title: TetDKO_shCtrl_Vc_E14_H3K27me3.BSseq

city: Boston

first: Hao

last: Wu

address: 149G Warren Alpert Building, 200 Longwood Avenue

institute: Harvard Medical School/HHMI

data_processing: Raw sequencing reads were first trimmed for low-quality bases and adaptor sequences using Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic). Data quality was then examined with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The trimmed reads were mapped against the mouse genome (mm9 build) with Bismark using the bowtie2 mode (http://www.bioinformatics.babraham.ac.uk/projects/bismark/). PCR duplicates were removed using the Picard program (http://picard.sourceforge.net/). Sequencing base quality was first recalibrated with BisSNP (http://epigenome.usc.edu/publicationdata/bissnp2011/) and CpGs with low quality were removed (minimum mapping quality [mmp] >=10 and minimum base quality [mbp] score >= 5). CpGs overlapping with cell-line-specific SNPs in the mouse genome (dbSNP build 132) were removed from downstream analysis with BisSNP.  All programs were performed with default setting (unless otherwise specified). For MAB-seq analysis, raw signals were calculated as % of T/(C+T) at each called CpG. For BS-seq analysis, raw signals were calculated as % of C/(C+T) at each called CpG.

source_name: mouse embryonic stem cells

growth_protocol: V6.5 (control and Tdg knockdown), E14Tg2A (control, Tdg knockdown and Tet1/2–/–), and J1 (Dnmt1/3a/3b–/–) mouse embryonic stem cell (mESC) lines were cultured in feeder-free gelatin-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) (GIBCO, 11995) supplemented with 15% FBS (GIBCO), 2 mM L-glutamine (GIBCO), 0.1 mM 2-mercaptoethanol (Sigma), nonessential amino acids (GIBCO), 1,000 units/ml LIF (Millipore, ESG1107). The culture was passaged every 2-3 days using 0.05% Trypsin (GIBCO).

extract_protocol:
For whole genome (WG) MAB-seq analysis, genomic DNA was extracted from mESCs using the DNeasy Blood & Tissue Kit (Qiagen 69504). To capture H3K4me1- or H3K27me3-enriched chromatin for genome-scale MAB-seq/BS-seq analysis, ~15 million cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature followed by exposure to 0.125 M glycine. After two washes with cold PBS, cells were collected and stored at -80 °C before use. Chromatin were extracted and lysed sequentially with lysis buffer (LB3, 10 mM Tris-HCl, pH8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine). Chromatin was sonicated using a microtip (Branson sonifier 450) until the DNA fragments were reduced to 200-1000 bp in length. 10 μg antibodies were immobilized with 100 μl Dynal protein-G beads (Invitrogen) for at least 6 hours. Immunoprecipitation was performed overnight at 4 °C with antibody-conjugated protein-G beads. DNA/protein complexes were washed with RIPA buffer (50 mM Hepes-KOH, pH7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) for five times and reverse cross-linked at 65 °C overnight. The DNA was treated sequentially with RNase A and proteinase K, and purified by phenol/chloroform extraction and ethanol precipitation. Following antibodies were used in ChIP assays: anti-H3K4me1 (ab8895, Abcam) and anti-H3K27me3 (07-449, Millipore).
For genome-scale MAB-seq or BS-seq, 200-500 ng of ChIP DNA (H3K4me1- or H3K27me3-enriched) was first spiked-in with unmethylated lambda DNA (1:400), which was then repaired and ligated to methylated (5mC) custom adapters (forward 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’; reverse 5’-/5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTC-3’; the asterisk denotes phosphorothioate bond) with the NEBNext Ultra DNA Library Prep kit from Illumina (NEB). Adaptor-ligated DNA was then purified with 1.2x AMPure XP beads (Beckman Coulter). For BS-seq, methylated-adpator-ligated DNA was directly subjected to bisulfite conversion using Qiagen EpiTect DNA Bisulfite Kit (Qiagen, 59104) per manufacturer’s instructions, except that the thermal cycle was repeated twice. For MAB-seq, methylated adpator-ligated DNA was treated by M.SssI (New England Biolabs, M0226M) in a 50-µL reaction for two rounds. In each round of treatment, DNA was first incubated with 1.0 unit/µL M.SssI methylase (New England Biolabs, M0226M) for 4 hours in 25-µL reaction [1.25 µL of 20 unit/µL M.SssI and 0.5 µL of 32 mM SAM (final concentration: 640 µM)], and additional 25-µL containing same concentration of M.SssI (1.0 unit/µL) and SAM (640 µM) was supplemented to treat DNA for another 8 hours (in 50-µL). Of note, the first round of M.SssI treatment was performed in Mg++-free reaction buffer [10 mM Tris-HCl (pH 8.0), 50 mM NaCl, 10 mM EDTA], while the second round was carried out with NEB buffer #2 [10 mM Tris-HCl (pH 7.9), 50 mM NaCl, 10 mM MgCl2, 1 mM DTT]. DNA was purified by sequential Phenol/Chloroform/Isoamyl Alcohol (PCI, 25:24:1) extraction and ethanol precipitation after each round of M.SssI treatment. M.SssI-treated, methylated adaptor-ligated DNA was then subjected to bisulfite conversion using the EpiTect DNA Bisulfite Kit (Qiagen) as described above. Bisulfite-treated DNA was pre-amplified for 5 cycles using KAPA HiFi Uracil+ HotStart ReadyMix (KAPA) with indexed and universal primers from NEBNext Multiplex Oligos for Illumina (Index Primers Set 1). The optimal PCR cycle numbers required to generate the final libraries were then determined by quantitative PCR. Final libraries were generated by scaled-up PCR reactions using the cycles determined above, and purified with 1.2x AMPure XP beads. For whole-genome MAB-seq analysis, 1 µg non-enriched genomic DNA was first spiked-in with unmethylated lambda DNA (1:400) and was then treated with M.SssI (1st round protocol). M.SssI-treated genomic DNA (in 50-µL) was fragmented to an average size of 300-400 bp with Covaris M220 (20% duty factor, 200 cycles per burst, 80 sec x 2) using microTUBE AFA Fiber Screw-Cap. Sheared DNA was purified (1.2x AMPure XP beads), end-repaired and ligated to methylated adapters as described for H3K4me1/H3K27me3-MAB-seq. Methylated-adaptor-ligated DNA was treated with M.SssI again (2nd round protocol) before bisulfite conversion (Qiagen EpiTect DNA Bisulfite Kit). Bisulfite-treated DNA was prepared for sequensing as described above.

treatment_protocol: Stable Tdg knockdown was achieved using a lentiviral system obtained from the National Institutes of Health (NIH) AIDS Research and Reference Reagent Program (https://www.aidsreagent.org/). This system allows selection of infected cells with puromycin. The expression of short hairpin RNA (shRNA) targeting Tdg (5'-GCAAGGATCTGTCTAGTAA-3') or the control shRNA (5'-GTTCAGATGTGCGGCGAGT-3') is under the control of U6 promoter. To generate lentiviruses, three transducing vectors (pTY, pNHP and pHEF1a-VSVG) were cotransfected into 293T cells. The supernatant containing lentiviruses was harvested at 48 and 60 hrs after transfection and concentrated using a centrifugal filter (EMD Millipore, Amicon Ultra 100k). To generate stable knockdown cells, mESCs were infected with lentivirus in the 12-well plate and puromycin (2 µg/ml) was added to the medium for selecting infected cells. For vitamin C (Sigma, A8960) treatment, control and Tdg knockdown mouse ESCs were treated with 100 µg/ml of vitamin C for 60 or 96hrs.

tag: cell line

value: Tet1/2 KO

tag: lentiviral infection

value: control knockdown (shCtrl)

tag: vitamin c treatment

value: 100 ug/ml, 60hrs


title: strand specific RNA-Seq for LRG replicate 2

status: Public on Nov 02 2014

type: SRA

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

country: Germany

institute: Max Planck Institute of Psychiatry

description: Processed data file: AllSamples_geneExpression.fpkm_tracking

library_source: transcriptomic

data_processing:
For RNA-Seq data processing, reads were trimmed to 80, 60 or 30bp depending on their per-base quality distribution in order to achieve maximum alignment rates. Reads were mapped to the human genome (hg19) using TopHat v2.0 (ref 9) (http://tophat.cbcb.umd.edu) employing the unfiltered gencode.v19.annotation.gtf annotation as the transcriptome reference. TopHat was run with default parameters except for the coverage search being turned off. Transcript expression was estimated with Cuffdiff 2 (ref 10). The workflow used to analyze the data is described in detail in Trapnell et al. (2012) (alternate protocol B)11.
Genome_build: hg19
Supplementary_files_format_and_content: All coordinates are based on hg19. ENCODE narrowPeak Format: chromosome,chromstart,chromend,peak name,macs2 integer score, strand, fold change over background,-log10pvalue,-log10qvalue,relative summit position to peak star  WGBS/RRBS  bed format, each row describes one CpG: chrom,chromstart,chromend,number of reads where CpG was methylated/total number of reads coverging CpG,numeric score for UCSC display,strand-ignore  RNA-Seq txt format: cuffdiff output file: cufflinks  ChIP-Seq bed format containing 1kb tiles above a minimal enrichmend level: chrom,chromstart,chromend

molecule: total RNA

organism: Homo sapiens

source_name: ES-derived neural progenitor cells

growth_protocol: Culturing undifferentiated human ES cells:  HES5::eGFP BAC transgenic human ES cells (H9; WA-09; Wicell) expressing GFP under the HES5 promoter were cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs) (Globalstem). Undifferentiated ES cells were maintained as described previously1 in medium containing DMEM/F12, 20% KSR, 1mM Glutamine, 1% Penicillin/Streptomycin, non essential amino acids and beta-mercaptoethanol.  Undifferentiated ES cells were purified with pluripotency markers Tra-1-60 and PE-conjugated SSEA-3 (BD Pharmingen).   Neural induction and long-term propagation of NPCs:  Neural differentiation of ES cells was performed as described previously1-3. Briefly, neuroectodermal cells were generated either by monolayer induction – with dissociated ES cells plated on Matrigel (BD biosciences), or by co-culture on MS5 stromal cells. In both cases neural fate was directed by dual SMAD inhibition protocol2. Neural rosettes were harvested mechanically beginning on day 8-10 of differentiation. Rosettes were replated on culture dishes pre-coated with 15 μg/mL polyornithine (Sigma), 1 μg/mL Laminin (BD Biosciences) and 1ug/ml Fibronectin (BD Biosciences) (Po/Lam/FN) in N2 medium composed of DMEM/F12 and N2 supplement (Invitrogen). N2 supplement contained Insulin, Apo-transferin, Sodium Selenite, Putrecine and Progesterone. This medium was supplemented with SHH (200 ng/mL), FGF8 (100 ng/mL) and BDNF (20 ng/mL) (all from R&D Systems) to maintain early anterior regionalization of the neural plate. These factors were gradually replaced by FGF2 (20 ng/mL) and EGF (20 ng/mL) in the following two weeks of differentiation in order to maintain a proliferative (FGF and EGF responsive) NPC state. NPCs from all stages were collected at indicated days and FACS purified for HES5::GFP (NE to L-RG) or EGFR for LNPs to purify for the highest NPC state for each stage. Neuroectodermal cells were collected at day 12 of differentiation, Neuroepithelial/early radial glial cells were collected at day 14, mid neurogenesis radial glial cells were collected at day 35, late gliogenic radial glial cells were collected at day 80, and long term NPCs were collected at day 220. At each stage cells were either split for the next passage or subjected to FACS purification for HES5::GFP as described. Cells were replated onto Po/Lam/FN culture dishes. For neuronal, astroglial or oligodendroglial differentiation, NPCs were seeded at high density and subjected to differentiated for 17 days in the presence of AA/BDNF, 5% Fetal Bovine Serum (FBS) (Invitrogen), or AA/BDNF/SHH/FGF8, respectively. For more details, please see Edri et al.3.

