title: 6 dpi PRV infected TBLN

city: Ames

first: Laura

last: Miller

state: Iowa

address: 1920 Dayton Ave

department: Virus and Prion Research Unit

institute: USDA-ARS-National Animal Disease Center

data_processing:
Illumina fastq files for the infected and control libraries were processed by a custom perl script that created the three column Filtered Tag Count File consisting of: the first 20 bases of the tag sequence, raw tag count, and the normalized tag count in units of Tag Per Million (TPM). A tpm (transcripts per million) value for a specified transcriptional unit (TU) was calculated by counting appearance of DEGTP tags for a given TU, divided by the total number of TU counts obtained from a particular tissue and normalized per million.
Using a customized perl script, the Filtered Tag Count File for each library was parsed into the Identitag database as well as sequencing library metadata as has been previously described (Harhay GP, Smith TP, Alexander LJ, et al. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biol. 2010;11(10):R102).
Genome_build: swine genome assembly SGSC Sscrofa10.2/susScr3
Supplementary_files_format_and_content: tab-delimited text files of tag counts

organism: Sus scrofa domesticus

growth_protocol: Forty conventionally raised 4-5 week old pigs, free of clinical disease, were purchased from a Porcine Circovirus 2-, Swine Influenza Virus-, Porcine Respiratory and Reproductive Virus -, and PRV-negative herd. Pigs were equally allotted to two equal treatment groups and each group was housed in an isolation room for about one week prior to the beginning of the experiment

extract_protocol:
One gram of TBLN from each pig was collected immediately upon necropsy, minced and stored in RNAlater at -80°C until homogenized for extraction of total RNA with MagMAX™-96 for Microarrays Total RNA Isolation Kit (Applied Biosystems, Carlsbad, CA) using the manufacturer's protocol. The integrity of the RNA was confirmed using a 2100 Bioanalyzer and RNA 6000 Nano-chip (Agilent, Santa Clara, CA). The samples used had an average RIN value of 7.8 and 28S:18S rRNA ratio of 1.9.Tag library preparation was performed at Iowa State University DNA facility using a DGETP DpnII Sample Prep kit and protocol (Illumina, Hayward, CA). In brief, total RNA aliquots (1 mg) were diluted in 50 mL of nuclease-free H2O and heated at 65°C for 5 min to disrupt secondary structure prior to incubation with magnetic oligo-dT beads to capture the poly-adenlyated RNA fraction. First and second-strand cDNA was synthesized and bead-bound cDNA was subsequently digested with DpnII to retain a cDNA fragment from the most 3‘ GATC to the poly(A)-tail. Unbound cDNA fragments were washed away prior to ligation with GEX DpnII adapter to the 5’ end of the bead-bound digested cDNA fragments. This adapter contains a restriction site for MmeI which cuts 17 bp downstream from the DpnII site. After subsequent digestion with MmeI, 21 bp tags starting with the DpnII recognition sequence were recovered from the beads and dephosphorylated prior to phenol/chloroform extraction. Then, a second adapter (GEX adapter 2) was ligated onto the 3’ end of the cDNA tag at the MmeI cleavage site. The adapter-ligated cDNA tags were enriched by a 15 cycle PCR amplification using Phusion polymerase (Finnzymes) and primers complementary to the adapter sequences. The resulting fragments were purified by excision from a 6% polyacrylamide TBE gel. The DNA was eluted from the gel debris with 1× NEBuffer 2 by gentle rotation for 2 h at room temperature. Gel debris were removed using Spin-X Cellulose Acetate Filter (2 ml, 0.45 µm) and the DNA was precipitated by adding 10 µl of 3 M sodium acetate (pH 5.2) and 325 µl of ethanol (–20°C), followed by centrifugation at 14,000 r.p.m. for 20 min. After washing the pellet with 70% ethanol, the DNA was resuspended in 10 µl of 10 mM Tris–HCl, pH8.5 and quantified with a Nanodrop 1000 spectrophotometer. Sequencing using Solexa/Illumina Whole Genome SequencerCluster generation was performed according to the manufacturer's instructions.
Tag library preparation was performed at Iowa State University DNA facility using a DGETP DpnII Sample Prep kit and protocol (Illumina, Hayward, CA). In brief, total RNA aliquots (1 mg) were diluted in 50 mL of nuclease-free H2O and heated at 65°C for 5 min to disrupt secondary structure prior to incubation with magnetic oligo-dT beads to capture the poly-adenlyated RNA fraction. First and second-strand cDNA was synthesized and bead-bound cDNA was subsequently digested with DpnII to retain a cDNA fragment from the most 3‘ GATC to the poly(A)-tail. Unbound cDNA fragments were washed away prior to ligation with GEX DpnII adapter to the 5’ end of the bead-bound digested cDNA fragments. This adapter contains a restriction site for MmeI which cuts 17 bp downstream from the DpnII site. After subsequent digestion with MmeI, 21 bp tags starting with the DpnII recognition sequence were recovered from the beads and dephosphorylated prior to phenol/chloroform extraction. Then, a second adapter (GEX adapter 2) was ligated onto the 3’ end of the cDNA tag at the MmeI cleavage site. The adapter-ligated cDNA tags were enriched by a 15 cycle PCR amplification using Phusion polymerase (Finnzymes) and primers complementary to the adapter sequences. The resulting fragments were purified by excision from a 6% polyacrylamide TBE gel. The DNA was eluted from the gel debris with 1× NEBuffer 2 by gentle rotation for 2 h at room temperature. Gel debris were removed using Spin-X Cellulose Acetate Filter (2 ml, 0.45 µm) and the DNA was precipitated by adding 10 µl of 3 M sodium acetate (pH 5.2) and 325 µl of ethanol (–20°C), followed by centrifugation at 14,000 r.p.m. for 20 min. After washing the pellet with 70% ethanol, the DNA was resuspended in 10 µl of 10 mM Tris–HCl, pH8.5 and quantified with a Nanodrop 1000 spectrophotometer. Sequencing using Solexa/Illumina Whole Genome SequencerCluster generation was performed according to the manufacturer's instructions. Image analysis and basecalling were performed using the Illumina Pipeline to create a fastq file for each library

