNA for H3K27Ac ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: SPM Input DNA for PU.1 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: Microglia H3K4me2 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked

value: H3K4me2 (Vendor:Millipore, cat# 07030, lot#2309072)


title: Microglia PU.1 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked

value: no treatment


title: SPM Input DNA for H3K4me2 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: Microglia Input DNA for H3K4me2 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: Microglia H3K4me2 ChIP-Seq NOD/ShiLtJ no treatment

description: formaldehyde cross-linked


title: Microglia H3K27Ac ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked

value: H3K27Ac (Vendor:Active Motif, cat# 39135, lot#39135)


title: SPM Input DNA for H3K27Ac ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: SPM H3K4me2 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: BMDM polyA RNA-Seq C57BL6/J no treatment


title: SPM H3K27Ac ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: LPM Input DNA for PU.1 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: LPM PU.1 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: LPM H3K4me2 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: LPM H3K27Ac ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: BMDM H3K27Ac ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked

value: H3K27Ac (Vendor:Abcam, cat# ab4729, lot# GR132150-Y)


title: CSR-Act_B_GRO-Seq

city: Boston

first: Feilong

last: Meng

state: MA

address: 300 Longwood Ave

department: PCMM

institute: Boston Children's Hospital

description:
Nascent RNA
Each raw file corresponds to one biological replicate.

data_processing:
Library strategy: Gro-Seq
GRO-Seq and ChIP-Seq data sets were aligned using Bowtie software to mouse genome build mm9/NCBI37 or human genome build hg19/NCBI37.
We used Homer software to de novo identify transcripts from both strands of the genome in the context of the GRO-Seq data, and considered broad sense/antisense overlap regions (>100bp) as ConvT regions.
We used the MACS1.4 software to identify regions of ChIP-Seq enrichment over background with a P value threshold of 10−5. We used ROSE software to identify SEs.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files were generated by using MACS2 and bedGraphtoBigWig tools.

source_name: CSR activated B cells

growth_protocol: Splenic naïve B cells were purified via an αCD43/αCD11c/αGL7 negative selection approach. The purified naïve B cells were further activated with αCD40 plus IL4 for 60 hours to generate CSR-activated B cells. The VHB1-8 or WT mice were immunized with sheep red blood cells (SRBCs) for 9 days.  Splenic GC B cells were purified from immunized spleens via an αCD43/αCD11c/αIgD negative selection.

extract_protocol:
GRO-Seq: BrU labelled nascent transcripts were extracted with Tripure reagent and affinity purified with anti-BrU antibody conjugated agarose beads.
GRO-Seq: BrU labelled nascent RNA transcripts were fragmented with NaOH, and RNA was decapped with Tobacco Acid Pyrophosphatase (TAP) and end-repaired with T4 polynucleotide kinase. Illumina Adapters were ligated to the RNA with T4 RNA ligase and cDNA was generated with Reverse Transcriptase. The libraries were PCR amplified with Illumina primers and subjected to Illumina Hiseq2000 or HiSeq2500.

value: splenic B cells actvated with antiCD40 plus IL4 at Day 2.5


title: BMDM H3K4me2 ChIP-Seq C57BL6/J no treatment

description: Mnase-treated genomic DNA


title: LPM Input DNA for H3K27Ac ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: BMDM Input DNA for Mnase ChIP-Seq C57BL6/J no treatment

description: Mnase-treated genomic DNA


title: GC_B_GRO-Seq

source_name: GC B cells

value: Germinal Center B cells purified from spleen


title: SPM PU.1 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: DGCR8KO_whole cell extract

city: Baltimore

first: Patrick

last: Cahan

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

description:
DGCR8KO_WCE
ChIP_Seq_population_mESC.csv

data_processing:
Alignment: A Bowtie index was created based on the UCSC knownGene transcriptome, and paired-end reads were directly aligned to this index.
Calculation of expression levels: RSEM was run on these alignments to generate expression level estimates, and these estimates (tau) were multiplied by 1,000,000 to yield estimates of transcripts per million (TPM) for each gene. These TPM estimates were then transformed into log space by taking ln(TPM+1), which we hereafter refer to in the Supplement as ln(TPM).
Genome_build: mm9
Supplementary_files_format_and_content: For single-cell RNA-Seq, tab-delimited text files providing RSEM ln-transformed transcript per million (TPM) values for each sample. For ChIP-Seq, total number of reads mapping to promoter regions +1500 bp to -500 bp from annotated transcription start sites.

source_name: Dgcr8 knockout mouse embryonic stem cells

growth_protocol: Described under 'culture conditions' in sample information.

extract_protocol:
mES or neural precursor cells were taken directly from culture, trypsinized, washed in PBS, spun down and resuspended at a concentration of 3 x 10^5 cell per mL of complete media, mixed 7:3 with C1 suspension reagent (Fluidigm), and loaded onto C1 Single-Cell Auto Prep chips (C1 chips; Fluidigm). After loading, each of the cell isolation chambers on the C1 chip was optically inspected for the presence of a cell.  Subsequently, these cells were lysed and SMART-Seq whole transcriptome amplified (WTA) products were prepared with the C1 System using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech) and protocols provided by Fluidigm (full details available at www.fluidigm.com).
WTA products were harvested from the C1 chip, diluted to a concentration of 0.15 ng/μL, and cDNA libraries were prepared using Nextera XT DNA Sample preparation reagents (Illumina) as per the manufacturer’s recommendations, with minor modifications. Specifically, reactions were run at ¼ the recommended volume, the tagmentation step was extended to 10 minutes, and the extension time during the PCR step was increased from 30s to 60s. After the PCR step, all 96 samples were pooled without library normalization, cleaned twice with 0.9x AMPure XP SPRI beads (Beckman Coulter), and eluted in buffer TE. The pooled libraries were quantified using Quant-IT DNA High-Sensitivity Assay Kit (Invitrogen) and examined using a high-sensitivity DNA chip (Agilent). Finally, samples were sequenced deeply using either a HiSeq 2000 or a HiSeq 2500 sequencer (25 bp paired-end reads).

tag: culture conditions

value: serum+LIF

tag: antibody

value: Whole cell extract


title: DGCR8KO_RNAP2

description:
DGCR8KO_RNAP2
ChIP_Seq_population_mESC.csv

value: Dgcr8 knockout mouse embryonic stem cells

value: RNAP2 antibody:Covance MMS-128P


title: DGCR8KO_H3K36me3

description:
DGCR8KO_H3K36me3
ChIP_Seq_population_mESC.csv

value: H3K36me3 antibody:Abcam ab9050


title: DGCR8KO_H3K9me3

description:
DGCR8KO_H3K9me3
ChIP_Seq_population_mESC.csv

value: H3K9me3 antibody:Abcam ab8898


title: 2i_whole cell extract

description:
2i_WCE
ChIP_Seq_population_mESC.csv

source_name: v6.5 mouse embryonic stem cells

value: v6.5 mouse embryonic stem cells


title: LPM Input DNA for H3K4me2 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: DGCR8KO_H3K27ac