extract_protocol:
RNA-Seq:RNA was extracted using the miRNeasy kit (Qiagen, 217004). Poly(A) RNA was isolated using Oligo d (T25) beads (NEB, E7490L).
RNA-Seq: The following steps of Illumina library construction (end-repair, addition of A-base, ligation of barcoded adaptors and PCR enrichment) we used a general SPRI cleanup procedure: addition of PEG buffer (20% PEG and 2.5 M NaCl), and extracted and washed as above. The enzymatic reactions were carried as follows: 1. DNA end-repair: T4 PNK and T4 polymerase (New England Biolabs) incubated 12C for 15 min, 25C for 15 min;  2. A-base addition: Klenow (3’->5’ exonuclease; New England Biolabs) incubated at 37C for 30 min. 3. Adaptor ligation: DNA ligase (New England Biolabs) and indexed oligo adaptors and incubated 25C for 15 min, followed by 0.7X SPRI/reaction to remove non-ligated adaptors. 4. PCR enrichment: PCR mastermix (primer set, dNTP mix, Pfu Ultra Buffer (Agilent), Pfu Ultra-II Fusion (Agilent), water), for 20 cycles. The PCR amplified libraries we cleaned up using 0.7X SPRI/reaction (size selection mode) to remove excessive primers. Roughly 5 picomoles of DNA library was then applied to each lane of the flow cell and sequenced on Illumina HiSeq 2000 sequencers according to standard Illumina protocols.

tag: cell type

value: ES-derived neural progenitor cells

tag: genetic background


title: NE_rep24h_rep1_shRNA screen

description:
Protocol: shRNA screen
Processed data file: shRNAScreen_rawCounts.txt

library_source: genomic

data_processing:
For the shRNA screen data analysis, we followed the protocol outlined by Dai et al. 2014 employing the R package limma. First, we extracted and counted the number of times each shRNA was observed in each library using the shRNA sequence as barcode and the R function processHairpinReads().
Supplementary_files_format_and_content: text file with raw counts for hairpin sequences

molecule: genomic DNA

source_name: neural precursor cell: neuroepithelial

extract_protocol:
shRNA screen: We selected 244 transcription factors and epigenetic modifiers that were differentially or continuously highly expressed during our in vitro differentiation time course in an otherwise unbiased fashion (Extended Data Table 4). In addition, we included GFP, RFP, lacZ and luciferase as internal controls.  We then obtained a sub-pool of the human 45K shRNA pool6 distributed by the Broad Institute Genomic Perturbations Platform and the RNAi Consortium (TRC) against these genes. For each gene, 5 distinct shRNAs were included as well as 5 scrambled and 3 empty control vectors, amounting to a total of 1230+8 shRNAs. The plasmid for shRNA expression under the control of the constitutive U6 shRNA promoter was the lentiviral vector pLKO.1. shRNA pool production and infection conditions were performed as previously described6. Subsequently, we performed calibration experiments to determine to optimal combination of MOI and Puromyocin concentration to ensure efficient selection. We identified MOI 0.4 and 1ug/ml of Puromycin as optimal parameters for all stages. We then infected 26 million cells at each stage of NE, ERG and MRG to ensure sufficient shRNA integration events to recover the complexity of the shRNA library. 24h post infection and prior to full expression but after integration of the lentivirus into the genome we collected 3 million cells to determine our baseline shRNA library representation. Subsequently, we subjected the cells to 5 days of Puromycin selection and then FACS sorted the resulting populations into HES5+ and HES5- compartments.
We assessed the representation of the shRNA library in each of the 9 populations by retrieving all shRNA integration events from genomic DNA isolated from each sample using PCR followed by next generation sequencing as previously described (Strezoska, Z. et al 2012). More specifically, we performed two rounds of PCR using the following primers for the primary PCR: Primary R :CTTTAGTTTGTATGTCTGTTGCTATTAT; Primary F: AATGGACTATCATATGCTTACCGTAAC.  For the second, nested PCR we used: Nested F: GGCTTTATATATCTTGTGGAAAGGA; Nested R: GGATGAATACTGCCATTTGTCTC.

value: HES5::eGFP BAC transgenic human ES cells (H9; WA-09; Wicell) expressing GFP under the HES5 promoter

tag: treatment

value: Infected cells collected 24h after infection and puero selection


title: NE_minus_rep4_shRNA screen

value: GFP negative population after 6 days of shRNA infection


title: WT_shTdg_Vc_v65_H3K27me3.BSseq

state: Massachusetts

department: Genetics

country: USA

organism: Mus musculus

tag: genotype

value: wild-type (WT)

value: Tdg knockdown (shTdg)

tag: chip antibody


title: strand specific RNA-Seq for LRG replicate 3


title: NE_minus_rep2_shRNA screen


title: MNC771_RNAseq

status: Public on Nov 03 2014

city: Montreal

first: Tony

last: Kwan

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Trimmomatic v0.22  was used for trimming reads for quality (phred33>=30) and length (n>=32)
For RNA-seq, filtered reads were aligned to hg19 using Tophat v1.4.1 and bowtie v0.12.8. Raw read counts were obtained using htseq-count v0.5.3p9. Normalized gene and transcript expression values are obtained using cufflinks v2.1.1
Genome_build: hg19

source_name: Monocytes

growth_protocol: Circulating monocytes were collected from healthy adult blood donors of European origin. CD14+ magnetic microbeads were used to isolate monocytes from whole blood.

extract_protocol:
Total RNA was extracted from cell lysates using the miRNeasy Mini Kit including a DNaseI treatment step and quality assessed by Agilent 2100 BioAnalyzer.
Libraries were prepared according to the Illumina TruSeq protocol, and quality assessed by Agilent 2100 BioAnalyzer.

value: monocyte


title: WT_shTdg_Vc_v65_WG.MABseq

description:
processed data file: shTdg_Vc_merged_WG.MABseq.txt
processed data file: mESC.5fC5caC.sites.mm9_pval0.00025_cov10_bedgraph.gz
processed data file: mESC.5fC5caC.sites.mm9_pval0.00025_cov5_bedgraph.gz
processed data file: mESC.MABseqRawSignal.mm9_cov5_bedgraph.gz
processed data file: mESC.coverage.mm9_cov5_bedgraph.gz

data_processing: Raw sequencing reads were first trimmed for low-quality bases and adaptor sequences using Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic). Data quality was then examined with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The trimmed reads were mapped against the mouse genome (mm9 build) with Bismark using the bowtie2 mode (http://www.bioinformatics.babraham.ac.uk/projects/bismark/). PCR duplicates were removed using the Picard program (http://picard.sourceforge.net/). Sequencing base quality was first recalibrated with BisSNP (http://epigenome.usc.edu/publicationdata/bissnp2011/) and CpGs with low quality were removed (minimum mapping quality [mmq] >=10 and minimum base quality [mbq] score >= 5). CpGs overlapping with cell-line-specific SNPs in the mouse genome (dbSNP build 132) were removed from downstream analysis with BisSNP.  All programs were performed with default setting (unless otherwise specified). For MAB-seq analysis, raw signals were calculated as % of T/(C+T) at each called CpG. For BS-seq analysis, raw signals were calculated as % of C/(C+T) at each called CpG.


title: WT_shCtrl_Vc_v65_H3K27me3.BSseq


title: TetDKO_shCtrl_Vc_E14_H3K27me3.MABseq


title: strand specific RNA-Seq for MRG replicate 2


title: strand specific RNA-Seq for MRG replicate 1


title: WT_shTdg_Vc_v65_exp2_H3K27me3.MABseq

description: processed data file: shTdg_Vc_merged_H3K27me3.MABseq.txt


title: strand specific RNA-Seq for ERG replicate 2


title: WT_shCtrl_Vc_v65_H3K27me3.MABseq


title: strand specific RNA-Seq for ERG replicate 1


title: strand specific RNA-Seq for NE replicate 2


title: TetDKO_shCtrl_Vc_E14_H3K4me1.MABseq

description: processed data file: NegCtrl_merged_H3K4me1.MABseq.txt


title: DnmtTKO_noVc_J1_H3K4me1.MABseq

value: Dnmt1/3a/3b KO

value: 0 ug/ml


title: strand specific RNA-Seq for ESCs replicate 2


title: WT_shTdg_Vc_v65_exp1_H3K4me1.MABseq

description: processed data file: shTdg_Vc_merged_H3K4me1.MABseq.txt


title: strand specific RNA-Seq for ESCs replicate 1


title: WT_shTdg_noVc_v65_H3K4me1.MABseq


title: reduced representation bisulfite sequencing for long term neural precursors

description: Processed data file: RRBS_cpgMethylation_LNP.RRBS.bed.gz

data_processing:
WGBS libraries were aligned using BSMap 2.7 (ref 12) to the hg19/GRCh37 reference assembly. Subsequently, CpG methylation calls were made using custom software as previously described13, excluding duplicate, low-quality reads as well as reads with more than 10% mismatches. Only CpGs with more than 5x coverage were considered for further analysis. In addition, all CpGs within the first 4bp of each read were ignored.
Genome_build: hg19
Supplementary_files_format_and_content: All coordinates are based on hg19. ENCODE narrowPeak Format: chromosome,chromstart,chromend,peak name,macs2 integer score, strand, fold change over background,-log10pvalue,-log10qvalue,relative summit position to peak star  WGBS/RRBS  bed format, each row describes one CpG: chrom,chromstart,chromend,number of reads where CpG was methylated/total number of reads coverging CpG,numeric score for UCSC display,strand-ignore  RNA-Seq txt format: cuffdiff output file: cufflinks  ChIP-Seq bed format containing 1kb tiles above a minimal enrichmend level: chrom,chromstart,chromend

source_name: neural precursor cell: long term neural precursor

extract_protocol:
ChIP_Seq:To extract DNA and create the Illumina library we used AMPure XP beads (Agencourt) Solid-phase reversible immobilization (SPRI). SPRI beads were added to the samples, mixed 15 times, incubated at room temperature for 2 minutes. Supernatant was extracted from the beads from the beads 4 minutes on a magnet. We used 70% ethanol to wash the beads and then dried for 4 minutes. 40 ul EB buffer (10 mM Tris-HCl pH 8.0) was used to elute the DNA.
ChIP_Seq:The following steps of Illumina library construction (end-repair, addition of A-base, ligation of barcoded adaptors and PCR enrichment) we used a general SPRI cleanup procedure: addition of PEG buffer (20% PEG and 2.5 M NaCl), and extracted and washed as above. The enzymatic reactions were carried as follows: 1. DNA end-repair: T4 PNK and T4 polymerase (New England Biolabs) incubated 12C for 15 min, 25C for 15 min;  2. A-base addition: Klenow (3’->5’ exonuclease; New England Biolabs) incubated at 37C for 30 min. 3. Adaptor ligation: DNA ligase (New England Biolabs) and indexed oligo adaptors and incubated 25C for 15 min, followed by 0.7X SPRI/reaction to remove non-ligated adaptors. 4. PCR enrichment: PCR mastermix (primer set, dNTP mix, Pfu Ultra Buffer (Agilent), Pfu Ultra-II Fusion (Agilent), water), for 20 cycles. The PCR amplified libraries we cleaned up using 0.7X SPRI/reaction (size selection mode) to remove excessive primers. Roughly 5 picomoles of DNA library was then applied to each lane of the flow cell and sequenced on Illumina HiSeq 2000 sequencers according to standard Illumina protocols.


title: WT_shTdg_Vc_v65_exp2_H3K4me1.MABseq


title: WT_shTdg_Vc_v65_exp1_H3K27me3.MABseq


title: strand specific RNA-Seq for ERG derived neuronal like populations replicate 1

source_name: neural precursor cell derived neuronal like cells


title: whole genome bisulfite sequencing of mid radial glial cells

description: Processed data file: BiSeq_cpgMethylation_MRG.bed.gz

source_name: neural precursor cell: mid radial glial


title: reduced representation bisulfite sequencing for late radial glial cells

description: Processed data file: RRBS_cpgMethylation_LRG.RRBS.bed.gz

source_name: neural precursor cell: late radial glial


title: whole genome bisulfite sequencing of early radial glial cells

description: Processed data file: BiSeq_cpgMethylation_ERG.bed.gz


title: WT_shCtrl_noVc_v65_H3K4me1.MABseq

description: processed data file: shCtrl_noVc_Vc_merged_H3K4me1.MABseq.txt


title: strand specific RNA-Seq for LRG replicate 1


title: strand specific RNA-Seq for NE replicate 1


title: ChIP-Seq for OTX2 in MRG

description: Processed data file: MRG_OTX2_final_peaks.bed

data_processing:
ChIP-Seq data was aligned to the hg19/GRCh37 reference genome using MAQ14 version 0.7.1 with default parameter settings or Bowtie 2 version 2.05 (ref 15). Reads were filtered for duplicates and extended by 200 bp at the end of the read. Visualization of read count data was performed by converting raw bam files to .tdf files using IGV tools16 and normalizing to 1 million reads. Fragment length extended, duplicate and quality-filtered reads were used for subsequent analysis.
For H3K27ac and H3K4me3 histone marks, the Irreproducible Discovery Rate (IDR) framework20 with a cutoff of 0.1 in combination with the MACS221 peak caller version 2.1 was used to identify peaks taking advantage of both replicates for each condition. For MACS2 peak calling, we used an initial p-value cutoff of 0.01 and the corresponding whole cell extract (WCE) control library as background.
Genome_build: hg19
Supplementary_files_format_and_content: All coordinates are based on hg19. ENCODE narrowPeak Format: chromosome,chromstart,chromend,peak name,macs2 integer score, strand, fold change over background,-log10pvalue,-log10qvalue,relative summit position to peak star  WGBS/RRBS  bed format, each row describes one CpG: chrom,chromstart,chromend,number of reads where CpG was methylated/total number of reads coverging CpG,numeric score for UCSC display,strand-ignore  RNA-Seq txt format: cuffdiff output file: cufflinks  ChIP-Seq bed format containing 1kb tiles above a minimal enrichmend level: chrom,chromstart,chromend