treatment_protocol: On 0 days post-inoculation (dpi) pigs received an intranasal challenge with 2 ml of either sham inoculum (n = 20), prepared from swine testicle cell culture, or virus inoculum ( n = 20), of the Florida strain isolate (FS 268) of feral swine PRV6 at 1 x 106 cell culture infectious dose 50% (CCID50) per pig. Five pigs from each group were euthanized and necropsied on 1, 3, 6, and 14 dpi

value: Tracheobronchial lymph node

tag: breed

value: Cross-bred

value: 5 weeks

tag: inoculation

value: FS268 Pseudorabies virus 106 CCID50


title: 1 dpi PRV infected TBLN

status: Public on Oct 30 2015

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: age


title: 3 dpi PRV infected TBLN


title: 14 dpi Control TBLN

value: Control sham swine testicle cell culture media


title: 3 dpi Control TBLN


title: 1 dpi Control TBLN


title: 14 dpi PRV infected TBLN


title: Input_Zfp217 shRNA

city: New York

first: Martin

middle: J.

last: Walsh

state: NY

address: One Gustave L. Levy Pl.

department: Structural and Chemical Biology

institute: Mount Sinai School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.4
read sequences were done QC filtering by FASTX ( -q 20 -p 90 )
MeRIP-seq reads were aligned to the mm9 genome assembly using bowtie2
peaks were called either using MACS version 1.4 or using exomePeak and dis-regulated peaks in zfp217 KO meRIP were detected using exomePeak
Genome_build: mm9
Supplementary_files_format_and_content: bed file were generated using exomePeak

organism: Mus musculus

source_name: CCE

growth_protocol: Mouse ES cell line CCE was cultured in feeder-free on 0.1% gelatin-coated plates in ES cell medium (Dulbecco's modified Eagle's medium (DMEM; Hi-Glucose), 15% fetal bovine serum , non-essential amino acids, L-glutamine, β-mercaptoethanol, penicillin/streptomycin, sodium pyruvate and leukemia inhibitory factor (LIF; Millipore).