description:
DGCR8KO_H3K27ac
ChIP_Seq_population_mESC.csv

value: H3K27ac antibody:Abcam ab4729


title: DGCR8KO_H3K4me3

description:
DGCR8KO_H3K4me3
ChIP_Seq_population_mESC.csv

value: H3K4me3 antibody:Millipore 07-473


title: 2i_H3K9me3

description:
2i_H3K9me3
ChIP_Seq_population_mESC.csv


title: BMDM PU.1 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: 2i_RNAP2

description:
2i_RNAP2
ChIP_Seq_population_mESC.csv


title: 2i_H3K27ac

description:
2i_H3K27ac
ChIP_Seq_population_mESC.csv


title: BMDM Input DNA for PU.1 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: 2i_H3K4me3

description:
2i_H3K4me3
ChIP_Seq_population_mESC.csv


title: FBSLIF_H3K36me3

description:
FBSLIF_H3K36me3
ChIP_Seq_population_mESC.csv


title: FBSLIF_RNAP2

description:
FBSLIF_RNAP2
ChIP_Seq_population_mESC.csv


title: FBSLIF_whole cell extract

description:
FBSLIF_WCE
ChIP_Seq_population_mESC.csv


title: Naïve_B_GRO-Seq

source_name: Naïve B cells

value: Naive B cell purified from slpeen


title: DGCR8KO_H3K27me3

description:
DGCR8KO_H3K27me3
ChIP_Seq_population_mESC.csv

value: H3K27me3 antibody:Upstate 07-449


title: 2i_H3K36me3

description:
2i_H3K36me3
ChIP_Seq_population_mESC.csv


title: FBSLIF_H3K27ac

description:
FBSLIF_H3K27ac
ChIP_Seq_population_mESC.csv


title: FBSLIF_H3K4me3

description:
FBSLIF_H3K4me3
ChIP_Seq_population_mESC.csv


title: FBSLIF_H3K27me3

description:
FBSLIF_H3K27me3
ChIP_Seq_population_mESC.csv


title: Dgcr8_TC2

description:
Dgcr8_TC2
RnaSeq_population_mESC_TPM.csv


title: mESCs_Plate2_TC

description:
mESCs_Plate2_TC
RnaSeq_population_mESC_TPM.csv


title: 2iLif_TC

description:
2iLif_TC
RnaSeq_population_mESC_TPM.csv


title: FBSLIF_H3K9me3

description:
FBSLIF_H3K9me3
ChIP_Seq_population_mESC.csv


title: Dgcr8_TC1

description:
Dgcr8_TC1
RnaSeq_population_mESC_TPM.csv


title: Dgcr8KO_H5

description:
Dgcr8KO_H5
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_A8

description:
Dgcr8KO_A8
RnaSeq_single_cell_mESC_TPM.csv


title: 2i_H3K27me3

description:
2i_H3K27me3
ChIP_Seq_population_mESC.csv


title: mESCs_Plate1_TC

description:
mESCs_Plate1_TC
RnaSeq_population_mESC_TPM.csv


title: Dgcr8KO_H2

description:
Dgcr8KO_H2
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_G7

description:
Dgcr8KO_G7
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_H9

description:
Dgcr8KO_H9
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_F11

description:
Dgcr8KO_F11
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_A9

description:
Dgcr8KO_A9
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_H6

description:
Dgcr8KO_H6
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_A7

description:
Dgcr8KO_A7
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_F8

description:
Dgcr8KO_F8
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_F6

description:
Dgcr8KO_F6
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_G8

description:
Dgcr8KO_G8
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_G9

description:
Dgcr8KO_G9
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_G4

description:
Dgcr8KO_G4
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_H3

description:
Dgcr8KO_H3
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_H7

description:
Dgcr8KO_H7
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_H1

description:
Dgcr8KO_H1
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_G11

description:
Dgcr8KO_G11
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_G12

description:
Dgcr8KO_G12
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_G3

description:
Dgcr8KO_G3
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_E9

description:
Dgcr8KO_E9
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_E7

description:
Dgcr8KO_E7
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_F5

description:
Dgcr8KO_F5
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_G1

description:
Dgcr8KO_G1
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_E12

description:
Dgcr8KO_E12
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_F12

description:
Dgcr8KO_F12
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_H8

description:
Dgcr8KO_H8
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_A6

description:
Dgcr8KO_A6
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_E11

description:
Dgcr8KO_E11
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_E8

description:
Dgcr8KO_E8
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_E6

description:
Dgcr8KO_E6
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_F3

description:
Dgcr8KO_F3
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_D9

description:
Dgcr8KO_D9
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_E10

description:
Dgcr8KO_E10
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_E5

description:
Dgcr8KO_E5
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_E4

description:
Dgcr8KO_E4
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_F1

description:
Dgcr8KO_F1
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_G2

description:
Dgcr8KO_G2
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_A5

description:
Dgcr8KO_A5
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_D11

description:
Dgcr8KO_D11
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_E1

description:
Dgcr8KO_E1
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_D6

description:
Dgcr8KO_D6
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_D10

description:
Dgcr8KO_D10
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_D8

description:
Dgcr8KO_D8
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_C12

description:
Dgcr8KO_C12
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_D1

description:
Dgcr8KO_D1
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_D7

description:
Dgcr8KO_D7
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_E3

description:
Dgcr8KO_E3
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_C8

description:
Dgcr8KO_C8
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_C9

description:
Dgcr8KO_C9
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_D2

description:
Dgcr8KO_D2
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_A4

description:
Dgcr8KO_A4
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_E2

description:
Dgcr8KO_E2
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_D5

description:
Dgcr8KO_D5
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_C11

description:
Dgcr8KO_C11
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_F7

description:
Dgcr8KO_F7
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_C7

description:
Dgcr8KO_C7
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_C1

description:
Dgcr8KO_C1
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_C2

description:
Dgcr8KO_C2
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_B11

description:
Dgcr8KO_B11
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_B12

description:
Dgcr8KO_B12
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_C3

description:
Dgcr8KO_C3
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_C6

description:
Dgcr8KO_C6
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_B9

description:
Dgcr8KO_B9
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_B8

description:
Dgcr8KO_B8
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_B10

description:
Dgcr8KO_B10
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_C10

description:
Dgcr8KO_C10
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_A3

description:
Dgcr8KO_A3
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_D4

description:
Dgcr8KO_D4
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_C5

description:
Dgcr8KO_C5
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_B3

description:
Dgcr8KO_B3
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_B4

description:
Dgcr8KO_B4
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_B2

description:
Dgcr8KO_B2
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_A12

description:
Dgcr8KO_A12
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_D12

description:
Dgcr8KO_D12
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_B7

description:
Dgcr8KO_B7
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_B5

description:
Dgcr8KO_B5
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_B6

description:
Dgcr8KO_B6
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_A11

description:
Dgcr8KO_A11
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_B1

description:
Dgcr8KO_B1
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_C4

description:
Dgcr8KO_C4
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_A2

description:
Dgcr8KO_A2
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_A10

description:
Dgcr8KO_A10
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_H7

description:
TwoiLIF_H7
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_H5

description:
TwoiLIF_H5
RnaSeq_single_cell_mESC_TPM.csv


title: Dgcr8KO_A1

description:
Dgcr8KO_A1
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_H4

description:
TwoiLIF_H4
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_H8

description:
TwoiLIF_H8
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_H6

description:
TwoiLIF_H6
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_A9

description:
TwoiLIF_A9
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_H10

description:
TwoiLIF_H10
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_G9

description:
TwoiLIF_G9
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_G10

description:
TwoiLIF_G10
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_H11