tag: chip-antibody


title: RNA-seq from mouseembryonic fibroblast

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm10 reference genome (index downloaded from bowtie) using TopHat version 2.0.10.
To estimate expression levels of all genes we used HTSeq-count software, version 0.6.0 ,that was ran with mm10 gtf file downloaded from ensemble.
To get normalized expression levels (FPM) we used DESeq R library
Genome_build: mm10

molecule: polyA RNA

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Maintenance of grounds state naïve murine pluripotent cells was conducted in FBS free N2B27-based media, and included 10μg recombinant human LIF and small-molecule inhibitors CHIR99021 (CH, 1-3 μM- Axon Medchem) and PD0325901 (PD, 1 μM - TOCRIS) termed 2i. For embryoied bodies formation 5x10^6 ESCs were disaggregated with trypsin and transfer to low non-adherent palte and culture in MEF medium (DMEM supplemented with 1% L-Glutamine, 1% Non-essential amino acids, 1% penicillin/streptomycin and 15% FBS) for 8-21 days. MEF generation: E13.5 mouse embryo was decapitated and disaggregated with trypsin and culture in MEFs medium until MEFs population were expended.

extract_protocol:
Cells were harvested and RNA was extracted using the 5 PRIME PerfectPure RNA Cell culture Kit (cat#2302340 ), according to manufacturer's manual
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit v2 ( RS-122-2001).

value: WT

value: Mouse Embryonic Fibroblasts

tag: strain


title: RNA-seq from Mettl3-KO EBs, replicate A

source_name: Embroid bodies

value: Embroid bodies


title: RNA-seq from Mettl3-KO ESCs, replicate C

description: used for SILAC analysis

source_name: Embryonic Stem Cells

value: Embryonic Stem Cells


title: RNA-seq from Mettl3-KO EBs, replicate B


title: ChIP-Seq for OTX2 in NE

description: Processed data file: NE_OTX2_PE_final_peaks.bed


title: whole genome bisulfite sequencing of neuroepithelial cells

description: Processed data file: BiSeq_cpgMethylation_NE.bed.gz

source_name: human embryonic stem cell line H9


title: WT_shCtrl_Vc_v65_H3K4me1.MABseq


title: RNA-seq from Mettl3-KO ESCs, replicate A


title: RNA-seq from WT EBs, replicate B


title: MRG_rep2_H3K4me3

description: Processed data file: FinalIDR_MRG_H3K4me3_macs2.regionPeak.narrowpeak


title: MRG_rep2_WCE

value: none (Input)


title: MRG_rep2_H3K4me1

description: Processed data file: MRG_H3K4me1_peakSet_qval_005_FC_1_5.bed


title: RNA-seq from WT EBs, replicate A


title: RNA-seq from Mettl3-KO ESCs, replicate B


title: MRG_rep2_H3K27ac

description: Processed data file: FinalIDR_MRG_H3K27ac_macs2.regionPeak.narrowpeak


title: RNA-seq from WT ESCs, replicate C

description: used for SILAC analysis


title: Ribo-Seq Mettl3-KO EBs

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We trimmed trailing adapterns from reads using in-house script
We collapsed identical reads with fastx_collapser software, and finally filtered the reads by their length, keeping reads which are between 24 to 35 nucleotides.
We aligned reads to mm10 reference genome (index downloaded from bowtie) using TopHat version 2.0.10.
To estimate translation levels of all genes we used HTSeq-count software, version 0.6.0 ,that was run with mm10 gtf file downloaded from UCSC. The translation level was estimated from coding region alone (-t CDS flag), which is defined from 50bpb upstream to ATG to stop codon.
To get normalized expression levels (FPM) we used DESeq R library
Genome_build: mm10
Supplementary_files_format_and_content: bam, contains aligned reads following the described pre-processing steps

growth_protocol: Maintenance of grounds state naïve murine pluripotent cells was conducted in FBS free N2B27-based media, and included 10μg recombinant human LIF and small-molecule inhibitors CHIR99021 (CH, 1-3 μM- Axon Medchem) and PD0325901 (PD, 1 μM - TOCRIS) termed 2i. For embryoied bodies formation 5x10^6 ESCs were disaggregated with trypsin and transfer to low non-adherent palte and culture in MEF medium (DMEM supplemented with 1% L-Glutamine, 1% Non-essential amino acids, 1% penicillin/streptomycin and 15% FBS) for 8-21 days.

extract_protocol:
Cells were lysed with 0.5% Triton, and the lysate was cleared by centrifugation, treated with RNase I for 45min and then loaded on a sucrose cushion. RNA was then isolated from cells using the acid:phenol extraction method.
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circularized and PCR amplified.


title: RNA-seq from WT ESCs, replicate B


title: Ribo-Seq Mettl3-KO ESCs


title: MRG_rep1_H3K4me1


title: MRG_rep1_WCE


title: RNA-seq from WT ESCs, replicate A


title: MRG_rep2_H3K27me3

description: Processed data file: MRG_H3K27me3_peakSet_qval_005_FC_1_5.bed


title: m6A-seq in MEFs, replicate B: Input

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm10 reference genome (downloaded from ensemble) using TopHat version 2.0.10. Flags used: -M
We identified enriched intervals using MACS version 1.4.1, while using the input as control in order to define a background model.
Final peak list includes peaks that appaer in at least 2 out of 3 replicates (or 2 out of 2 in MEF),  their MACS fold-change is >2, and FDR < 5%, and they fall in annotated gene whose expression level was equal or over the first quartile of the expression level of all genes.
Genome_build: mm10
Supplementary_files_format_and_content: final_peaks.xlsx: final list of peaks in ESC, EBs and MEFs, and their mapping to genes

source_name: MEF cells

extract_protocol:
Cells were harvested and RNA was extracted using the 5 PRIME PerfectPure RNA Cell culture Kit (cat#2302340 ), according to manufacturer's manual
Libraries were prepared according to NEB's instructions accompanying the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (Cat# 7530).

tag: antibody

value: Input

value: MEF cells


title: ERG_rep2_H3K4me3

description: Processed data file: FinalIDR_ERG_H3K4me3_macs2.regionPeak.narrowpeak

source_name: neural precursor cell: early radial glial


title: MRG_rep1_H3K27me3


title: m6A-seq in MEFs, replicate B: IP


title: Ribo-Seq WT EBs


title: ERG_rep2_H3K4me1

description: Processed data file: ERG_H3K4me1_peakSet_qval_005_FC_1_5.bed


title: Ribo-Seq WT ESCs


title: ERG_rep2_H3K27me3

description: Processed data file: ERG_H3K27me3_peakSet_qval_005_FC_1_5.bed


title: MRG_rep1_H3K27ac


title: ERG_rep1_WCE

description: Processed data file: none


title: ERG_rep2_WCE


title: ERG_rep1_H3K4me3


title: ERG_rep2_H3K27ac

description: Processed data file: FinalIDR_ERG_H3K27ac_macs2.regionPeak.narrowpeak


title: m6A-seq in EBs, replicate B: Input

source_name: BVSC Embryoid Bodies

value: BVSC Embryoid Bodies


title: m6A-seq in MEFs, replicate A: IP


title: ERG_rep1_H3K4me1

value: ES-derived neural progenitor cells


title: m6A-seq in EBs, replicate C: IP


title: ERG_rep1_H3K27me3

value: HES5::eGFP BAC transgenic human ES cells (H9; WA-09; Wicell) expressing GFP under the HES5 promoter


title: MRG_rep1_H3K4me3


title: m6A-seq in EBs, replicate A: Input


title: NE_rep2_H3K4me3

description: Processed data file: FinalIDR_NE_H3K4me3_macs2.regionPeak.narrowpeak


title: m6A-seq in EBs, replicate A: IP


title: NE_rep2_WCE


title: m6A-seq in ESCs, replicate C: IP

source_name: BVSC Embryonic Stem Cells

value: BVSC Embryonic Stem Cells


title: m6A-seq in ESCs, replicate C: Input


title: ERG_rep1_H3K27ac


title: NE_rep2_H3K4me1

description: Processed data file: NE_H3K4me1_peakSet_qval_005_FC_1_5.bed


title: m6A-seq in ESCs, replicate B: IP


title: NE_rep2_H3K27me3

description: Processed data file: NE_H3K27me3_peakSet_qval_005_FC_1_5.bed


title: m6A-seq in ESCs, replicate B: Input


title: NE_rep2_H3K27ac

description: Processed data file: FinalIDR_NE_H3K27ac_macs2.regionPeak.narrowpeak


title: m6A-seq in ESCs, replicate A: Input


title: m6A-seq in MEFs, replicate A: Input


title: NE_rep1_H3K4me3


title: NE_rep1_WCE

description: Processed data file: none


title: m6A-seq in ESCs, replicate A: IP


title: m6A-seq in EBs, replicate B: IP


title: WT ESCs 8h after Actinomycin treatment

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to bowtie mm10 index, using bowtie2, version 2.1.0
Gene expression levels were estimated in the following way: each gene was divided to 50-bp bins, from its transcription-start-site and to 3kb after its transcription-end-site (based on UCSC “refGene” table). The number of reads in each bin was counted, and the bin with the highest number of reads was chosen as the representative expression level of that gene.
These expression levels were normalized by the sample size, such that each level represents RPM.
Genome_build: mm10

extract_protocol:
Total RNA was fragmented into average size of 300 nucleotides by incubation of the RNA in 95oC for 4:30 minutes (NEBNext Magnesium RNA Fragmentation Module). The 3’ polyadenylated fragments were enriched by selection on poly dT beads (Dynabeads Invitrogen).
Strand specific cDNA was synthesized using a poly T-VN oligo (18 T) and Affinity Script RT enzyme (Agilent). Double strand DNA was obtained using Second strand synthesis kit (NEBNext second strand synthesis module). DNA was purified by adding paramagnetic SPRI beads (Agencourt AMPure XP, Beckman Coulter) pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a 96-well magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction. DNA ends are first repaired by T4 polymerase (NEBNext), next, T4 polynucleotide kinase (NEB) adds a phosphate group at the 5′ ends. An adenosine base is then added to the blunt-ended fragments, using Klenow enzyme (NEB), and a barcode Illumina compatible adaptor (IDT) was ligated to each fragment using T4 quick ligase (NEB). DNA fragments were amplified by 12 cycles of PCR (Kapa HiFi) using specific primers (IDT) to the ligated adaptors. Library quantity was determined by Qubit Fluorometric Quantitiation (Life Technologies) and the quality of each library was analyzed by Tapestation (Agilent).