extract_protocol:
Total RNA for each condition was extracted with Trizol (Invitrogen) and treated with RNAse free DNAseI (Roche). RNA was fragmented chemically to ~100 nts long fragments and subjected to IP using anti-m6A antibody (Synaptic systems, 202003).
Library construction was prepared following the manufacturer's recommendation (TruSeq RNA Sample Preparation kit, Illumina RS-122-2001)

treatment_protocol: Cells were infected with either control or Zfp217 shRNA. 4 days post-infection, cells were selected with 1 microgram/ mL puromycin (Sigma) for 5 more days and harvested for RNA extraction

tag: cell line

value: CCE

tag: cell type

value: mouse stem cells


title: Input_control shRNA


title: METTL3-RIP-seq

data_processing:
Basecalls performed using CASAVA version 1.4
Raw RIP-seq reads are aligned against the aforementioned custom contaminant list (including mouse mitochondria genome, ribosomal RNA and Illumina adapter) using bowtie2 to filter contaminant (aligned) reads
RIP-seq reads were aligned to the mm9 genome assembly using TopHat (version 2.0.8)
Cufflinks/Cuffdiff was used to compute FPKM values for each Ensembl transcript and fold-change difference of gene expression between the RIP and control libraries.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for expressed transcripts in RIP

extract_protocol:
Cell nuclei were isolated, nuclear lysate was prepared and incubated overnight with 10 µg of Zfp217 antibody (Santa Cruz Biotechnology, SC-55351x) or 10 µg of Mettl3 antibody (Bethyl, A301-567A) for 2x10E6. Afterwards, the RNA-protein complexes were immunoprecipitated with protein G magnetic beads and the RNA fraction was extracted using Trizol reagent.
Library construction was prepared following the manufacturer's recommendation (TruSeq RNA Sample Preparation kit, Illumina RS-122-2001)

treatment_protocol: No treatment

tag: rip antibody

tag: rip antibody vendor

value: Bethyl

tag: rip antibody cat. #


title: Zfp217 shRNA-Zfp217 IP

tag: antibody

value: m6A antibody

tag: antibody vendor

value: Synaptic systems

tag: antibody cat. #


title: control shRNA-Zfp217 IP


title: Day 0

data_processing:
Illumina Casava1.7 software used for basecalling.
After filtering contaminant (aligned) reads, sequenced reads were then mapped to mm9 genome, RefSeq exons, splicing junctions using BWA v0.7.3 alignment algorithm
The filtered reads that are uniquely aligned to the exon and splicing-junction sites for each transcript were then counted as expression level for a corresponding transcript and was further subjected to log2 transformation  and global median normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each transcript in each sample

growth_protocol: Mouse ES cell line CCE was cultured in feeder-free on 0.1% gelatin-coated plates in ES cell medium (Dulbecco's modified Eagle's medium (DMEM; Hi-Glucose), 15% fetal bovine serum , non-essential amino acids, L-glutamine, β-mercaptoethanol, penicillin/streptomycin, sodium pyruvate and leukemia inhibitory factor (LIF; eBiosciences).

extract_protocol:
Total RNA for each condition was extracted with Trizol (Invitrogen) and treated with RNAse free DNAseI (Roche)
RNA-seq libraries were prepared from Tryzol extracted RNA samples from which rRNA was removed using Ribo-ZeroTM and following the TruSeq Stranded Total RNA Sample Prep kit protocol (Illumina).

treatment_protocol: To induce differentiation with retinoic acid (RA), LIF (eBioscience) was removed and RA (Sigma-Aldrich) was added at a concentration of 5 μM.  Medium was changed every other day. Cells were harvested for extraction of total RNA at the indicated time points.

tag: cell line background

value: ESC

tag: treated with

value: DMSO


title: Day 4

value: D4 differentiated ESC

value: 5 microM Retinoic acic (Sigma) for 4 days


title: Day 6

value: D6 differentiated ESC

value: 5 microM Retinoic acic (Sigma) for 6 days


title: 6 dpi Control TBLN


title: CP4-1-in vitro

city: Guelph

first: Valeria

middle: Regina

last: Parreira

state: ON

address: 50 Stone Rd E

department: Pathobiology

country: Canada

institute: University of Guelph

data_processing:
Illumina Casava1.8.2. software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C. perfringens strain CP4 whole genome using bowtie2 version 2.1.0 using default parameters.
Raw reads counts were generated for each gene using HTSeq software version 0.5.4p1, using the HTSeq counting mode “union”
Estimates of absolute expression (rpkm, reads per kilobase per million read) were generated using the edgeR function rpkm
Genome_build: C. perfringens CP4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Clostridium perfringens