description:
TwoiLIF_H11
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_H2

description:
TwoiLIF_H2
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_A8

description:
TwoiLIF_A8
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_G7

description:
TwoiLIF_G7
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_G6

description:
TwoiLIF_G6
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_G8

description:
TwoiLIF_G8
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_H9

description:
TwoiLIF_H9
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_H1

description:
TwoiLIF_H1
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_G5

description:
TwoiLIF_G5
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_G4

description:
TwoiLIF_G4
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_G12

description:
TwoiLIF_G12
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_F11

description:
TwoiLIF_F11
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_A7

description:
TwoiLIF_A7
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_H12

description:
TwoiLIF_H12
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_F10

description:
TwoiLIF_F10
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_F6

description:
TwoiLIF_F6
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_F9

description:
TwoiLIF_F9
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_G11

description:
TwoiLIF_G11
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_G2

description:
TwoiLIF_G2
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_F8

description:
TwoiLIF_F8
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_G1

description:
TwoiLIF_G1
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_F5

description:
TwoiLIF_F5
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_F7

description:
TwoiLIF_F7
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_F12

description:
TwoiLIF_F12
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_F4

description:
TwoiLIF_F4
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_E11

description:
TwoiLIF_E11
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_A6

description:
TwoiLIF_A6
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_E8

description:
TwoiLIF_E8
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_E7

description:
TwoiLIF_E7
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_F3

description:
TwoiLIF_F3
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_E6

description:
TwoiLIF_E6
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_E10

description:
TwoiLIF_E10
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_F1

description:
TwoiLIF_F1
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_D12

description:
TwoiLIF_D12
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_E1

description:
TwoiLIF_E1
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_E9

description:
TwoiLIF_E9
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_A5

description:
TwoiLIF_A5
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_G3

description:
TwoiLIF_G3
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_D9

description:
TwoiLIF_D9
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_D11

description:
TwoiLIF_D11
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_D8

description:
TwoiLIF_D8
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_E3

description:
TwoiLIF_E3
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_D10

description:
TwoiLIF_D10
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_E2

description:
TwoiLIF_E2
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_E4

description:
TwoiLIF_E4
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_E12

description:
TwoiLIF_E12
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_F2

description:
TwoiLIF_F2
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_D1

description:
TwoiLIF_D1
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_D6

description:
TwoiLIF_D6
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_D2

description:
TwoiLIF_D2
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_D3

description:
TwoiLIF_D3
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_C10

description:
TwoiLIF_C10
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_C9

description:
TwoiLIF_C9
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_C8

description:
TwoiLIF_C8
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_D4

description:
TwoiLIF_D4
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_A4

description:
TwoiLIF_A4
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_D5

description:
TwoiLIF_D5
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_C4

description:
TwoiLIF_C4
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_C2

description:
TwoiLIF_C2
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_C3

description:
TwoiLIF_C3
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_B11

description:
TwoiLIF_B11
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_C1

description:
TwoiLIF_C1
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_C7

description:
TwoiLIF_C7
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_B12

description:
TwoiLIF_B12
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_B10

description:
TwoiLIF_B10
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_C11

description:
TwoiLIF_C11
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_A3

description:
TwoiLIF_A3
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_C5

description:
TwoiLIF_C5
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_C12

description:
TwoiLIF_C12
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_B3

description:
TwoiLIF_B3
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_B8

description:
TwoiLIF_B8
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_B1

description:
TwoiLIF_B1
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_B5

description:
TwoiLIF_B5
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_A12

description:
TwoiLIF_A12
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_A10

description:
TwoiLIF_A10
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_B9

description:
TwoiLIF_B9
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_A2

description:
TwoiLIF_A2
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_B7

description:
TwoiLIF_B7
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_B6

description:
TwoiLIF_B6
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_B4

description:
TwoiLIF_B4
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_H8

description:
FBSLIF_Plate1_H8
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_A1

description:
TwoiLIF_A1
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_A9

description:
FBSLIF_Plate1_A9
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_H7

description:
FBSLIF_Plate1_H7
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_H4

description:
FBSLIF_Plate1_H4
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_H3

description:
FBSLIF_Plate1_H3
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_H12

description:
FBSLIF_Plate1_H12
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_H5

description:
FBSLIF_Plate1_H5
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_C6

description:
TwoiLIF_C6
RnaSeq_single_cell_mESC_TPM.csv


title: TwoiLIF_B2

description:
TwoiLIF_B2
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_H10

description:
FBSLIF_Plate1_H10
RnaSeq_single_cell_mESC_TPM.csv


title: glut12 MO_2

city: Bad Nauheim

first: Rubén

last: Marín-Juez

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute

data_processing:
Base calling was done by the Illumina HCS version 2.0.12
Data analysis was performed using Genetiles software (www.genetiles.com)
Genome_build: Zv9_toplevel
Supplementary_files_format_and_content: tab-delimited text files include read values for each Sample

organism: Danio rerio

source_name: Whole embryo_glut12

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol:
Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 4 days post fertilization

value: whole embryo

tag: morpholino


title: glut12 MO_3


title: TwoiLIF_A11

description:
TwoiLIF_A11
RnaSeq_single_cell_mESC_TPM.csv


title: Control MO_2

source_name: Whole embryo_control

value: control


title: FBSLIF_Plate1_G10

description:
FBSLIF_Plate1_G10
RnaSeq_single_cell_mESC_TPM.csv


title: Control MO_3


title: glut12 MO_1


title: FBSLIF_Plate1_A8

description:
FBSLIF_Plate1_A8
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_G9

description:
FBSLIF_Plate1_G9
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_G7

description:
FBSLIF_Plate1_G7
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_G6

description:
FBSLIF_Plate1_G6
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_G4

description:
FBSLIF_Plate1_G4
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_H1

description:
FBSLIF_Plate1_H1
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_H11

description:
FBSLIF_Plate1_H11
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_G11

description:
FBSLIF_Plate1_G11
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_G3

description:
FBSLIF_Plate1_G3
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_G12

description:
FBSLIF_Plate1_G12
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_F10

description:
FBSLIF_Plate1_F10
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_F9

description:
FBSLIF_Plate1_F9
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_H2

description:
FBSLIF_Plate1_H2
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_F8

description:
FBSLIF_Plate1_F8
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_F6

description:
FBSLIF_Plate1_F6
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_G8

description:
FBSLIF_Plate1_G8
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_G2

description:
FBSLIF_Plate1_G2
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_F5

description:
FBSLIF_Plate1_F5
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_F7

description:
FBSLIF_Plate1_F7
RnaSeq_single_cell_mESC_TPM.csv


title: Control MO_1


title: FBSLIF_Plate1_F4

description:
FBSLIF_Plate1_F4
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_E10

description:
FBSLIF_Plate1_E10
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_E11

description:
FBSLIF_Plate1_E11
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_A6

description:
FBSLIF_Plate1_A6
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_E9

description:
FBSLIF_Plate1_E9
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_E8

description:
FBSLIF_Plate1_E8
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_E7

description:
FBSLIF_Plate1_E7
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_F3

description:
FBSLIF_Plate1_F3
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_G5

description:
FBSLIF_Plate1_G5
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_F11

description:
FBSLIF_Plate1_F11
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_F1

description:
FBSLIF_Plate1_F1
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_F2

description:
FBSLIF_Plate1_F2
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_E5

description:
FBSLIF_Plate1_E5
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_A5

description:
FBSLIF_Plate1_A5
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_E1

description:
FBSLIF_Plate1_E1
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_G1

description:
FBSLIF_Plate1_G1
RnaSeq_single_cell_mESC_TPM.csv


title: MnaseSeq_2_(20120131_7)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Chd1 input, 10' MNase

data_processing: 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. The Illumina sample was a mixture of yeast DNA and fly DNA so we also mapped the reads to release 5.30 of D.melanogaster (Sep 2010) obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads that were only mapped to yeast (Supplementary file .bed).