tag: time after treatment


title: NE_rep1_H3K4me1


title: WT ESCs 4h after Actinomycin treatment


title: NE_rep1_H3K27ac


title: NE_rep1_H3K27me3


title: WT ESCs 0h after Actinomycin treatment


title: ESC_rep2_H3K4me3

description: Processed data file: FinalIDR_hESC_H3K4me3_macs2.regionPeak.narrowpeak

value: embryonic stem cells


title: m6A-seq in EBs, replicate C: Input


title: WT EBs 4h after Actinomycin treatment


title: WT EBs 0h after Actinomycin treatment


title: ESC_rep2_H3K4me1

description: Processed data file: hESC_H3K4me1_peakSet_qval_005_FC_1_5.bed


title: ESC_rep2_H3K27ac

description: Processed data file: FinalIDR_hESC_H3K27ac_macs2.regionPeak.narrowpeak


title: ESC_rep2_H3K27me3

description: Processed data file: hESC_H3K27me3_peakSet_qval_005_FC_1_5.bed


title: Mettl3-KO ESCs 4h after Actinomycin treatment


title: ESC_rep1_WCE


title: Mettl3-KO ESCs 8h after Actinomycin treatment


title: Mettl3-KO ESCs 0h after Actinomycin treatment


title: Mettl3-KO EBs 4h after Actinomycin treatment


title: Mettl3-KO EBs 8h after Actinomycin treatment


title: Mettl3-KO EBs 0h after Actinomycin treatment


title: ESC_rep1_H3K27me3


title: ESC_rep1_H3K27ac


title: ESC_rep1_H3K4me1


title: WT_shTdg_Vc_E14_WG.MABseq

description:
processed data file: shTdg_Vc_merged_WG.MABseq.txt
processed data file: mESC.5fC5caC.sites.mm9_pval0.00025_cov10_bedgraph.gz
processed data file: mESC.5fC5caC.sites.mm9_pval0.00025_cov5_bedgraph.gz
processed data file: mESC.MABseqRawSignal.mm9_cov5_bedgraph.gz
processed data file: mESC.coverage.mm9_cov5_bedgraph.gz

value: wild-type (WT)

value: 100 ug/ml, 96hrs


title: h yhet m14

status: Public on Nov 01 2014

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

description: processed data in Series supplementary file parabiosis.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
alignment: tophat with deafult parameters
Expression table done using ESAT http://garberlab.umassmed.edu/software/esat/
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Choroid plexus of young heterochronic parabiont 14

tag: selection marker

value: age and type of parabiosis (hetero- vs. isochronic)

tag: organ

value: Choroid plexus

tag: age

value: 3 months

value: heterochonic parabiosis

tag: tissue isolation

value: excised from PBS-perfused mouse and snap frozen on dry ice


title: e oiso m21

source_name: Choroid plexus of old isochronic parabiont 21

value: 22 months

value: isochronic parabiosis


title: i yhet m11

source_name: Choroid plexus of young heterochronic parabiont 11


title: g yhet m9

source_name: Choroid plexus of young heterochronic parabiont 9


title: k ohet m29

source_name: Choroid plexus of old heterochronic parabiont 29


title: d oiso m19

source_name: Choroid plexus of old isochronic parabiont 19


title: l ohet m34

source_name: Choroid plexus of old heterochronic parabiont 34


title: f oiso m23

source_name: Choroid plexus of old isochronic parabiont 23


title: c yiso m5

source_name: Choroid plexus of young isochronic parabiont 5


title: WT EBs 8h after Actinomycin treatment

value: WT

value: Embroid bodies


title: MD Y3 WT TH

description: processed data in Series supplementary file Y_vs_O_tissues_o.txt

source_name: Thymus of young mouse 3

value: age and organ

value: Thymus


title: a yiso m1

source_name: Choroid plexus of young isochronic parabiont 1


title: MD Y1 WT TH

source_name: Thymus of young mouse 1


title: ESC_rep1_H3K4me3

source_name: human embryonic stem cell line H9


title: MD Y3 WT SP

source_name: Spleen of young mouse 3

value: Spleen


title: MD Y3 WT MLN

source_name: Mesenteric Lymph nodes of young mouse 3

value: Mesenteric Lymph nodes


title: MD Y2 WT SP

source_name: Spleen of young mouse 2


title: MD Y1 WT MLN

source_name: Mesenteric Lymph nodes of young mouse 1


title: MD Y1 WT SP

source_name: Spleen of young mouse 1


title: MD Y3 WT Lung

source_name: Lung of young mouse 3

value: Lung


title: MD Y2 WT Lung

source_name: Lung of young mouse 2


title: MD Y2 WT Liver

source_name: Liver of young mouse 2

value: Liver


title: MD Y1 WT Lung

source_name: Lung of young mouse 1


title: MD Y3 WT Liver

source_name: Liver of young mouse 3


title: MD Y1 WT ILN

source_name: Inguinal lymph nodes of young mouse 1

value: Inguinal lymph nodes


title: MD Y2 WT HC

source_name: Hippocampus of young mouse 2

value: Hippocampus


title: MD Y2 WT ILN

source_name: Inguinal lymph nodes of young mouse 2


title: MD Y1 WT HC

source_name: Hippocampus of young mouse 1


title: MD Y2 WT Colon

source_name: Colon of young mouse 2

value: Colon


title: b yiso m3

source_name: Choroid plexus of young isochronic parabiont 3

value: age and type of parabiosis (hetero- vs. isochronic)

value: Choroid plexus


title: MD Y3 WT CLN

source_name: cervical lymph nodes of young mouse 3

value: cervical lymph nodes

value: 3 months


title: MD Y1 WT CP

source_name: Choroid plexus of young mouse 1

value: excised from PBS-perfused mouse and snap frozen on dry ice


title: MD Y2 WT TH

source_name: Thymus of young mouse 2


title: MD Y3 WT CP

source_name: Choroid plexus of young mouse 3


title: MD Y2 WT CLN

source_name: cervical lymph nodes of young mouse 2


title: MD Y1 WT Colon

source_name: Colon of young mouse 1


title: MD Y3 WT BM

source_name: bone marrow of young mouse 3

value: bone marrow

value: bone marrow was flushed with PBS from tibia and femur from PBS-perfused mouse and snap-frozen on dry ice


title: MD Y2 WT BM

source_name: bone marrow of young mouse 2


title: MD O3 WT TH

source_name: thymus of aged mouse 3

value: thymus

value: 22 months


title: MD Y1 WT BM

source_name: bone marrow of young mouse 1

value: age and organ


title: MD O1 WT TH

source_name: thymus of aged mouse 1


title: whole genome bisulfite sequencing of human embryonic stem cells

description: Processed data file: BiSeq_cpgMethylation_hESC.bed.gz

source_name: human embryonic stem cells

value: ES-derived neural progenitor cells

value: HES5::eGFP BAC transgenic human ES cells (H9; WA-09; Wicell) expressing GFP under the HES5 promoter


title: MD Y3 WT HC

source_name: Hippocampus of young mouse 3


title: MD Y1 WT Liver

source_name: Liver of young mouse 1


title: MD O2 WT SP

source_name: spleen of aged mouse 2

value: spleen


title: MD O3 WT SP

source_name: spleen of aged mouse 3


title: MD O1 WT SP

source_name: spleen of aged mouse 1


title: MD O2 WT MLN

source_name: mesenteric lymph nodes of aged mouse 2

value: mesenteric lymph nodes


title: MD Y3 WT Colon

source_name: Colon of young mouse 3


title: MD Y2 WT CP

source_name: Choroid plexus of young mouse 2


title: MD Y2 WT MLN

source_name: Mesenteric Lymph nodes of young mouse 2

value: Mesenteric Lymph nodes


title: MD O3 WT Liver

source_name: liver of aged mouse 3

value: liver


title: MD O1 WT Lung

source_name: lung of aged mouse 1

value: lung


title: MD O2 WT Lung

source_name: lung of aged mouse 2


title: MD O1 WT MLN

source_name: mesenteric lymph nodes of aged mouse 1


title: MD O1 WT Liver

source_name: liver of aged mouse 1


title: MD O2 WT ILN

source_name: inguinal lymph nodes of aged mouse 2

value: inguinal lymph nodes


title: MD O3 WT Colon

source_name: colon of aged mouse 3

value: colon


title: MD O3 WT HC

source_name: hippocampus of aged mouse 3

value: hippocampus


title: MD O1 WT HC

source_name: hippocampus of aged mouse 1


title: MD O2 WT HC

source_name: hippocampus of aged mouse 2


title: MD O2 WT Colon

source_name: colon of aged mouse 2


title: MD O1 WT Colon

source_name: colon of aged mouse 1


title: MD O3 WT CP

source_name: choroid plexus of aged mouse 3

value: choroid plexus


title: MD O1 WT ILN

source_name: inguinal lymph nodes of aged mouse 1

value: excised from PBS-perfused mouse and snap frozen on dry ice


title: MD O3 WT MLN

source_name: mesenteric lymph nodes of aged mouse 3


title: MD O3 WT CLN

source_name: Cervical lymph nodes of aged mouse 3

value: Cervical lymph nodes


title: MD O1 WT CLN

source_name: Cervical lymph nodes of aged mouse 1


title: MD O1 WT CP

source_name: choroid plexus of aged mouse 1


title: MD O3 WT BM

source_name: bone marrow of aged mouse 3

value: bone marrow

value: bone marrow was flushed with PBS from tibia and femur from PBS-perfused mouse and snap-frozen on dry ice


title: MD O2 WT BM

source_name: bone marrow of aged mouse 2

value: 22 months


title: MD O2 WT CLN

source_name: Cervical lymph nodes of aged mouse 2

value: age and organ


title: MD O2 WT TH

source_name: thymus of aged mouse 2

value: thymus


title: MD O1 WT BM

source_name: bone marrow of aged mouse 1


title: Msx1-2 (f-f) WT  - LCM RNA-Seq - Stroma

city: Cincinnti

first: SK

last: Dey

address: 3333 Burnet Ave

department: Reproductive Sciences

institute: Cincinnati Children's Hospital

description: Laser capture microdissected

data_processing:
Illumina Casava v1.8.2 software was used for basecalling.
Sequenced reads were mapped to the UCSC mouse mm9 genome using tophat v2.0.5.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.0.2 package, following a protocol from "Trapnell C. et al., Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocol, 2012 Mar 1;7(3):562-78.".
Genome_build: mm9
Supplementary_files_format_and_content: text files with RPKM with statistics for identifying differentially expressed genes

source_name: uterus (stroma cells)

extract_protocol:
Laser capture microdissection of indicated cell type onto CapSure HS LCM caps, extracted with Arcturus PicoPure kit following manufacturers instructions
TruSeq Stranded Total RNA Sample Prep kit with Ribo-Zero Deplete treatment

treatment_protocol: Extracted on day 4 of pregnancy after mating with vasectomized male

value: Control (f/f)

tag: tissue

value: uterus

value: Stroma


title: Msx1-2 (d-d) KO  - LCM RNA-Seq - Stroma

description: Laser capture microdissected

value: Knockout (d/d)


title: MD O3 WT Lung

source_name: lung of aged mouse 3


title: Msx1-2 (d-d) KO  - LCM RNA-Seq - Luminal Epithelium

description: Laser capture microdissected

source_name: uterus (luminal epithelial cells)

value: Luminal Epithelium


title: SMah37Z12.Ks

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

data_processing:
Basecalls performed using Illumina RTA software.
Basecalls and quality scores were converted to fastq format.
Individual libraries were demultiplexed.
reads filtered for adaptor sequence and low quality calls
alignment to genome by tophat2
expression estimates by cuffdiff
Genome_build: v5.3.1 (Phytozome v9) available at http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9
Supplementary_files_format_and_content: tab delimited file of expression estimate by FPKM for all genes in all samples

organism: Chlamydomonas reinhardtii

source_name: Zn resupply - 12 hours

growth_protocol: Algae were grown from an inoculum of 1 x 10^5 cells/ml in Tris-acetate-phosphate (TAP) medium containing our revised micronutrient composition (Kropat et al., 2011) at 24°C under continuous light (~90 µmol m-2 s-1) with shaking (180 rpm).  The desired lighting spectra were achieved by mixing 2 cool white fluorescent bulbs at 4100K for each 1 warm white fluorescent bulb at 3000K.

extract_protocol:
A volume of culture containing 5 x 10^7 cells was transferred to a 15 ml Falcon tube and centrifuged at 2500 xg for 2 min at room temperature. The supernatant was immediately decanted and the pellets resuspended in 1 ml freshly made lysis buffer (50 mM Tris-HCl pH 7.5, 200 mM NaCl, 20 mM EDTA, 2% sodium dodecyl sulfate). Samples were centrifuged at 600 xg for 3 min at room temperature to pellet starch. The resulting supernatant was snap-frozen in liquid N2 and stored at -80°C for later processing. Upon thawing at room temperature, 10 ml TRIzol (Life Technologies, Carlsbad, California) was added, and the lysates were thoroughly mixed. Samples were incubated for 5 min at room temperature before being transferred to MaXtract HD (QIAgen, Hilden, Germany) tubes. 2 mL of chloroform was added and mixed again. After a 5 min incubation at room temperature, MaXtract HD tubes were centrifuged at 1500 xg for 5 min at room temperature, and the nucleic acid-containing aqueous phase was collected. To extract RNA, samples were processed using the miRNeasy Mini Kit (QIAgen, Hilden, Germany) according to manufacturer’s instructions. To remove contaminating DNA, samples were digested on-column using the RNase-Free DNase Set (QIAgen, Hilden, Germany) according to manufacturer’s instructions. RNA samples were subjected to an ethanol precipitation according to standard laboratory protocol (300 mM sodium acetate and 2.5 volumes of 100 % ethanol) to remove carry-over contaminants from the QIAgen buffers before being resuspended in 50 µL dH2O.
We used the Illumina TruSeq Stranded mRNA Sample Prep LS kit according to the manufacturer's instructions (Protocol Rev. D from SEP-2012).