source_name: lab culture

extract_protocol:
RNAlater was added to chicken intestinal contentes and bacterial cultures and  frozen at -70C. RNA from C. perfringens were isolated using silica column kits.
RNA libraries were prepared using Illumina HiSeq 2500 with TruSeq v3 chemistry

tag: strain

tag: features

value: virulent


title: Day 3

value: D3 differentiated ESC

value: 5 microM Retinoic acic (Sigma) for 3 days


title: Luciferase control shRNA

treatment_protocol: Cells were infected with either control or Zfp217 shRNA. 4 days post-infection, cells were selected with 1mg/mL puromycin (Sigma) for 5 more days and harvested for RNA extraction

tag: infected with

value: Luciferase control shRNA

tag: selected with

value: puromycin (1mg/mL) for 5 days


title: Day 5

value: D5 differentiated ESC

value: 5 microM Retinoic acic (Sigma) for 5 days


title: Zfp217_RIP-seq

value: CCE

value: mouse stem cells

value: Santa Cruz


title: Input_ChIP-seq

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
read sequences were done QC filtering by FASTX ( -q 20 -p 90 )
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
peaks were called using MACS2 using Input as control with the following setting: QVALUE threshold (0.05), MFOLD (5, 50).
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS.

molecule: genomic DNA

extract_protocol:
After cross-linking cells for 10 min with 1% formaldehyde and sonicating chromatin with a Diagenode Bioruptor, chromatin was immunoprecipitated using 10 µg of Zfp217 antibody (Santa Cruz Biotechnology, SC-55351x) for 10E6 cells.
ChIP-DNA was end repaired with T4 DNA polymerase and polynucleotide kinase. An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 200-300bp size fractions were excised from 2% agarose gel stained with GelStar. Adaptor-modified fragments were enriched by 16 cycles of PCR amplification. The DNA library prep was validated in Bioanalyzer for quantity and size.


title: Zfp217 shRNA

value: Zfp217 shRNA


title: WT_mono_nucleosomes_biorep2

city: Cardiff

first: Nicholas

last: Kent

address: Museum Avenue

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

description: Genomic mono-nucleosome map: frequency distribution of 150bp CPSA size class paired-read mid-point positions, in 10bp bins, 3-bin moving average.

data_processing:
Paired reads were aligned to the ASM294v1.17 reference genome using Bowtie 0.12.7 with command line flags: -n 0 --trim3 64 --maxins 5000 --fr -k 1 --sam. Reads in the .bam files are therefore trimmed to 36bp.
Aligned read pairs for each fission yeast strain were sorted according to chromosome using grep, and into a range of size classes based on the SAM format ISIZE value (difference between 5’ end of the mate read and the 5’ end of the first mapped read) plus or minus 20% using scripts described in Kent et al., (2011,Nucleic Acids Res. 39:e26) . E.g. Mono-nucleosome-sized reads are, therefore, represented as 150bp ± 30bp.
To define the genomic position of MNase-resistant chromatin entities we mapped the mid-point position of the read pairs in a particular size class. Frequency distributions of the mid-point positions, were then calculated using 10bp bins, and the distributions lightly smoothed to a 3 bin moving average using scripts decribed in Kent et al., (2011,Nucleic Acids Res. 39:e26).
Note: WT_7 is a re-analysis of wild-type S. pombe MNase-seq data previously published in Gal C., Moore K.M., Paszkiewicz K., Kent N.A., Whitehall S.K. (2015) The impact of the HIRA histone chaperone upon global nucleosome architecture. Cell Cycle 14:123-134. Raw paired-end sequence (rather than .bam alignment) available under SRA: SRS712792
Genome_build: ASM294v1.17
Supplementary_files_format_and_content: After unzipping, the files describe nucleosome mid point position frequency distributions as zero-referenced, chromosome base, three-column tab-delimited text files. The three columns are: chromosome number; bin position; 3MA mid-point frequency value. By adding the file extension .sgr (an Affymetrix file format) these files can be rendered directly using the Integrated Genome Browser.