organism: Saccharomyces cerevisiae

source_name: Chd1 input

extract_protocol: Nuclear isolation, chromatin preparation, and immunoprecipitation were performed as described (PMID 23468649). Sequencing libraries were prepared as described (PMID 22025700), except that TruSeq adapters were used for multiplexing and the ratio of sample to Ampure beads was changed from 5:9 to 1:1 in the two cleanup steps to compensate for the longer length of the TruSeq adapters.

tag: cell

value: nuclei

value: MATa ade2-1 can1-100 his3-11, 15 leu2-3, 112 trp1-1 ura3-1 RAD5+ CHD1-3FLAG-kanMX4


title: MnaseSeq_3_(20121019_4_12)

description: Isw1 Flag input, 10' MNase

data_processing: 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads that were only mapped to yeast (Supplementary file .bed).

source_name: Isw1 Flag input

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ ISW1-3FLAG-kanMX4


title: MnaseSeq_1_(20120131_5)

description: Isw1 input, 10' MNase

source_name: Isw1 input


title: FBSLIF_Plate1_D12

description:
FBSLIF_Plate1_D12
RnaSeq_single_cell_mESC_TPM.csv

value: serum+LIF


title: FBSLIF_Plate1_D11

description:
FBSLIF_Plate1_D11
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_D9

description:
FBSLIF_Plate1_D9
RnaSeq_single_cell_mESC_TPM.csv


title: GCt_B_H3K27Ac_ChIP-Seq - input

description: Each raw file corresponds to one biological replicate.

data_processing:
GRO-Seq and ChIP-Seq data sets were aligned using Bowtie software to mouse genome build mm9/NCBI37 or human genome build hg19/NCBI37.
We used Homer software to de novo identify transcripts from both strands of the genome in the context of the GRO-Seq data, and considered broad sense/antisense overlap regions (>100bp) as ConvT regions.
We used the MACS1.4 software to identify regions of ChIP-Seq enrichment over background with a P value threshold of 10−5. We used ROSE software to identify SEs.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files were generated by using MACS2 and bedGraphtoBigWig tools.

extract_protocol:
ChIP-Seq: Cell Lysates were sonicated and histone-DNA complexes were isolated with anti H3K27Ac antibody.
ChIP-Seq: Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Preparation Kit. The libraries were sequenced on Illumina HiSeq2500.

value: Germinal Center B cells purified from spleen

value: input


title: FBSLIF_Plate1_D8

description:
FBSLIF_Plate1_D8
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_D7

description:
FBSLIF_Plate1_D7
RnaSeq_single_cell_mESC_TPM.csv


title: CSR-Act_B_H3K27Ac_ChIP-Seq - input

value: splenic B cells actvated with antiCD40 plus IL4 at Day 2.5


title: FBSLIF_Plate1_E6

description:
FBSLIF_Plate1_E6
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_E3

description:
FBSLIF_Plate1_E3
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_F12

description:
FBSLIF_Plate1_F12
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_A7

description:
FBSLIF_Plate1_A7
RnaSeq_single_cell_mESC_TPM.csv


title: MEF_GRO-Seq

description:
Nascent RNA
Each raw file corresponds to one biological replicate.

source_name: MEFs

value: mouse embryonic fibroblasts


title: GCt_B_H3K27Ac_ChIP-Seq

value: H3K27Ac (abcam, ab4729)


title: FBSLIF_Plate1_D10

description:
FBSLIF_Plate1_D10
RnaSeq_single_cell_mESC_TPM.csv

value: v6.5 mouse embryonic stem cells


title: FBSLIF_Plate1_D2

description:
FBSLIF_Plate1_D2
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_D3

description:
FBSLIF_Plate1_D3
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_C12

description:
FBSLIF_Plate1_C12
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_D1

description:
FBSLIF_Plate1_D1
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_E2

description:
FBSLIF_Plate1_E2
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_C11

description:
FBSLIF_Plate1_C11
RnaSeq_single_cell_mESC_TPM.csv


title: Ubi_Il21r

description: 4C from Il21r viewpoint in Il4raU/U activated B cells

data_processing:
base-calling: Illumina CASAVA 1.8.0 to 1.8.2
ChIP-Seq_density: alignment: bowtie-0.12.8/bowtie -S -m 1 -p 20 -a --best --strata -n 2
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.18/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
ChIP-Seq_SE: alignment: bowtie-0.12.8/bowtie -S -m 1 -p 20 -a --best --strata -n 2
ChIP-Seq_SE: peak calling: MACS 1.4.2 with the flag ‘-p 1e9’
ChIP-Seq_SE: Super-enhancer calling:    ROSE (https://bitbucket.org/young_computation/rose.git) with ‘TSS_EXCLUSION_ZONE_SIZE=2000’
ChIP-Seq_mutations: align and fix read group: bwa  0.6.2-r126 ‘bwa aln –B 3 –n 2’ and ‘bwa samse –r <new_read_group_string>’
ChIP-Seq_mutations: flag and sort bam files: ‘samtools view –S –b –F4’ and 'samtools sort'
ChIP-Seq_mutations: deduplicate: picard 1.7.9 MarkDuplicates with ‘REMOVE_DUPLICATES=true
ChIP-Seq_mutations: GATK, version 2.5-2 RealignerTargetCreator (default settings)
ChIP-Seq_mutations: GATK, version 2.5-2 IndelRealigner with the flag ‘--consensusDeterminationModel KNOWNS_ONLY’
ChIP-Seq_mutations: GATK, version 2.5-2 BaseRecalibrator  (default settings)
ChIP-Seq_mutations: GATK, version 2.5-2 PrintReads  (default settings)
ChIP-Seq_mutations: GATK, version 2.5-2 UnifiedGenotyper with the flags ‘-stand_call_conf 4 -stand_emit_conf 4’
ChIP-Seq_mutations: hard filtering : custom software (python, bash) > 5bp from known indels; QUAL >= 20; GQ >= 20; DP >=3; callable in both WT replicates >=1 mutant sample
ChIP-Seq_mutations:  SNP counts:  custom software (R version 3.1.1 (2014-07-10)) remove AIDmm positions, count SNPs and callable bases per peak, obtain p-values using binomial distribution, BH correction
RNA-Seq: alignment: gsnap v. 2013-05-09
RNA-Seq: alignment:  normalized coverage: custom software
4C: bowtie-1.0; create bowtie index of all mm9 DpnII restriction fragment ends (40 bp from cut site)
4C: custom software; analyzed read pairs for presence of  correct bait sequence
4C: bowtie 1.0; if bait sequence present, align second read to DpnII fragment ends
4C: custom software, count number of hits to the left and right  end of each DpnII fragment
4C: For the analysis of local data, fragment densities were normalized  and displayed as described in [Van de Werken et al., PMID: 22961246]
ChIA-PET: Chia-PET tool: collapse redundant reads into non-redundant PET sequence
ChIA-PET: Chia-PET tool : analyze linker barcode composition to estimate error rate
ChIA-PET: Chia-PET tool: trim linkers
ChIA-PET: BatMis 3.0: align to mm9 reference, only perfectly and uniquely aligned reads are retained
ChIA-PET: Chia-PET tool: remove PCR duplicate (merge tags mapping within +/-2bp into one PET)
ChIA-PET: Chia-PET tool: categorize reads as either a self-ligation PET (two ends of the same DNA fragment) or and inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex)
ChIA-PET: Chia-PET tool : classify inter-ligation PETs as intrachromosomal or interchromosomal PETs
ChIA-PET: Chia-PET tool : intrachromosomal PET connections supported by at least 2 independent PETs are provided in bed12 format with the thick ends representing the PET clusters on either end of the connection
ChIA-PET: Chia-PET processing pipeline is described in greater detail in Li et al., 2010 (PMCID: PMC2872882)
Genome_build: mm9 (if mouse) or hg19 (if human)

Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
ChIP-Seq: .SuperEnhancers.bed files contain super-enhancer intervals called based on H3K27Ac ChIP-Seq
ChIP-Seq: .SNPs.bed files contain the positions of mutations
ChIP-Seq:  the file k4me3.1kbmerge.pool.bed.gz contains the peak calls from pooled and downsampled RAMOS IP's used to identify hotspots
ChIP-Seq: the file me1.Nipbl.pos.bed.gz contains regulatory elements in RAMOS cells, called based on H3K4me1 and Nipbl ChIP-Seq
RNA-seq: .bigWig files contain extenden tag coverage in 100 nt windows divided by library size in millions to obtain normalized read coverage (rpm)
4C: *.tab files contain counts per fragment for DpnII fragments. Columns: chrom, start, end, counts_left_end, counts_right_end, norm_total_counts
ChIA-PET: .bed files show the significant connections that are supported by 2 or more independent PETs in a bed12 format

source_name: activated B cell

value: spleen


title: WT_IL4ra

description: 4C from Il4ra viewpoint in WT activated B cells

value: WT


title: Ubi_IL4ra


title: FBSLIF_Plate1_C9

description:
FBSLIF_Plate1_C9
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_D5

description:
FBSLIF_Plate1_D5
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_C8

description:
FBSLIF_Plate1_C8
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_D6

description:
FBSLIF_Plate1_D6
RnaSeq_single_cell_mESC_TPM.csv


title: CSR-Act_B_H3K27Ac_ChIP-Seq

description: Each raw file corresponds to one biological replicate.


title: FBSLIF_Plate1_A4

description:
FBSLIF_Plate1_A4
RnaSeq_single_cell_mESC_TPM.csv


title: WT_Il21r

description: 4C from Il21r viewpoint in WT activated B cells


title: RNAseq_Il4ra_WT_rep2

description: WT control for Il4rau/u mice.


title: RNAseq_Il4ra_UU_rep3

description: Knock-in of the Ubc promoter into the Il4ra promoter.


title: RNAseq_Il4ra_WT_rep1

description: WT control for Il4rau/u mice.


title: RNAseq_Il4ra_UU_rep1


title: RNAseq_Il4ra_WT_rep3

description: WT control for Il4rau/u mice.


title: Input_aB

description:
Input for H3K27Ac_aB
processed data file: aB_H3K27Ac_SuperEnhancers.bed.gz


title: FBSLIF_Plate1_C3

description:
FBSLIF_Plate1_C3
RnaSeq_single_cell_mESC_TPM.csv


title: H3K27Ac_aB_rep3

description:
the 3 H3K27Ac replicates were pooled for SE calling
processed data file: aB_H3K27Ac.bw; aB_H3K27Ac_SuperEnhancers.bed.gz

value: Anti-Histone H3 (acetyl K27) antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: FBSLIF_Plate1_C7

description:
FBSLIF_Plate1_C7
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_C4

description:
FBSLIF_Plate1_C4
RnaSeq_single_cell_mESC_TPM.csv


title: H3K27Ac_aB_rep1

tag: genotype/variation


title: NPCs_H7

description:
NPCs_H7
RnaSeq_single_cell_NPC_TPM.csv

value: Neural precursor cells derived from in vitro differentiation of v6.5 mouse embryonic stem cells

value: Selection in ITSFn, followed by expansion in N2+bFGF / laminin


title: H3K27Ac_aB_rep2


title: NPCs_H4

description:
NPCs_H4
RnaSeq_single_cell_NPC_TPM.csv


title: siTSU-RZ

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

data_processing:
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
N-containing reads were discarded
reads were trimmed to bases 6-50 using fastx-trimmer and filtered for multi mapping reads against the genome with bowtie allowing 3MM
genome uniquely mapping reads were mapped against the transcriptome of dm3-r5.56 with bowtie (up to 3MM) and RPKM values were calculated (mapped reads per kb per 1M genome uniquely mapped reads) - average of all transcript isoform RPKMs per gene
reads not mappable to the transcriptome were mapped against the intron reference of dm3-r5.56 with bowtie (up to 3MM) and intron-RPKMs were calculated (mapped reads per kb per 1M genome uniquely mapped reads)
Supplementary_files_format_and_content: format: txt; content: RPKM tables
for the creation of bigWig tracks trimmed reads got mapped to the genome with GSNAP allowing splicing of reads and up to 3MM. Uniquely mapped reads got processed into bigwig using Homertools.
Supplementary_files_format_and_content: format: bigWig; content: tracks of genome uniquely mapping reads
Genome_build: dmel_release 5

organism: Drosophila melanogaster

source_name: Ovarian Somatic Cells (OSC)

growth_protocol: OSC were grown at 27 degrees on M3 medium

extract_protocol:
total RNA was depleted of rRNA by RiboZero, fragmented and reverse transcribed with random hexamers. Strand-specific libraries were prepared using the UDG-digestion-based strategy and cloned with NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (NEB)
total RNA was isolated with Trizol
see in the SAMPLES section

treatment_protocol: siRNAs were transfected with Cell Line Nucleofector kit V (Amaxa Biosystems; program T-029)

value: Ovarian Somatic Cells (OSC)

tag: transfected sirna

value: siRNA tsu

tag: rrna depletion method

value: depletion of rRNA with RiboZero


title: FBSLIF_Plate1_B12

description:
FBSLIF_Plate1_B12
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_C1

description:
FBSLIF_Plate1_C1
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_D4

description:
FBSLIF_Plate1_D4
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_B11

description:
FBSLIF_Plate1_B11
RnaSeq_single_cell_mESC_TPM.csv


title: RNAseq_Il4ra_UU_rep2

tag: tissue


title: FBSLIF_Plate1_B10

description:
FBSLIF_Plate1_B10
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_C10