treatment_protocol: Zn limitation was induced by inoculating cells from a nutrient-replete culture to a number of 10^5 cells/ml into 100 ml culture medium without supplemented Zn (“first round culture”), and then into medium without supplemented Zn (“second round culture”). ZnCl2 was resupplied at 2.5 µM to these limited cultures where described when they reached a density of 1 x 10^6 cells/ml (“t0h” of zinc resupply).

tag: time point

value: 12h after Zn resupply


title: Msx1-2 (f-f) WT  - LCM RNA-Seq - Luminal Epithelium

description: Laser capture microdissected


title: MD O3 WT ILN

source_name: inguinal lymph nodes of aged mouse 3

value: inguinal lymph nodes


title: SMah37Z3.0Ks

source_name: Zn resupplly - 3.0 hours

value: 3h after Zn resupply


title: SMah37Z4.5Ks

source_name: Zn resupply - 4.5 hours

value: 4.5h after Zn resupply


title: SMah37ZRLtKs

source_name: Zn replete - late

value: Zn replete - late


title: SMah37ZM00Ks

source_name: Zn minus

value: Zn deficient - t0


title: MD O2 WT CP

source_name: choroid plexus of aged mouse 2

value: choroid plexus

value: excised from PBS-perfused mouse and snap frozen on dry ice


title: SMah37Z1.5Ks

source_name: Zn resupply - 1.5 hours

value: 1.5h after Zn resupply


title: SMah37ZRErKs

source_name: Zn replete - early

value: Zn replete - early


title: Ser5P-RNAPII ChIPseq

city: La Jolla, San Diego

first: conchi

last: estaras

state: CA

address: 10010 N Torrey Pines Rd

department: Regulatory Biology

institute: The Salk Institute

data_processing:
Peak calling was performed using Homer software
Genome_build: hg19
Supplementary_files_format_and_content: wig files

source_name: human embryonic stem cells

growth_protocol: hESCs were grown in feeder-free layer conditions in TeSR media.

extract_protocol:
For ChIPseq, DNA was extracted Qiaquick PCR extraction kit (cat 28106, Qiagen). For GROseq, nascent RNA purification was done using Trizol LS (Invitrogene).
For ChIPseq, libraries were done with Illumina reagents. For GROseq, libraries were prepared with NEBnext kit (E7300S)

treatment_protocol: For ChIPseq, non specific treatments were applied. For GROseq, hESCs were transfected with control or Ssu72 specific siRNAs for 48h. Lipofectamine RNAimax from Invitrogene was used for transfection.

tag: state

value: pluripotent

tag: passage

tag: cell line


title: Na12hrR1

city: Ames

first: Steven

middle: B

last: Cannon

state: IA

address: Crop Genome Informatics Laboratory #1017, Iowa State University

institute: United States Department of Agriculture - Agricultural Research Service, Corn Insects and Crop Genetics Research Unit

description: Salt stress 12 hr replicate 1

data_processing:
The reads were aligned with GSNAP (Wu TD and Nacu S, Bioinformatics, 2010) using default settings with a maximum of 4 mis-matches allowed.
The uniquely mapped reads that mapped to a single location in the genome were analyzed for differential gene expression between the control and treatment samples using the R package DESeq v1.7.10 (Anders S and Huber W, Genome Biology, 2010).
Genome_build: Glycine max genome assembly and annotation v1.01 from Phytozome (JGI Glyma1.0 gene calls).
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts for each gene
Supplementary_files_format_and_content: tab-delimited text file includes DESeq normalized counts for each gene

organism: Glycine max

source_name: roots

growth_protocol: The seeds of G. max cv. Williams 82 were germinated on moist germination paper and were allowed to grow until the v1 stage (first trifoliolate stage) in a growth chamber maintained at 77 F and 60% humidity throughout the experiment.

extract_protocol:
Root tissue was harvested, flash frozen in liquid nitrogen, and total RNA was isolated using Qiagen RNeasy® Plant mini kit per the manufacturer’s protocol. The RNA samples were treated with Ambion® TURBO DNA-free™ DNase to get rid of any DNA contamination in the RNA samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The salt treatment was applied by transferring the seedlings into 100 mM NaCl solution. For the dehydration treatment, plants were removed from the germination paper and left in air under water-limiting conditions to impose dehydration stress.

value: Williams 82

tag: developmental stage

value: V1 stage seedlings

value: root


title: Na12hrR2

description: Salt stress 12 hr replicate 2


title: siSsu72 GROseq

description: nascent RNA

data_processing:
Library strategy: GRO-seq
Peak calling was performed using Homer software
Genome_build: hg19
Supplementary_files_format_and_content: wig files


title: Na6hrR3

description: Salt stress 6 hr replicate 3


title: SQR9_root exudates_48 h

city: Nanjing

first: Dongqing

last: Yang

state: Jiangsu

address: Weigang 1#, Xuanwu district

country: China

institute: Nanjing Agricultural University

data_processing:
clean reads obtained from the Illumina sequencing data (at least half of the bases with a quality > 5, not including N)
mapped to the B. amyloliquefaciens SQR9 genome using bowtie2 with paramenters --phred64 -x 9 --very-fast --ff -1
Collected reads from different samples of each gene were transformed into RPM (Reads Per Kilo bases per Million reads) values (Mortazavi, et al., 2008).
Genes exhibiting statistically significant expression changes between the control and treatment conditions were identified using MARS model from the DEGseq program package using the  false discovery rate (FDR) control method
Only genes that met the following filter conditions were regarded as significantly expressed between control and treatment: (i) fold-change>=1.5; (ii) q-value<=0.001
Genome_build: CP006890
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Bacillus amyloliquefaciens

source_name: SQR9_root exudates_48 h

growth_protocol: Incubated at 37°C in 48-well microtiter plates filled with 1/2 MSgg medium, without shaking

extract_protocol:
RNA was extracted by E.Z.N.A. @ Bacterial RNA Kit (OMEGA, bio-tek, USA), mRNA was depleted using a Ribo-ZeroTM rRNA Removal kit (Epicenter, USA), cDNA was synthesised by Superscript II reverse transcriptase (Invitrogen, America).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Addition of the concentrated maize root exudates into the wells, control wells were treated with water

tag: incubation time

tag: treatment

value: addition of maize root exudates


title: Na12hrR3

description: Salt stress 12 hr replicate 3

tag: genotype


title: Na1hrR3

description: Salt stress 1 hr replicate 3


title: SQR9_control_24 h

source_name: SQR9_control_24 h

value: control


title: SQR9_control_48 h

source_name: SQR9_control_48 h


title: Na6hrR2

description: Salt stress 6 hr replicate 2


title: Ssu72 ChIPseq

description:
antibodies used for ChIPseq:
Ssu72 Genetex catalog number: GTX116436
Ser5P-RNAPII: Millipore catalog number:  05-623


title: Na6hrR1

description: Salt stress 6 hr replicate 1


title: Na1hrR1

description: Salt stress 1 hr replicate 1


title: Na1hrR2

description: Salt stress 1 hr replicate 2


title: SMah37Z24.Ks

source_name: Zn resupply - 24 hours

value: 24h after Zn resupply


title: De12hrR3

description: Dehydration stress 12 hr replicate 3


title: siCtrl GROseq

description: nascent RNA


title: De12hrR2

description: Dehydration stress 12 hr replicate 2


title: De6hrR2

description: Dehydration stress 6 hr replicate 2


title: SQR9_root exudates_24 h

source_name: SQR9_root exudates_24 h


title: De6hrR3

description: Dehydration stress 6 hr replicate 3


title: De6hrR1

description: Dehydration stress 6 hr replicate 1


title: De12hrR1

description: Dehydration stress 12 hr replicate 1


title: De1hrR1

description: Dehydration stress 1 hr replicate 1


title: Co0hrR3

description: Control 0 hr replicate 3


title: De1hrR2

description: Dehydration stress 1 hr replicate 2


title: De1hrR3

description: Dehydration stress 1 hr replicate 3


title: Co0hrR2

description: Control 0 hr replicate 2


title: Co0hrR1

description: Control 0 hr replicate 1


title: HBM_11_uninfected

city: Palo Alto

first: Dedeepya

last: Vaka

address: 265 Campus Drive

department: Pediatrics

institute: Stanford

data_processing:
DNA Nexus
Sequenced reads were mapped to hg19 whole genome using DNA Nexus.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using ngsutils
Genome_build: hg19
Supplementary_files_format_and_content: FPKM tracking file with FPKM for each sample

source_name: primary bone marrow derived mesenchymal progenitor cells

growth_protocol: Cells were grown in aMEM supplemented with 20% FBS.

extract_protocol:
TriZol RNA extraction. PolyA selected, linker ligated and size excluded cDNA was used.
3seq

treatment_protocol: Cells were treated with 1ug/ml Doxycycline for 13 days prior to RNA extraction.

value: 16 years old


title: HBM_10_EWS-Fli

value: primary bone marrow derived mesenchymal progenitor cells

value: 20 years old


title: HBM_12_uninfected

value: 13 years old


title: HBM_12_EWS-Fli


title: Mut+ [Mut_P_16]

city: Paris cedex 15

first: Christian

last: MUCHARDT

address: 25 rue du Dr-Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur Paris

description:
RNA-SEQ_MUT1_Plus_vs_MUT1_Minus.xlsx
Mut_P_16

data_processing:
RNA-Seq data analysis was performed by GenoSplice (http://www.genosplice.com).
First, reads were aligned onto the mouse genome (mm9) using STAR v.2.3.0, with an exon-exon junction database built using annotations from version 2013_2 of FAST-DB (see http://www.easana.com).
For each gene present in FAST DB v2013_2, reads aligning on constitutive regions (that are not prone to alternative splicing) were counted.
Based on these read counts, normalization and differential gene expression were performed using DESeq (v1.12.0 on R v3.0.0).
EASANA was used for visualization of results
Genome_build: mm9

source_name: HP1g null + pREV-HP1g S83A

extract_protocol: Total RNA was depleted from ribosomal RNA then sequenced by Next Generation sequencing with a 50+bp standard.

treatment_protocol: MEF-derived cells either HP1g null or re-complemented with either HP1g WT or HP1gS83A were either not stimulated or exposed to PMA for 1h.

value: mixed 129/Sv x C57BL/6 background

tag: cell type

value: Derived from HP1g null MEFs

tag: stimulation

value: 60 min.  with PMA


title: Mut+ [Mut_P_18]

description:
RNA-SEQ_MUT1_Plus_vs_MUT1_Minus.xlsx
Mut_P_18

tag: strain


title: HP1- [HP1_M_9]

description:
RNA-SEQ_HP1_Plus_vs_HP1_Minus.xlsx
HP1_M_9

source_name: HP1g null + pREV-HP1g

value: No PMA


title: HP1- [HP1_M_8]

description:
RNA-SEQ_HP1_Plus_vs_HP1_Minus.xlsx
HP1_M_8


title: HBM_11_EWS-Fli


title: Mut- [Mut_M_14]

description:
RNA-SEQ_MUT1_Plus_vs_MUT1_Minus.xlsx
Mut_M_14


title: Mut- [Mut_M_13]

description:
RNA-SEQ_MUT1_Plus_vs_MUT1_Minus.xlsx
Mut_M_13


title: HP1+ [HP1_P_11]

description:
RNA-SEQ_HP1_Plus_vs_HP1_Minus.xlsx
HP1_P_11


title: HP1+ [HP1_P_10]

description:
RNA-SEQ_HP1_Plus_vs_HP1_Minus.xlsx
HP1_P_10


title: HP1+ [HP1_P_12]

description:
RNA-SEQ_HP1_Plus_vs_HP1_Minus.xlsx
HP1_P_12


title: Mut- [Mut_M_15]

description:
RNA-SEQ_MUT1_Plus_vs_MUT1_Minus.xlsx
Mut_M_15


title: CTL+ [Rev_P_6]

description:
RNA-SEQ_CTLPlus_vs_CTLMinus.xlsx
Rev_P_6

source_name: HP1g null + pREV


title: CTL+ [Rev_P_5]

description:
RNA-SEQ_CTLPlus_vs_CTLMinus.xlsx
Rev_P_5


title: CTL+ [Rev_P_4]

description:
RNA-SEQ_CTLPlus_vs_CTLMinus.xlsx
Rev_P_4


title: CTL- [Rev_M_1]

description:
RNA-SEQ_CTLPlus_vs_CTLMinus.xlsx
Rev_M_1


title: CTL- [Rev_M_2]