organism: Schizosaccharomyces pombe

source_name: Cross-linked in vivo chomatin

growth_protocol: Cells (100 ml) were grown to OD595= 0.75-8.0 in YE5S at 30°C

extract_protocol:
Reactions were incubated at 65°C overnight with 0.2 mg/ml proteinase K and 10 μg RNAse. DNA was purified by extracting twice with phenol:chloroform followed by ethanol precipitation (0.1 volumes of 3 M sodium acetate followed by 2 volumes of ethanol). Pellets were washed in 70% ethanol and resuspended in water containing 10 μg/ml RNase and incubated at 37°C for 30 min. Triplicate digests were pooled and treated with with 100 U unmodified T4 polynucleotide kinase (NEB) for 30 min at 37°C to remove 3′-phosphate groups left by MNase. DNA was extracted once more with phenol:chloroform, re-precipitated with sodium acetate and propan-2-ol, washed with 80% ethanol, dried and re-suspended in TE (pH 7.5).
DNA fragments were end repaired, 3′-adenylated and ligated to indexed adapters without size selection using Nextflex reagents (Newmarket Scientific, UK). Libraries were amplified with 8 cycles PCR using Kapa HiFi PCR master mix (Anachem), primers removed with GeneRead size selection protocol (QIAgen) before quantification by Bioanalyser DNA 7500 assay. Libraries were pooled, denatured, diluted to 6 nM before clustering in a single lane of a high output Illumina flowcell.  Sequencing (100nt) was undertaken on a HiSeq 2500 using TruSeq SBS v3 reagents (Illumina).

treatment_protocol: Cells were crosslinked for 20 min at 30°C using 1% formaldehyde and quenched by the addition of glycine to 125 mM. Cells were washed once in CES buffer (50 mM citric acid/50 mM Na2HPO4 [pH 5.6], 40 mM EDTA [pH 8.0], 1.2 M sorbitol and 10 mM β-mercaptoethanol) and resuspended in 500 μl of CES buffer with 0.5mg Zymolase 100-T. Cells were spheroplasted at 30°C for up to 1 h and then washed twice with ice cold 1.2M sorbitol. Spheroplasts were then resuspended in 800 μl NP-S buffer (1.2 M sorbitol, 10 mM CaCl2, 100 mM NaCl, 1 mM EDTA pH 8.0, 14 mM β-mercaptoethanol, 50 mM Tris pH 8.0, 0.075% NP-40, 5 mM spermidine, 0.1 mM PMSF, 1% Sigma Protease inhibitors cocktail [Sigma P8215]). Spheroplasts were then divided into four 200 μl aliquots and each aliquot was mixed with 300 μl of NP-S buffer. Three aliquots were digested with 187.5 units of MNase (USB) for 10 min at 37°C. The fourth was retained as an undigested control. MNase digestion was terminated by adding EDTA [pH 8.0] to a final concentration of 50 mM and SDS to 0.2%.

tag: genotype

value: h-


title: abo1_mono_nucleosomes_biorep2

value: h-, abo1::KanMX


title: Day 2

value: D2 differentiated ESC

value: 5 microM Retinoic acic (Sigma) for 2 days


title: Zfp217_ChIP-seq

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody cat. #


title: Prox1 GFP minus

city: San Diego

first: Son

last: Pham

state: California

address: 10010 N Torrey Pines Rd

department: LOG

institute: Salk Institute

description:
Single-end, 50bp on HiSeq2500v3.
Processed data file: cpm.txt, column PROX1GFPPLUS

data_processing:
Reads from all libraries were mapped to the human reference genome (GRCh37) using STAR version 2.3.0. The assignment of reads to gene regions was performed by htseq-count, version 0.5.4 p5. The raw counts are normalized to obtain cpm.
Genome_build: GRCh37
Supplementary_files_format_and_content: cpm.txt: tab-delimited text file containing normalized cpm (count per million) for each sample.

organism: Homo sapiens

source_name: iPSC-derived neurons

growth_protocol: DG-like hippocampal iPSC-derived neurons cultured as described (Yu DX et al. Stem Cell Reports 2014).

extract_protocol:
FACSorting into Trizol-LS; standard Trizol RNA extraction.
PolyA pulldown, stranded, according to Illumina protocol.

treatment_protocol: Lentiviral expression of Prox1-promoter-driven GFP.

tag: cell type

value: iPSC-derived neurons

value: minus


title: Prox1 GFP plus

description:
Single-end, 50bp on HiSeq2500v3.
Processed data file: cpm.txt, column PROX1GFPMINUS

value: plus


title: Blood_Platelets_Lung-L65

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Selection of intron-spanning reads was performed using Picard-tools (version 1.115)
Read summarization was performed using HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Genome_build: hg19
Supplementary_files_format_and_content: Samples in the tab-delimited text file were processed according to the described protocol and data of all samples was merged in a comprehensive read count matrix.