description:
FBSLIF_Plate1_C10
RnaSeq_single_cell_mESC_TPM.csv


title: NPCs_H11

description:
NPCs_H11
RnaSeq_single_cell_NPC_TPM.csv


title: siACN-RZ

value: siRNA Acn


title: NPCs_H10

description:
NPCs_H10
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_G9

description:
NPCs_G9
RnaSeq_single_cell_NPC_TPM.csv


title: siGFP-RZ

value: siRNA GFP


title: FBSLIF_Plate1_C2

description:
FBSLIF_Plate1_C2
RnaSeq_single_cell_mESC_TPM.csv

value: serum+LIF


title: NPCs_G4

description:
NPCs_G4
RnaSeq_single_cell_NPC_TPM.csv


title: TwoiLIF_E5

description:
TwoiLIF_E5
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_C6

description:
FBSLIF_Plate1_C6
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_B9

description:
FBSLIF_Plate1_B9
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_A3

description:
FBSLIF_Plate1_A3
RnaSeq_single_cell_mESC_TPM.csv


title: NPCs_H8

description:
NPCs_H8
RnaSeq_single_cell_NPC_TPM.csv


title: siTSU-PA-rep1

molecule: polyA RNA

extract_protocol:
mRNA from siRNA transfected OSCs was selected with Dynabeads Oligo(dT) (Invitrogen) from total RNA, fragmented and reverse transcribed with random hexamers. Strand-specific libraries were prepared using the UDG-digestion-based strategy and cloned with NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB)
total RNA was isolated with Trizol
see in the SAMPLES section

value: isolation of PolyA RNA


title: FBSLIF_Plate1_C5

description:
FBSLIF_Plate1_C5
RnaSeq_single_cell_mESC_TPM.csv


title: NPCs_G3

description:
NPCs_G3
RnaSeq_single_cell_NPC_TPM.csv


title: siAcn-PA-rep2


title: NPCs_G2

description:
NPCs_G2
RnaSeq_single_cell_NPC_TPM.csv


title: siAcn-PA-rep1


title: NPCs_G12

description:
NPCs_G12
RnaSeq_single_cell_NPC_TPM.csv


title: FBSLIF_Plate1_B5

description:
FBSLIF_Plate1_B5
RnaSeq_single_cell_mESC_TPM.csv


title: siGFP-PA-rep2


title: FBSLIF_Plate1_B4

description:
FBSLIF_Plate1_B4
RnaSeq_single_cell_mESC_TPM.csv


title: NPCs_G10

description:
NPCs_G10
RnaSeq_single_cell_NPC_TPM.csv


title: FBSLIF_Plate1_B3

description:
FBSLIF_Plate1_B3
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_B2

description:
FBSLIF_Plate1_B2
RnaSeq_single_cell_mESC_TPM.csv


title: NPCs_G11

description:
NPCs_G11
RnaSeq_single_cell_NPC_TPM.csv


title: siGFP-PA-rep1


title: RNAseq_RAMOS_rep2

organism: Homo sapiens

source_name: RAMOS

tag: genotype

value: Burkitt's lymphoma cell line


title: RNAseq_RAMOS_rep3


title: NPCs_F9

description:
NPCs_F9
RnaSeq_single_cell_NPC_TPM.csv

tag: cell type


title: NPCs_F7

description:
NPCs_F7
RnaSeq_single_cell_NPC_TPM.csv


title: FBSLIF_Plate1_B1

description:
FBSLIF_Plate1_B1
RnaSeq_single_cell_mESC_TPM.csv


title: NPCs_F3

description:
NPCs_F3
RnaSeq_single_cell_NPC_TPM.csv


title: RNAseq_RAMOS_rep1


title: FBSLIF_Plate1_A11

description:
FBSLIF_Plate1_A11
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_A12

description:
FBSLIF_Plate1_A12
RnaSeq_single_cell_mESC_TPM.csv


title: FBSLIF_Plate1_A10

description:
FBSLIF_Plate1_A10
RnaSeq_single_cell_mESC_TPM.csv


title: NPCs_F11

description:
NPCs_F11
RnaSeq_single_cell_NPC_TPM.csv


title: siTSU-PA-rep2


title: Ramos_GRO-Seq

description:
Nascent RNA
Each raw file corresponds to one biological replicate.

data_processing:
Library strategy: Gro-Seq
GRO-Seq and ChIP-Seq data sets were aligned using Bowtie software to mouse genome build mm9/NCBI37 or human genome build hg19/NCBI37.
We used Homer software to de novo identify transcripts from both strands of the genome in the context of the GRO-Seq data, and considered broad sense/antisense overlap regions (>100bp) as ConvT regions.
We used the MACS1.4 software to identify regions of ChIP-Seq enrichment over background with a P value threshold of 10−5. We used ROSE software to identify SEs.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated by using MACS2 and bedGraphtoBigWig tools.

source_name: Ramos cell line (msh2-/-)

value: human Burkitt's lymphoma cell line; B lineage cell

tag: cell line

value: Ramos


title: NPCs_F10

description:
NPCs_F10
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_E4

description:
NPCs_E4
RnaSeq_single_cell_NPC_TPM.csv


title: H3K4me3_ramos_rep1

description:
Unmodified parent RAMOS cell line used as reference for calling genetic variants in the gentically modified clones.
processed data file: RAMOS.SNPs.bed.gz; Hotspots.AIDtgMSH2mmUgi.bed.gz; RAMOS_H3K4me3.wig.gz; RAMOS_H3K4me3.peaks.bed.gz

tag: chip antibody

value: Anti-trimethyl-Histone H3 (Lys4)

value: Millipore


title: H3K4me3_ramos_rep2

value: WT


title: FBSLIF_Plate1_A2

description:
FBSLIF_Plate1_A2
RnaSeq_single_cell_mESC_TPM.csv

value: v6.5 mouse embryonic stem cells


title: FBSLIF_Plate1_B7

description:
FBSLIF_Plate1_B7
RnaSeq_single_cell_mESC_TPM.csv


title: H3K4me3_AIDtg_clone26

description:
Genetically engineered RAMOS cell line.  Cells have a defect in missmatch and base excision repair and overexpress AID to reveal AID dependent mutations.
processed data file: AIDtgMSH2mmUgi.SNPs.bed.gz; Hotspots.AIDtgMSH2mmUgi.bed.gz; RAMOS_H3K4me3.wig.gz; RAMOS_H3K4me3.peaks.bed.gz

value: MSH2-/-; AIDtg; UGItg


title: H3K4me3_AIDtg_clone25


title: FBSLIF_Plate1_A1

description:
FBSLIF_Plate1_A1
RnaSeq_single_cell_mESC_TPM.csv


title: NPCs_E2

description:
NPCs_E2
RnaSeq_single_cell_NPC_TPM.csv

value: Neural precursor cells derived from in vitro differentiation of v6.5 mouse embryonic stem cells