description:
RNA-SEQ_CTLPlus_vs_CTLMinus.xlsx
Rev_M_2


title: HBM_10_uninfected


title: Mut+ [Mut_P_17]

description:
RNA-SEQ_MUT1_Plus_vs_MUT1_Minus.xlsx
Mut_P_17


title: BMDM_4

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description:
Untreated macrophage
B8

data_processing:
Image analysis and base calling was performed using Illumina’s real time analysis (RTA) software version 1.13.48.
Reads were filtered to remove those with low base call quality using Illumina’s default chastity criteria. The results were then demultiplexed and converted to fastq format files by CASAVA version 1.8.2.
100nt paired-end reads from 8 samples (4 IL4 stimulated, 4 non-treated) were then mapped to mm9 reference genome using Tophat software version 2.0.9 (Trapnell et al., 2012), with default options, using mm9 UCSC reference genes GTF (Karolchik et al., 2003)
An ab initio transcript reconstruction was performed using Cufflinks, version 2.1.1 with default parameters (Trapnell et al., 2012)
The resulting GTFs were merged using Cuffmerge, version 2.1.1 (Roberts et al., 2011), using option –g with mm9 UCSC GTF as reference, allowing to distinguish between known and novel transcripts.
Count data by gene was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/, version 0.5.4p3)
Genome_build: mm9
Supplementary_files_format_and_content: Count data by gene (gene_counts.txt) and transcript (merged_isoforms_FPKM.txt), exon coordinates (merged.gtf), tab-delimited format

source_name: Bone marrow-derived macrophage

extract_protocol:
Untreated and IL-4-treated BMDMs were lysed in Qiazol and total RNA extracted. The average yield was 20-50 µg of total RNA for each sample. RNA was DNaseI treated (New England Biolabs) and concentrated using RNAclean XP (Beckman Coulter). RNA was then depleted of rRNA using the Ribo-Zero Magnetic Gold kit (Epicentre Biotechnologies) followed by concentration using RNA Clean & Concentrator -5 columns (Zymo Research).
Illumina sequencing libraries were prepared according to the TruSeq RNA Sample Preparation Guide (Revision A), starting at the RNA fragmentation step. RNA fragmentation with “Elute, Prime, Fragment Mix” was performed for 4 minutes at 94ºC

value: Bone marrow-derived macrophage


title: IL4-treated BMDM_1

description:
IL4-treated macrophage
BL5


title: BMDM_2

description:
Untreated macrophage
B6


title: BMDM_3

description:
Untreated macrophage
B7


title: shGFP-2

data_processing:
STAR 2.3.0 cufflinks 2.1.1
Sequenced reads were mapped to hg19 whole genome using STAR aligner.Genome generation is from iGenomes
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks 2.1.1 software
Genome_build: hg19
Supplementary_files_format_and_content: FPKM tracking file with FPKM for each sample

source_name: A673 Ewing's sarcoma cells

extract_protocol:
Trizol
RNA-Seq

value: A673 Ewing's sarcoma cells

value: shGFP

value: 15 year old


title: HP1- [HP1_M_7]

description:
RNA-SEQ_HP1_Plus_vs_HP1_Minus.xlsx
HP1_M_7


title: shEWS-FLI3

value: shEWS-FLI


title: shEWS-FLI4


title: shlnc277-1


title: shEWS-FLI1


title: shGFP-3


title: shGFP-4


title: IL4-treated BMDM_2

description:
IL4-treated macrophage
BL6


title: shlnc277-2


title: shlnc277-4


title: IL4-treated BMDM_4

description:
IL4-treated macrophage
BL8


title: CTL- [Rev_M_3]

description:
RNA-SEQ_CTLPlus_vs_CTLMinus.xlsx
Rev_M_3


title: IL4-treated BMDM_3

description:
IL4-treated macrophage
BL7


title: A673 shhnRNPK-2

source_name: A673 Ewing cells expressing an shRNA targeting hnRNPK

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS.

extract_protocol:
5 days post infection, RNA was extracted using TRIzol.
NuGen Encore Complete kit

treatment_protocol: Cells were infected with lenti-virus containing shRNA either for GFP or hnRNPK and selected with puromycin.

value: Ewing's sarcoma


title: shlnc277-6


title: shlnc277-7


title: shlnc277-5


title: shlnc277-3


title: A673 shGFP-2

source_name: A673 Ewing cells expressing control shRNA


title: A673 shhnRNPK-1


title: A673 shGFP-1


title: BRD4 ChIP

first: Hufeng

last: Zhou

address: 181 Longwood Ave,

department: Department of Microbiology and Molecular Genetics

institute: Harvard Medical School

description: ChIP-seq

data_processing:
genome build: hg19
Supplementary_files_format_and_content: wig file

source_name: Lymphoblast Cell Line

growth_protocol: Cells were grown in RPMI media supplemented witth 10% FetalPlex, 2 mM glutamine, penicillin and streptomycin.

extract_protocol:
Cells were fixed with 1% formaldehyde. After wash with PBS, the cells were lyzed in ChIP lysis buffer. Lysates were sonicated and cleared by centrifugation. After pre-clear with protein A beads, antibody (Bethyl Labs A301-985A lot A301-985A-1) was incubated with the lysate overnight at 4°C. Protein A was used to capture the protein DNA complex. The eluted protein DNA complexes were reverse crosslinked and DNA was purified by a Qiagen PCR purification column.
Libraries were prepared using ChIP-Seq Library Prep Reagent Set for Illumina from NEB. Briefly, DNA was end-repaired. 3' A base was added and ligated to adaptors. After PCR amplification, DNA was purified and analyzed with Illumina HiSeq.

value: EBV-infected B Lymphocytes

tag: chip antibody

value: Bethyl Labs A301-985A lot A301-985A-1


title: shEWS-FLI2


title: shGFP-1


title: targetedDNaseHiC-lincRNA-H1-rep2

city: Riverside

first: Wenxiu

last: Ma

address: 900 University Ave

institute: University of California Riverside

description: library strategy: targeted DNase Hi-C

data_processing:
First, we performed an exhaustive search and cleaning of the Illumina primer and adaptor sequences in the 150 bp full-length reads and extracted the remaining read fragments of various lengths from 25-80 bp.
We then mapped each end of these cleaned paired-end reads separately to the human genome (GRCh37/hg19 assembly, obtained from the UCSC Genome Browser) using BWA/v0.5.9. We only retained the reads that mapped uniquely, allowing at most 3 mismatches and requiring mapping quality MAPQ >= 30.
To eliminate the bias due to the PCR duplication step, we removed redundant paired-end reads. We define two reads as redundant if both ends of the reads are mapped to identical locations in the genome.
For targeted DNase Hi-C data we performed an additional filtering step to keep only the paired-end reads for which at least one end mapped to or within 150 bp from one of the captured target regions.
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: txt files, containing uniquely mapped and non-redundent read pairs. The files are tab-delimited. The columns are #1 read identifier, #2 strand of the 1st end, #3 mapped chr of the 1st end, #4 mapped coordinate of the 1st end, #5 sequence of 1st end, #6 strand of the 2nd end, #7 mapped chr of the 2nd end, #8 mapped coordinate of the 2nd end, #9 sequence of 2nd end.

source_name: Targeted DNase Hi-C experiment on H1 cells, lincRNA promoter library, biological replicate 2

growth_protocol: Two cell lines, namely, human embryonic stem cell H1 and human erythromyeloblastoid leukemia cell K562, were grown under standard culture conditions and harvested at log phase.

extract_protocol:
DNase Hi-C or targeted DNase Hi-C:  Cells are cross-linked with formaldehyde; chromatin is then randomly fragmented by DNase I. The resulting chromatin fragments are end-repaired and dA-tailed, then marked with a biotinylated internal adaptor; and proximity ligation is carried out by burying the biotin-labeled fragments inside solidified agarose gel to favor ligation events between the cross-linked DNA fragments. The resulting DNA sample contains ligation products consisting of chimeric DNA fragments that were originally in close spatial proximity in the nucleus, marked with biotin at the junction. A whole-genome chromatin interaction library is created by shearing the DNA and selecting the biotin-containing fragments with streptavidin magnetic beads. After linear library amplification, a DNase Hi-C library is generated and sequenced to identify whole-genome chromatin contacts. For targeted DNase Hi-C, the chromatin contacts associated with a specific group of loci of interest are then enriched by a bait library targeting the loci via in-solution hybridization-based DNA capture. Finally, quantitation of the enriched chromatin interactions is achieved through massively parallel deep sequencing.
DNase Hi-C or targeted DNase Hi-C

value: H1 ES cells

tag: library

value: lincRNA-P

tag: replicate


title: targetedDNaseHiC-lincRNA-H1-rep1

description: library strategy: targeted DNase Hi-C

source_name: Targeted DNase Hi-C experiment on H1 cells, lincRNA promoter library, biological replicate 1


title: targetedDNaseHiC-pe-H1-rep1

description: library strategy: targeted DNase Hi-C

source_name: Targeted DNase Hi-C experiment on H1 cells, 220kb P-E library, biological replicate 1

value: P-E


title: DNaseHiC-WG-H1

description: library strategy: DNase Hi-C

source_name: DNase Hi-C experiment on H1 cells

value: whole-genome


title: targetedDNaseHiC-pe-K562-rep1

description: library strategy: targeted DNase Hi-C

source_name: Targeted DNase Hi-C experiment on K562 cells, 220kb P-E library, biological replicate 1

value: K562 cells


title: HIF2a_Normoxy_IL10 1

status: Public on Oct 31 2014

city: Regensburg

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

description: Chromatin IP against HIF2a

data_processing:
Sequence tags were mapped to the human reference sequence (GRCh27/hg19) using Bowtie1 and only uniquely mapped tags were used for downstream analyses. Parameters:  -q --best -m 1
Genome_build: hg19
Supplementary_files_format_and_content: alignment files produced with bowtie

source_name: macrophage

growth_protocol: monocytes were isolated from human buffy coats and differentiated into macrophages with medium containing 5% human serum for 7 days and achieved approximately 80% concluence

extract_protocol:
Chromatin Immunoprecipitation
DNA from chromatin immunoprecipitation was adapter-ligated and PCR amplified using NEBNext DNA Sample Prep Reagent Set1 (NEB E6000L) and Adapter Oligo Mix and PCR primers from Illumina following the manufacturer’s protocol. ChIP fragments were sequenced for 36 cycles on Illumina Genome Analyzers

treatment_protocol: 16h with IL-10 [20 ng/ml] ± 4h 1% O2

tag: donor

tag: stress

value: Normoxy 20% O2


title: HIF2a_Normoxy_IL10 2

description: Chromatin IP against HIF2a


title: HIF1a_Hypoxy_IL10 1

description: Chromatin IP against HIF1a

value: Hypoxy 1% O2 4 hours


title: HIF1a_Hypoxy_IL10 2

description: Chromatin IP against HIF1a


title: HIF1a_Normoxy_IL10 2

description: Chromatin IP against HIF1a


title: HIF2a_Normoxy 1

description: Chromatin IP against HIF2a


title: HIF2a_Hypoxy_IL10 1

description: Chromatin IP against HIF2a


title: HIF2a_Normoxy 2

description: Chromatin IP against HIF2a


title: HIF1a_Normoxy_IL10 1

description: Chromatin IP against HIF1a


title: HIF2a_Hypoxy 1

description: Chromatin IP against HIF2a


title: MiRNAs in tobacco roots after topping

city: zhengzhou

first: hongxiang

last: guo

address: 95 wenhua road

institute: henan agricultural university

data_processing: Only small RNA reads that passed the Illumina pipeline quality control and contained clear adaptor sequences were considered good reads for further processing. After adaptor sequence was trimmed, clean small RNA reads of 18nt or more were combined into unique sequences. Reads that match known plant repeats, rRNAs, tRNAs, snRNAs, and snoRNAs were removed. The unique small RNA reads were used to do a Blastn search against the four genomic sequence resources：317, 49 tobacco ESTs (www.ncbi.nlm.nih.gov)，300,158 tobacco genomic sequences (ftp.solgenomics.net/tobacco_genome), 44,561 tobacco shotgun sequences (ftp.tigr.org/pub/data/plantta/Nicotiana_tabacum), and 1,420,595 tobacco Genome Survey Sequences (GSS，www.ncbi.nlm.nih.gov). Perfect match was required. Results of these BLASTn searches were then subjected to secondary structure analysis using UNAFOLD version 3.8. We then examined the secondary structure, and a result was considered as a genuine miRNA candidate if it met the miRNA criteria [24]. To identify the conserved miRNAs in tobacco, these miRNA candidates were used to do a Blastn search against the miRNA database (miRBase17.0, http://www.mirbase.org), and only the perfectly matched sequences (number of mismatch<3) were considered to be conserved miRNAs. Except for these conserved miRNAs, other miRNA candidates were considered to be new miRNAs. The sequence reads of each miRNA in two libraries were normalized, and then the fold change of miRNAs between two libraries was obtained.