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA (Bioanalyzer RIN values >7 and/or distinctive rRNA curves) diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v1 (Clontech, cat. nr. 634936) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations (8-12 samples per Hiseq lane) and submitted for 100 bp Single Read sequencing on the Hiseq 2500 platform (Illumina).

tag: patient id

tag: cancer type

value: Lung

tag: batch

tag: mutational subclass

value: KRAS

tag: tissue

value: blood

value: thrombocytes


title: Input_RIP-seq

tag: cell line


title: Day 1

tag: cell line background

value: D1 differentiated ESC

value: 5 microM Retinoic acic (Sigma) for 1 day


title: Blood_Platelets_Lung-L40


title: Blood_Platelets_Lung-L39


title: Blood_Platelets_Lung-L25

value: EGFR


title: Blood_Platelets_Lung-L22


title: Blood_Platelets_Lung-L23


title: Blood_Platelets_Lung-L20


title: Blood_Platelets_Lung-L19


title: Blood_Platelets_Lung-L18


title: Blood_Platelets_Lung-L12


title: Blood_Platelets_Lung-L59


title: Blood_Platelets_Lung-L07


title: Blood_Platelets_Lung-L03


title: Blood_Platelets_Lung-L11


title: Blood_Platelets_Lung-L58


title: Blood_Platelets_Lung-L01


title: Blood_Platelets_CRC-BRAF6

value: CRC

value: wt


title: Blood_Platelets_Lung-59


title: Blood_Platelets_CRC-BRAF5


title: Blood_Platelets_CRC-412


title: Blood_Platelets_Breast-H84

value: Breast


title: Blood_Platelets_Lung-49


title: Blood_Platelets_Lung-L51


title: Blood_Platelets_CRC-368


title: Blood_Platelets_Lung-57


title: Blood_Platelets_Breast-H92


title: Blood_Platelets_Chol-BRAF4

value: Hepatobiliary


title: Blood_Platelets_Breast-H81


title: Blood_Platelets_Breast-H76


title: Blood_Platelets_Breast-H75


title: Blood_Platelets_Breast-H68


title: Blood_Platelets_Breast-H63


title: Blood_Platelets_Breast-H66


title: Blood_Platelets_Breast-H59


title: Blood_Platelets_Breast-H38


title: Blood_Platelets_Breast-H89


title: Blood_Platelets_Breast-H31


title: Blood_Platelets_Breast-H11


title: Blood_Platelets_Panc-597

value: Thrombocytes

value: Pancreas


title: Blood_Platelets_Breast-H83


title: Blood_Platelets_Panc-593


title: Blood_Platelets_Panc-503


title: Blood_Platelets_Panc-553


title: Blood_Platelets_Panc-512


title: Blood_Platelets_Panc-493


title: Blood_Platelets_Panc-498


title: H3K27ac ChIP-seq from BN369 P1 cells

city: Rennes

first: Gilles

last: Salbert

address: Avenue du Général Leclerc

department: Biology

country: France

institute: University of Rennes 1

data_processing:
SCL-seq fastq files were mapped to human hg19 genome assembly using Bowtie with parameters l=32 bp, n=1, m=1, strata, best, and Samtools.
The bam files were then processed to generate .wig files using MACS 1.4.0.
Genome_build: hg19
Supplementary_files_format_and_content: wig files

source_name: in vitro differentiated plasmablasts

growth_protocol: Naive B cells from healthy donors were purified by negative selection using magnetic cell separation (Miltenyi Biotech) and cultured at 7.5.105 cells/ml with the stimulation cocktail 1 (2,6 µg/ml Fab'2 anti-Ig, 100 ng/ml CD40 Ligand, 1 µg/ml CpG ODN 2006 and 50 U/ml IL2) for 4 days. Activated B cells were then washed and further cultured at 4.105 cells/ml with the differentiation cocktail 2 (50 U/ml IL2, 5 ng/ml IL4, 10 ng/ml IL10)