title: NPCs_E11

description:
NPCs_E11
RnaSeq_single_cell_NPC_TPM.csv

value: Selection in ITSFn, followed by expansion in N2+bFGF / laminin


title: NPCs_E12

description:
NPCs_E12
RnaSeq_single_cell_NPC_TPM.csv


title: H3K4me3_AIDtg_clone22


title: H3K4me3_AIDtg_clone23


title: NPCs_E10

description:
NPCs_E10
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_D8

description:
NPCs_D8
RnaSeq_single_cell_NPC_TPM.csv


title: H3K4me3_AIDtg_clone21


title: H3K4me3_AIDtg_clone24


title: H3K4me3_AIDtg_clone19


title: H3K4me3_AIDtg_clone20


title: NPCs_D6

description:
NPCs_D6
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_D7

description:
NPCs_D7
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_D4

description:
NPCs_D4
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_D12

description:
NPCs_D12
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_D3

description:
NPCs_D3
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_D5

description:
NPCs_D5
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_E3

description:
NPCs_E3
RnaSeq_single_cell_NPC_TPM.csv


title: H3K4me3_AIDtg_clone15


title: H3K4me3_AIDtg_clone16


title: NPCs_D11

description:
NPCs_D11
RnaSeq_single_cell_NPC_TPM.csv


title: H3K4me3_AIDtg_clone17


title: H3K4me3_AIDtg_clone14


title: NPCs_D1

description:
NPCs_D1
RnaSeq_single_cell_NPC_TPM.csv


title: H3K4me3_AIDtg_clone12


title: H3K4me3_AIDtg_clone13


title: NPCs_C8

description:
NPCs_C8
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_C9

description:
NPCs_C9
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_C7

description:
NPCs_C7
RnaSeq_single_cell_NPC_TPM.csv


title: H3K4me3_AIDtg_clone11


title: H3K4me3_AIDtg_clone9


title: H3K4me3_AIDtg_clone7


title: NPCs_C3

description:
NPCs_C3
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_C5

description:
NPCs_C5
RnaSeq_single_cell_NPC_TPM.csv


title: H3K4me3_AIDtg_clone18


title: H3K4me3_AIDtg_clone6


title: H3K4me3_AIDtg_clone10


title: H3K4me3_AIDtg_clone8


title: NPCs_C12

description:
NPCs_C12
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_B8

description:
NPCs_B8
RnaSeq_single_cell_NPC_TPM.csv


title: H3K4me3_AIDtg_clone5


title: NPCs_B7

description:
NPCs_B7
RnaSeq_single_cell_NPC_TPM.csv


title: H3K4me3_AIDtg_clone4


title: NPCs_B6

description:
NPCs_B6
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_B4

description:
NPCs_B4
RnaSeq_single_cell_NPC_TPM.csv


title: H3K4me3_AIDtg_clone1


title: Nipbl_ramos_rep1

description:
Used to classify regulatory elements. Replicates were pooled
processed data file: RAMOS_RE.bed.gz

value: Rabbit anti-NIPBL Antibody

value: Bethyl


title: H3K4me3_AIDtg_clone2


title: Nipbl_ramos_rep2


title: NPCs_B5

description:
NPCs_B5
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_B2

description:
NPCs_B2
RnaSeq_single_cell_NPC_TPM.csv


title: H3K4me3_AIDtg_clone3


title: NPCs_B1

description:
NPCs_B1
RnaSeq_single_cell_NPC_TPM.csv


title: H3K4me1_ramos

description:
Used to classify regulatory elements
processed data file: RAMOS_RE.bed.gz

value: Anti-Histone H3 (mono methyl K4) antibody

value: Abcam


title: NPCs_C6

description:
NPCs_C6
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_A9

description:
NPCs_A9
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_A8

description:
NPCs_A8
RnaSeq_single_cell_NPC_TPM.csv


title: ChiaPET_RAMOS_rep1

description:
Replicate data sets were pooled for the final analysis
processed data file: RAMOS_RNAPol2_ChiaPET.gz

value: RNA Polymerase II 8WG16 Monoclonal Antibody

value: Covance


title: ChiaPET_RAMOS_rep2


title: NPCs_A2

description:
NPCs_A2
RnaSeq_single_cell_NPC_TPM.csv


title: NPCs_A7

description:
NPCs_A7
RnaSeq_single_cell_NPC_TPM.csv


title: RNA-seq siTUT47 ActD 4h (biological replicate #2)

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

description: RNA-seq for HeLa total RNA 4h after actinomycin D treatment to TUT4/7 knockdown cells

data_processing:
The sequence reads were aligned to the spike-in RNA sequences (GenBank accessions M24537.1, X04603.1, L38424.1, and X17013.1) by Bowtie2 (Langmead and Salzberg, 2012) using  options “--end-to-end --sensitive -k 4”.
Scaling factor of a sample was calculated as geometric mean of ratios for valid spike-ins between geometric mean of read counts in all samples and read counts in the sample.
Spike-in RNAs with insufficient read counts (< 500) in any sample were excluded from the calculation. The reads not aligned to any spike-in RNAs were aligned to UCSC hg19 genome assembly using STAR (Dobin et al., 2013) with an option “--outFilterScoreMin 3” and splicing junction annotations generated from the NCBI RefSeq and the UCSC knownGene. The reduced RefSeq transcript set for non-overlapping representation was prepared as previously described (Chang et al., 2014b).
Reads mapped to each transcript were counted using BEDTools multicov (Quinlan and Hall, 2010) with default options. The read counts were scaled by the factors calculated from spike-in read counts. Transcripts not detected with enough reads (< 1,000 normalized reads in the siControl 0 hr sample) were removed to reduce noises.
Genome_build: hg19
Supplementary_files_format_and_content: A spreadsheet file contain normalized read counts by spike-in scaling; RS2-normalized-readcount.csv is for biological replicate #2 samples.

growth_protocol: HeLa cells were maintained in DMEM (Welgene) supplemented with  10% fetal bovine serum (Welgene).

extract_protocol:
Total RNAs were extracted by TRIzol (Invitrogen), and the quality was checked by  Bioanalyzer 2100 (Agilent).
The same amount of control poly(A) spike-in (Affymetrix,  #900433) was mixed with each sample with the same amount of total RNA, and  subsequently rRNA was depleted by Ribo-Zero (Epicentre). RNA-seq libraries were  constructed using Illumina TruSeq RNA sample preparation kit v2.

treatment_protocol: HeLa cells were transfected twice with 40 nM of siRNAs using  Lipofectamine 2000 (Invitrogen). To block transcription, HeLa cells were treated with actinomycin D (Sigma, 4  μg/ml).

value: HeLa

value: human cervical cancer cell line


title: RNA-seq siTUT47 ActD 2h (biological replicate #2)

description: RNA-seq for HeLa total RNA 2h after actinomycin D treatment to TUT4/7 knockdown cells