organism: Nicotiana tabacum

source_name: tobacco roots after topping

growth_protocol: Tobacco plants were grown in the fields.

extract_protocol: Total RNA was isolated from roots tissue using Trizol agent (TaKaRa, Dalian, China), according to the manufacturer’s instructions. MiRNA cloning was performed as described previously by Sunkar and Zhu [23]. Briefly, 0.5 M NaCl and 10% PEG8000 were used to precipitate and enrich RNAs with low molecular weight. Next, a 15% polyacrylamide denaturing gel was employed to separate the low-molecular weight RNA. During gel electrophoresis, about 100 μg of total RNA was applied to the gel and two labeled RNA oligonucleotides, approximately 18 and 26 nt in length, were used as size standards. After gel electrophoresis, small RNAs with 18-26 nt were excised from the gel and eluted with 0.4 M NaCl overnight at 4°C. The RNA was dephosphorylated using alkaline phosphatase (New England Biolabs, Beijing China) and recovered by ethanol precipitation. The isolated small RNAs were then sequentially ligated to 5’- and 3’-chimeric oligonucleotide adapters, reversely transcribed, and amplified by PCR. Finally, Solexa sequencing technology was employed to sequence the small RNAs from tobacco roots samples (Beijing Genomics Institute, Shenzhen, Guangdong, China).

treatment_protocol: Topping treatment

tag: cultivar

tag: tissue

value: roots


title: BMDM_1

description:
Untreated macrophage
B5


title: HIF2a_Hypoxy_IL10 2

description: Chromatin IP against HIF2a


title: HIF2a_Hypoxy 2

description: Chromatin IP against HIF2a


title: targetedDNaseHiC-lincRNA-K562-rep2

description: library strategy: targeted DNase Hi-C

source_name: Targeted DNase Hi-C experiment on K562 cells, lincRNA promoter library, biological replicate 2


title: targetedDNaseHiC-lincRNA-K562-rep1

description: library strategy: targeted DNase Hi-C

source_name: Targeted DNase Hi-C experiment on K562 cells, lincRNA promoter library, biological replicate 1


title: HIF1a_Hypoxy 1

description: Chromatin IP against HIF1a


title: HIF1a_Hypoxy 2

description: Chromatin IP against HIF1a


title: HIF1a_Normoxy 2

description: Chromatin IP against HIF1a


title: HIF1a_Normoxy 1

description: Chromatin IP against HIF1a


title: DNaseHiC-WG-K562

description: library strategy: DNase Hi-C

source_name: DNase Hi-C experiment on K562 cells


title: WT rep2

city: Davis

first: Venkatesan

last: Sundaresan

address: One Shields Ave

department: Plant Biology

institute: University of California Davis

description: Transcriptional profiling

data_processing:
Illumina Casava1.7 software used for basecalling.
For the RNAseq experiment, the resulting non-partitioned barcoded Illumina fastq file was modified using a custom perl script to classify reads to one of four barcodes (ACCC, CGTA, GAGT, TTAG) demanding an exact match.
This fastq file was then mapped to the rice genome RGAP version 7.0 using tophat version 2.0.5 with default parameters except that a segment size of 18 was used.  The resulting accepted_hit.bam file was processed in conjunction with the RGAP 7.0 gene models file (all.gff3) using a custom perl script that only counted reads that mapped within exons of the defined gene models.
The resulting genome-unique reads count table for the first isoform of 'LOC_' genes was then analyzed for differentially expressed genes using the R package DESeq version 1.10.1 with use of relaxed gene dispersion estimation parameters (fitType = 'local' and sharingMode = 'fit-only'), and tested assuming a negative binomial distribution using the nbinomTest function.   A 10% false discovery rate (FDR) was used as a cutoff to define differentially expressed genes.
Genome_build: RGAP rice vs 7.0
Supplementary_files_format_and_content: The comma separated values (csv) file contains count data for reads mapping to exons for alternative transcript isoforms for Oryza sativa rice gene models for LOC_ loci from RGAP version 7.0

organism: Oryza sativa

source_name: WT

growth_protocol: All rice plants were grown in greenhouse conditions of 30oC daytime and 25oC nighttime temperatures. Light regimes were dictated by natural light conditions.

extract_protocol:
Inflorescence 7 stage, according to (Itoh et al., 2005) (0.3-1.5 cm) was dissected from wild type Dongjin and placed in liquid Nitrogen. Frozen tissue was homogenized using the Mini Beadbeater (BioSpec Products, Inc.). RNA was extracted with Trizol Reagent (Invitrogen) using the manufacturers recommended protocol. RNA was further purified with the QIAGEN RNAeasy Plant Mini kit (QIAGEN) following the manufacturers protocol for RNA cleanup including the optional DNase digestion. RNA was quantified on the ND 1000 Nanodrop Spectrophotometer (Thermo Fisher Scientific, Inc.).
cDNA was synthesized using the Ovation RNA-seq System (NuGEN) with a starting input of 10 ng of RNA. RNAseq libraries were created with the Encore NGS Multi Library Prep I kit (NuGEN).  Forty cycles of single-read Illumina high throughput sequencing was performed on an Illumina Genome Analyzer IIx

value: Dongjin

value: panicle

tag: age

value: WT


title: emf2b rep1

description: Transcriptional profiling


title: BAT_DMSO_day_7_TTB30

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

institute: F. Hoffmann-La Roche

description: BAT_DMSO_day 7

data_processing:
Base-calling was performed with the latest version (v1.8.2) of CASAVA
RNA-seq reads were first aligned to human transcriptome using bowtie2 (v2.1.0).
Unmapped reads were then aligned to human genome using bowtie2 (v2.1.0)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file with gene counts per sample

source_name: Human pluripotent stem-cell derived brown adipose cells

growth_protocol: MPCs were seeded at 75% confluency in 15 cm dishes, incubated overnight with lentiviral particles at an MOI of 50 for each virus and maintained in growth medium without virus for 24 hours.

extract_protocol:
Total RNA from adipocyte lysate was extracted and purified using the Rneasy mini kit (Qiagen) according to the manufacturer’s instructions.
For all samples high quality RNA was obtained (RIN between 8.1 and 9.8). RNA Sequencing libraries were prepared from 1μg of total RNA using the Illumina TruSeq RNA Sample preparation Kit v2 (Illumina) following the manufacturer’s instructions

treatment_protocol: PSC-WA received either DMSO, JAK3-inhibitor CP-690550 (2 μM) or SYK-inhibitor R406 (1 μM). PSC-BA and MPC received DMSO only.

value: BAT

value: DMSO

tag: time

value: 7 days

tag: librarybatch

value: B

tag: lane

tag: multiplex


title: WT rep1

description: Transcriptional profiling


title: BAT_DMSO_day_7_TTB29

description: BAT_DMSO_day 7

tag: treatment


title: emf2b rep2

description: Transcriptional profiling

tag: genotype


title: RAD21 WT ChIP

city: East Melbourne

first: Huiling

last: Xu

state: Victoria

address: St Andrew Place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
RNA-seq reads were mapped using bowtie version 0.12.8 & TopHat v1.4.1. Transcripts assembled using Cufflink. Reads count was performed with htseq-count (version 1.0.0)
ChIP-seq reads were mapped with BWA for Illumina (version 1.2.3).
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include limma-voom normalised log2 values for each Sample;
Supplementary_files_format_and_content: For ChIP-seq, peak calling was performed using MACS V3.1 with p value cutoff 1e-4 for peak detection and MFOLD 10 for enrichment ratio.

source_name: WT small intestinal crypts

extract_protocol:
Small intestinal crypts were isolated in PBS containing 3 mM EDTA, 0.5 mM DTT and protease inhibitor (Roche). Adenomas were dissected from the small intestine. RNA was extracted using RNaEasy kit (Qiagene).For ChIP-seq, crypts and adenoma in 1% formaldehyde for 10 Min at room temperature. Chromatin was sheared using the Covaris S2 system following the manufacturer’s instructions. ChIP was performed using a ChIP validated rabbit anti-Rad21 antibody (Ab992, Abcam) and Magna-ChIP A kit (Millipore).
Library preparations were performed using the TruSeq RNA Sample Preparation protocol (Illumina, San Diego, CA) and correct size established using the DNA 1000 kit (Agilent technologies, Santa Clara, CA). Libraries were quantified with qPCR, normalised and pooled to 2nM before sequencing with paired-end 50 bp reads using standard protocols on the HiSeq2000 (Illumina, San Diego, CA).

tag: strain background

tag: genotype/variation

value: Wild type

value: Small intestinal crypts

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: MPC_DMSO_day_7_TTB26

description: MPC_DMSO_day 7

source_name: Human pluripotent stem-cell derived mesenchymal progenitor cells

tag: cell type

value: MPC


title: WAT_DMSO_day_7_TTB18

description: WAT_DMSO_day 7

source_name: Human pluripotent stem-cell derived white adipose cells

value: WAT

tag: replicate


title: WAT_DMSO_day_7_TTB17

description: WAT_DMSO_day 7


title: WAT_SYKi_day_7_TTB24

description: WAT_SYKi_day 7

value: SYKi


title: WAT_SYKi_day_7_TTB23

description: WAT_SYKi_day 7


title: MPC_DMSO_day_7_TTB25

description: MPC_DMSO_day 7


title: WAT_JAK3i_day_7_TTB19

description: WAT_JAK3i_day 7


title: MPC_DMSO_day_7_TTB27

description: MPC_DMSO_day 7


title: BAT_DMSO_day_7_TTB28

description: BAT_DMSO_day 7


title: WAT_SYKi_day_7_TTB22

description: WAT_SYKi_day 7


title: WAT_JAK3i_day_7_TTB12

description: WAT_JAK3i_day 7


title: MiRNAs in tobacco roots before topping

source_name: tobacco roots before topping


title: WAT_DMSO_day_7_TTB16

description: WAT_DMSO_day 7


title: WAT_JAK3i_day_7_TTB20

description: WAT_JAK3i_day 7


title: BAT_DMSO_24_hours_TTB13

description: BAT_DMSO_24 hours

value: 24 hours

value: A


title: MPC_DMSO_24_hours_TTB10

description: MPC_DMSO_24 hours


title: BAT_DMSO_24_hours_TTB14

description: BAT_DMSO_24 hours


title: MPC_DMSO_24_hours_TTB11

description: MPC_DMSO_24 hours


title: BAT_DMSO_24_hours_TTB15

description: BAT_DMSO_24 hours


title: WAT_SYKi_24_hours_TTB09

description: WAT_SYKi_24 hours


title: MPC_DMSO_24_hours_TTB12

description: MPC_DMSO_24 hours


title: MD Y3 WT ILN

description: processed data in Series supplementary file Y_vs_O_tissues_o.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
alignment: tophat with deafult parameters
Expression table done using ESAT http://garberlab.umassmed.edu/software/esat/
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Inguinal lymph nodes of young mouse 3

tag: strain

tag: selection marker

value: age and organ

tag: organ

value: Inguinal lymph nodes

value: 3 months

tag: tissue isolation

value: excised from PBS-perfused mouse and snap frozen on dry ice


title: WAT_SYKi_24_hours_TTB08

description: WAT_SYKi_24 hours


title: WAT_JAK3i_24_hours_TTB06

description: WAT_JAK3i_24 hours


title: WAT_JAK3i_24_hours_TTB05

description: WAT_JAK3i_24 hours


title: WAT_JAK3i_24_hours_TTB04

description: WAT_JAK3i_24 hours


title: WAT_DMSO_24_hours_TTB03

description: WAT_DMSO_24 hours


title: WAT_SYKi_24_hours_TTB07

description: WAT_SYKi_24 hours


title: WAT_DMSO_24_hours_TTB02

description: WAT_DMSO_24 hours


title: WAT_DMSO_24_hours_TTB01

description: WAT_DMSO_24 hours


title: input_EV

first: Julien

last: Delafontaine

state: Vaud

address: Route Cantonale

department: SV

institute: EPFL

description: Sample 1

data_processing:
Fusion of overlapping pairs of paired-end reads (negative insert size) with FLASH
Mapping with Bowtie 1 v.0.12.7 on Wistar subtelomeres assembly. Options: "-Sam 20 --best --strata --chunkmbs 512" (cf. HTSstation)
Creation of read density profiles representing (~#reads/NH flag) at each genomic position (cf. HTSstation)
Read counting / RPKM calculation: 10^9 * (#reads/NH flag) / transcript_size / sample_lib_size. transcript_size is the TERRA size (5-10Kb) or the region spanned by the exons of a gene.
Genome_build: Wistar subtelomeres assembly v4.3.12, January 2012 (http://www.wistar.org/lab/harold-c-riethman-phd/page/subtelomere-assemblies - "htel_1-500K_1_10_12_v4_3_12fasta.TXT")
Supplementary_files_format_and_content: Read densities in bedGraph format.
Supplementary_files_format_and_content: all_rpkm_normalized.txt linked as supplementary file on Series record.