title: TAIL-seq exp #9 siTUT47

description: TAIL-seq for TUT4 and TUT7 knockdown HeLa cells, set #9

data_processing:
Library strategy: TAIL-Seq
The base calls and signal intensities were processed by Illumina RTA 1.17.21.3 for HiSeq 2500, or RTA 1.17.28 for MiSeq. The read 1 sequences were reanalyzed for more sensitive basecalling using AYB 2. The read 1 sequences were aligned to the common contaminants set, which is composed of rDNA repeat units (GenBank accession U13369.1), PhiX genome (GenBank accession J02482.1), Illumina TruSeq primer sequences, and all sequences for 5S and 5.8S rRNAs of respective species (retrieved from Rfam 11.0 of the Wellcome Trust Sanger Institute) using GSNAP 2013-03-31 with maximum 5% mismatches allowed. Clusters with any match to the contaminants were removed from the subsequent analyses. The sequences having completely identical nucleotides in the 21st to 35th cycle in read 1 (representative region of the insert) and the 1st to 15th cycle in read 2 (degenerate bases in 3′ adapter) are deduplicated by leaving only a cluster with the maximum PHRED quality sum of read 1. The degenerate and fixed delimiter sequence in 3′ adapter was clipped out from read 2 by searching perfect match of delimiter sequence (‘GTCAG’ as in the direction of read 2) between the 14th and 16th cycles in read 2. The clusters missing a delimiter sequence or having low diversity in degenerate region (at least two occurrences for all of A, C, G and T) were removed from further analyses.
The fluorescence signal intensities were processed into “Relative T signal” as described in our previous paper (Chang et al, 2014b). The signals from a spike-in sample were purified with an outlier filter based on robust Mahalanobis distance (mvoutlier package 1.9.9; quan=0.5, alpha=0.025). Random 500 clusters per each spike-in were chosen for parameter calculation of a Gaussian mixture hidden Markov model (GMHMM). We trained the model using Baum-Welch algorithm implemented in the GHMM library (http://ghmm.org) with topology and initial parameters shown in fig. S1A and table S7 and S8 (1,000 iterations). The procedure was iterated to maximize likelihood, not using any property (eg. designed length of poly(A) tail) of spike-ins. Relative T signals outside the range of [-5, 5] were clipped into the range for both training and later calculations.
The length of poly(A) tails were first measured with base call-based “Strategy II” described in fig. S1A. For clusters with the measured length is shorter than 8 nt, the length is called as the final poly(A) tail length. For the others, normalized T signals starting from the first position in T-stretch detected by Strategy II were analyzed with the GMHMM. The hidden states were decoded with the standard Viterbi algorithm implemented in the GHMM library. The number of cycles with state 1 and 2 was called as the length of poly(A) tail. For the estimation of performance, we applied the process to all spike-in samples except the clusters used for the parameter fitting of the model.
The remaining reads after contaminant filter and the first duplication filters were then aligned to the genome sequences (UCSC hg19, positions of splicing junctions were processed from the UCSC Genome Browser database for version of Jan 24, 2013) using GSNAP 2013-03-31. Three different versions of alignments to genome were used in this study. (1) R1 alignment: using only the full read 1 sequences which are 51 nt long. This was used for identification of a cluster. (2) R2 short alignment: using only 40 nt right next to the 3′ adapter of read 2. This was used in searching for the poly(A)-free 3′ hydroxyl ends. (3) paired alignment: using the full read 1 sequences and part of read 2 sequences trimmed of degenerate bases and delimiter. We filtered out poly(A) stretches encoded from genome using this alignment set. All the alignments were performed with maximum mismatches of 5%, minimum mapping quality of 3. All multi-mapped reads were removed. The remaining PCR artifacts with few mismatches were removed again using the R1 alignment with 15 degenerate bases inside the 3′ adapter region. To detect that kind of artifacts, we clustered the R1 alignments with maximum distance between mapped positions of 10 bp, they were then clustered again within the first cluster using degenerate bases from read 2 of respective reads with CD-HIT-EST 4.5.4 (word size=6, sequence identity=0.85). For a set of detected duplicates, we chose a read with maximum sum of PHRED quality in read 1 to leave.
For classification and transcript-level analyses, we compiled reference annotations for human and mouse using NCBI RefSeq, RepeatMasker, gtRNAdb, Rfam and miRBase databases (the first three were downloaded from the UCSC Genome Browser on Apr 25, 2013; Rfam version 11; miRBase version 19). The R1 alignments were annotated with intersection with the compiled annotations using BEDTools {Quinlan, 2010 #66}. When multiple annotations were overlapped to an alignment, we chose a class for the statistics requiring exclusive assignment of a genomic source type by the following priority: miRNA, rRNA, tRNA, Mt-tRNA, snoRNA, scRNA, srpRNA, snRNA, lncRNA, RNA, ncRNA, misc_RNA, Cis-reg, ribozyme, RC, IRES, frameshift_element, LINE, SINE, Simple_repeat, Low_complexity, Satellite, DNA, LTR, CDS, 3′ UTR, 5′ UTR, intron, Other, Unknown (higher priority first). The transcript-level analyses were performed using our custom non-redundant RefSeq (nrRefSeq) transcript set, which is a reduced set retaining only the longest isoform or transcript when regions overlap with each other. The positions of read 1 in nrRefSeq transcripts were positioned with BEDTools intersection between alignments to genome sequences and nrRefSeq annotation set, and then translated to the transcript-level coordination with in-house software.
As poly(A) tails were initially detected with a constraint that it must begin within the first 30 cycles, so the maximum detectable 3′ end modification of poly(A) tails was limited to the last 30 nucleotides of insert. To exclude A stretches obviously encoded from genomic sequence (with or without 3′ end modifications), we masked detected poly(A) tail ranges with read 2 alignments so that the 3′-most position of alignable (not clipped) is eliminated from poly(A) tail or its 3′ end modifications. All statistics regarding transcript-level modification rates were calculated for transcripts having more than 200 tags with poly(A) tails longer than 8 nt.
Genome_build: hg19
Supplementary_files_format_and_content: The spreadsheet files contain the poly(A) tail length distribution and 3' end modification frequencies next to poly(A) tails for all detected transcripts

extract_protocol:
Total RNAs were extracted from HeLa cells by TRIzol reagent (Invitrogen, 15596-018) and purified by RNeasy MinElute column (Qiagen, 74204) according to manufacturer’s instruction.
TAIL-seq was carried out as described previously (Chang et al., 2014b). Briefly, 25-50  ug of total RNAs (>200 nt) were extracted by TRIzol (Invitrogen), purified by RNeasy  MinElute column (Qiagen), and rRNA-depleted by using Ribo-zero kit (Epicentre). The  RNAs were ligated to the biotinylated 3′ adaptor, and partially digested by RNase T1.  The fragmented RNAs were pull-downed with streptavidin beads, phosphorylated at the  5′ end, and gel purified (500-1000 nt). The purified RNAs were ligated to the 5′ adaptor, reverse-transcribed, and amplified by PCR.

treatment_protocol: HeLa cells were transfected twice with 40 nM of siRNAs using  Lipofectamine 2000 (Invitrogen). A mixture of 2-4 different siRNAs was used  to knockdown each gene. In combinatorial knockdown, we mixed siRNA pools to have a  final concentration of 40 nM.


title: TAIL-seq exp #9 siCont

description: TAIL-seq for control knockdown HeLa cells, set #9


title: NPCs_A6

description:
NPCs_A6
RnaSeq_single_cell_NPC_TPM.csv


title: RNA-seq siTUT47 ActD 1h (biological replicate #2)

description: RNA-seq for HeLa total RNA 1h after actinomycin D treatment to TUT4/7 knockdown cells


title: NPCs_A10

description:
NPCs_A10
RnaSeq_single_cell_NPC_TPM.csv


title: RNA-seq siTUT47 ActD 0h (biological replicate #2)

description: RNA-seq for HeLa total RNA 0h after actinomycin D treatment to TUT4/7 knockdown cells


title: NPCs_B3

description:
NPCs_B3
RnaSeq_single_cell_NPC_TPM.csv


title: mESC_Plate2_June2014_H8

description:
mESC_Plate2_June2014_H8
RnaSeq_single_cell_mESC_TPM.csv

value: serum+LIF


title: RNA-seq siCont ActD 4h (biological replicate #2)

description: RNA-seq for HeLa total RNA 4h after actinomycin D treatment to control knockdown cells


title: mESC_Plate2_June2014_H9

description:
mESC_Plate2_June2014_H9
RnaSeq_single_cell_mESC_TPM.csv