source_name: HeLa cells, without TERRA enrichment by IP

growth_protocol: HeLa cells were transfected using Lipofectamine 2000 according to the manufacturer's protocol (Invitrogen). Puromycin (2 μg/ml) (InvivoGen) or blasticidin (10 μg/ml) (InvivoGen) was added to the medium 24 h after transfection of pSuper-Puro and/or pSuper-Blast constructs. Puromycin and blasticidin selection was maintained for 4 days.

extract_protocol:
Affinity purification of 5’ capped RNAs was performed by incubating nuclear RNA with GST-eIF4E. Nuclear RNA pulled down with GST-eIF4E was then incubated with 125 pmol of biotinylated oligonucleotide (CCCTAA)3 [5'-biotin-TAATACGA CCCTAA CCCTAA CCCTAA-3'. TAATACGA is part of T7 promoter sequence with no similarity in human genome (confirmed by BLAST analysis) and serves as spacer. The oligo is complementary to TERRA transcripts and was used for TERRA enrichment.] in 5 mM Tris-HCl pH7.5, 0.5 mM EDTA and subsequently heated to 75°C for 5 min to denature the RNA secondary structures. NaCl was added to a final concentration of 1M and the sample was cooled down to 50°C over a period of 30 min. Then, 25ml of Dynabeads (10mg/ml) (Invitrogen) were added and the mixture was incubated at 50°C for 3 hours. After washing the beads, the RNA was eluted by adding 100 ml of 10 mM Tris-HCl pH8 and heating to 80°C for 3 min.
Libraries were prepared starting from 100 ng of RNA using the PE-102-1002-Paired-end kit from Illumina (Illumina, San Diego, CA, US) according to manufacturer recommendations. Ligation products of around 250 bp were gel purified before PCR amplification (15 cycles). 100 ng of libraries were then normalized according to the Illumina DSN protocol using the Duplex-specific nuclease from Evrogen (JSC, Moscow, Russia). 12 PCR cycles were performed using PCR PE 1.0 and 2.0 primers to enrich DNA fragments. DSN libraries were loaded on a HiSeq 2000 (Illumina) at 6 pM and paired-end sequenced using the 100 bp protocol.

tag: cell line

value: HeLa

tag: affinity purification reagent

value: control

value: wild type


title: IP_T

description: Sample 4

source_name: HeLa cells, with TERRA enrichment by IP

value: Streptavidin-coupled Dynabeads (Invitrogen, catalog# 65001)

value: TRF-2 KO


title: P8 Dmrt6 Null Testis Replicate 1

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
Null_CGATGT
processed data file: dmrt6_log2_cpm_rna_seq.csv

data_processing:
Mapped RNA-Seq samples to mm9 with STAR_2.3.0e
Mapped Chip-Seq samples to mm9 with Bowtie2
Duplicates were removed from both experiments with Picard.
ChIP Peaks were Identified with MACS
macs14 -t DM6_chip_dedup.bam -c DM6_input_dedup.bam -f BAM -s 25  -g 1.87e9 -p 1e-05 --slocal 100 --llocal 1000 -n DM6_dedup_macs14_pe05
Genome_build: mm9
Supplementary_files_format_and_content: The RNA-Seq data is summarized as a table of normalized, log2 counts per million (cpm) values using the default paramters in EdgeR.  The bed file is a list of peaks with scores identified by MACS1.4.

source_name: P8 Dmrt6 Null Testis_RNA-seq

extract_protocol:
Testes were harvested in Trizol for RNA-Seq, and fixed with formaldehyde for ChIP-Seq
Rabbit polyclonal antibodies to DMRT6 were raised against a purified DMRT6 fusion protein containing glutathione-S-transferase (GST) fused to the C-terminal 148 amino acids of DMRT6. Antibodies to GST were removed by GST-affigel 10 chromatography and the antiserum was then purified by GST-DMRT6-affigel 10 chromatography
RNA libraries were made using Illumina TruSeq Protocol.  The ChIP libraries were made from the input and the material immuniprecipitated with the Dmrt6 antibody described in this paper.   Chromatin fragments were blunted with Lucigen DNA terminator enyme mix (Lucigen# 40035).  Blunted fragments were adenylated with Exo- Klenow (NEB #MO2125).  Illumina adapters (Illumina #100521) were diluted 1:50 and ligated to adenylated fragments with T4 ligase (NEB #NEB M0202T).  Products were amplified with 18 rounds of PCR using Phusion Polymerase (NEB M0530s) using barcoded oligonucleotides.  DNA fragments between 150 and 250 were purified by agarose gel electrophoresis.

value: Dmrt6 Null

tag: developemental stage

tag: tissue

value: testis


title: IP_EV

description: Sample 3


title: P8 Wildtype Testis Replicate 3

description:
WT_TGACCA
processed data file: dmrt6_log2_cpm_rna_seq.csv

source_name: P8 Wildtype Testis_RNA-seq


title: P8 Wildtype Testis Replicate 1

description:
WT_ATCACG
processed data file: dmrt6_log2_cpm_rna_seq.csv


title: Adenoma Input DNA

source_name: Apc Min small intestinal adenoma

value: Apc min/+

value: small intestinal adenoma


title: DSA-3

source_name: Apc Min Rad21+/- double mutant small intestinal adenomas

value: Apc min/+ Rad21+/-


title: P8 Dmrt6 Null Testis Replicate 2

description:
Null_ACAGTG
processed data file: dmrt6_log2_cpm_rna_seq.csv


title: input_T

description: Sample 2


title: P8 Wildtype Testis Replicate 2

description:
WT_TTAGGC
processed data file: dmrt6_log2_cpm_rna_seq.csv


title: Exp 4 Wk 0 CD34+ MIG+

city: Sydney

first: Jason

last: Wong

state: NSW

address: Level 2, Lowy Cancer Research Centre, University of New South Wales

institute: UNIVERSITY OF NEW SOUTH WALES

data_processing:
Base-calling: Illumina Real Time Analysis, scoring metric v1.5
Raw reads were prefiltered to remove all reads that have 3 or more bases with a quality score of less than Q13
All provided cleaned data have had adaptors clipped
Alignments were all made against hg19. mRNA-seq: tophat (version 1.3.1) -g 25 -r 20 --segment-length 45 -G "hg19_refseq.gtf" --solexa1.3-quals
Genome_build: hg19
Supplementary_files_format_and_content: Exon read counts in text format generated using analyzeRNA.pl from the HOMER package

source_name: CD34+ cells

extract_protocol:
Bone marrow (BM) samples were harvested from normal volunteers with informed consent in accordance with local ethical guidelines.  The CD34+ fraction was obtained by magnetic bead separation using an automated CliniMACS cell separation system (Miltenyi Biotec, Cologne).  Cell purity was assessed by flow cytometry and was ≥ 98%. ChIP assays were performed with 15 x 10^6 per condition. Total RNA extraction and purification was performed using miRNeasy mini kits (QIAGEN). The small RNA fraction (<200nt) was collected in a separate fraction from total RNA, as per manufacturer’s standard instructions. Total RNA was amplified using the Ovation RNA-seq system V2 (NuGEN) prior to sequencing.
Library construction was performed as per Illumina protocol Rev A 11257047

value: CD34+ cells


title: Exp 5 Wk 0 CD34+ MIG+ GFP+

value: ERG overexpression


title: Input

description:
dmrt6_input
processed data file: DM6_dedup_macs14_pe05_peaks.bed

source_name: Input

value: C57BL/6, Mixed

value: adult


title: WT input DNA

value: Wild type

value: Small intestinal crypts


title: Dmrt6 ChIP

description:
dmrt6_chip
processed data file: DM6_dedup_macs14_pe05_peaks.bed

source_name: Dmrt6 ChIP

tag: chip antibody

value: Rabbit polyclonal antibodies to DMRT6


title: DSA-2


title: Exp 5 Wk 0 CD34+ MIG+

tag: treatment


title: P8 Dmrt6 Null Testis Replicate 3

description:
Null_GCCAAT
processed data file: dmrt6_log2_cpm_rna_seq.csv


title: RAD21 Adenoma ChIP

value: Abcam


title: Ade 3


title: DSA-1


title: Ade 2


title: DHS-4

source_name: Apc Min Rad21+/- double mutant small intestinal crypts


title: DHS-3


title: DHS-2


title: Ade 1


title: Min 3

source_name: Apc Min small intestinal crypts


title: Min 2


title: Rad-4

source_name: Rad21+/- small intestinal crypts


title: WT 3

source_name: WT small intestinal crypts


title: Rad-2


title: Rad-3


title: Exp 4 Wk 0 CD34+ MIG+ GFP+


title: WT 1


title: mouse_nmp1_positive_sorted

city: Shanghai

first: Qing Cissy

last: Yu

address: 320 Yue Yang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institute of Biological Sciences

description: mRNA

data_processing:
Basecalling using Illumina Casava 1.8.2 software.
Around 32 million 1×100 single reads for each sample were obtained and uniquely mapped to the mm9 mouse genome with more than 70% of mapping rate for both samples using TopHat v1.3.3.
Bam to Bedgraph using genomeCoverageBed v2.17.0.
BedGraph to bigwig using UCSC bedGraphToBigWig V4.
Differential gene expression analysis using Cuffdiff 2.0.2.
Genome_build: MGSCv37
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format; http://genome.ucsc.edu/goldenPath/help/bigWig.html). The .bw file reports the abundance score at each genomic position if there is RNA-seq signal.

source_name: Freshly sorted Procr+ mouse mammary myoepithelium

extract_protocol:
Total RNA from freshly isolated Lin-, CD24+, CD29hi, Procr+ cells and Lin-, CD24+, CD29hi, Procr- cells were extracted with Trizol.
RNA-seq libraries were prepared according to the manufacturer's instructions (Illumina) and then applied to sequencing on Illumina HiSeq 2000 in CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai.

treatment_protocol: Cells were freshly sorted from mouse mammary gland.

tag: strain/background

value: mammary gland myoepithelium

value: Lin-, CD24+, CD29hi, Procr+ cells

tag: developmental stage

value: adult virgin 8wk


title: mouse_control_sorted

description: mRNA

source_name: Freshly sorted Procr- mouse mammary myoepithelium

value: Lin-, CD24+, CD29hi, Procr- cells


title: Control 6

city: Los Angeles

first: Atsushi

last: Nakano

address: 615 Charles E. Young Dr. South

department: MCDB/BSCRC

institute: UCLA

description:
C6
Illumina Solexa 1.3

data_processing:
Alignment to mm9 assembly using Tophat 2.0.4, using Ensembl annotation as junction library, allowing unique reads only and up to 2 mismatches
Counting and annotating reads through HTSeq 0.5.4p3, using "non-empty intersection" method
Calculating p-values using DESeq with default parameters, method of estimating dispersions to be "blind"
Calculating RPKM values by dividing raw reads as reported by HTSeq by total number of aligned reads as reported by Tophat (in millions) and the length of each gene as calculated by the union length of all possible exons (in kilobases)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited .txt format, contains common name of gene, Ensembl ID, genomic coordinates, gene function, type of coding region, location in cell as annotated experimentally and predicted in other annotations, calculated length of gene as union length of exons, counts per sample, RPKM per sample, log base 2 ratio, p-value, and p-value adjusted for false discovery rate

source_name: atrial tissue

extract_protocol:
Atrial tissues were disolved in Trizol, followed by RNeasy column purification.
Illumina TruSeq RNA Sample Prep Kit was used with 250ng of total RNA for the construction of RNA-sequencing libraries under standard Illumina protocols.

value: atria

tag: genotype/variation

value: SLN-Cre; Nkx2-5-flox/+ (control)


title: Mutant 5

description:
M5
Illumina Solexa 1.3

value: SLN-Cre; Nkx2-5-flox/flox (mutant)


title: Control 2

description:
C2
Illumina Solexa 1.3


title: Control 4

description:
C4
Illumina Solexa 1.3


title: Mutant 7

description:
M7
Illumina Solexa 1.3


title: Min 1

tag: strain background

value: Apc min/+