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA mini kit (Qiagen) after cell-sorting (FACS Aria, BD) of blood or lymph node naive B cells and of in vitro differentiated plasmablasts (day 6 of the culture). For ChIP experiments, cells were fixed with 1% formaldehyde prior to cell sorting.
Genomic DNA (7 μg) from naïve B cells and plasmablasts was fragmented to 200 to 500 bp by sonication (Bioruptor, Diagenode) before incubation with β-glucosyltransferase and azide-glucose. Glucosylated 5hmCs were then labeled with biotin before enrichment of the biotinylated DNA fragments with streptavidin-coated magnetic beads. All steps used reagents from the Hydroxymethyl Collector kit (Active Motif). After elution from the beads, purified DNA was precipitated and processed for sequencing on a Highseq2000 (Illumina). Library preparations and sequencing reactions were run at the IGBMC genomic platform (Strasbourg, France). ChIP-seq was performed in P1 cells as follows. Cells were fixed for 8 minutes in 1% formaldehyde at room temperature and chromatin was sonicated for 15 minutes with the Bioruptor Sonication System (Diagenode). Immunoprecipitation was carried out with antibodies from Diagenode against H3K4me1 (pAb-194-050, lot: A1863-001P) and H3K27ac (pAb-196-050, lot: A1723-0041D) using approximately 500,000 cells per antibody. ChIP-seq libraries were constructed using the Kapa Hyper Prep Kit (Kapa Biosystems) and sequenced with an Illumina HiSeq1500 sequencer.

value: plasmablasts

tag: origin

value: differentiation of NBC from buffy coat (healthy donor)


title: Blood_Platelets_Panc-461


title: Input DNA from BN369 P1 cells


title: Blood_Platelets_Panc-451


title: Blood_Platelets_Panc-477


title: Input DNA from BN358 P1 cells


title: Blood_Platelets_Panc-501


title: H3K27ac ChIP-seq from BN358 P1 cells


title: Blood_Platelets_Panc-449


title: H3K4me1 ChIP-seq from BN369 P1 cells


title: Blood_Platelets_Breast-H74


title: Blood_Platelets_Panc-448


title: Blood_Platelets_Panc-435


title: Blood_Platelets_Panc-431


title: H3K4me1 ChIP-seq from BN358 P1 cells


title: Blood_Platelets_Panc-390


title: Blood_Platelets_Panc-391


title: Blood_Platelets_Panc-389


title: Blood_Platelets_Panc-388


title: Blood_Platelets_Panc-488


title: Blood_Platelets_Panc-387


title: Blood_Platelets_Panc-382


title: Blood_Platelets_Panc-380


title: Blood_Platelets_Panc-371


title: Blood_Platelets_Panc-369


title: Blood_Platelets_Panc-370


title: Blood_Platelets_Panc-335


title: Blood_Platelets_Panc-367


title: Blood_Platelets_Panc-331


title: Blood_Platelets_Panc-328


title: Blood_Platelets_Lung-L.33


title: Blood_Platelets_Lung-L.4


title: Blood_Platelets_Lung-L.26


title: Blood_Platelets_Panc-260


title: Blood_Platelets_Panc-327


title: Blood_Platelets_Lung-62


title: Blood_Platelets_Lung-61

value: EGFR, MET


title: Blood_Platelets_Lung-L.13


title: Blood_Platelets_Panc-286


title: Blood_Platelets_Lung-74


title: Blood_Platelets_Lung-L.15


title: Blood_Platelets_Lung-46


title: Blood_Platelets_Panc-314


title: Blood_Platelets_Lung-42

value: KRAS, MET


title: Blood_Platelets_Lung-40

value: Lung


title: Blood_Platelets_Panc-434


title: Blood_Platelets_Lung-58


title: Blood_Platelets_Lung-271


title: Blood_Platelets_Lung-25


title: Blood_Platelets_Lung-29


title: Blood_Platelets_Lung-30


title: Blood_Platelets_Lung-37

value: KRAS


title: Blood_Platelets_Lung-24-1

value: blood


title: Blood_Platelets_Lung-20-1


title: Blood_Platelets_Lung-26


title: Blood_Platelets_Lung-20


title: Blood_Platelets_Lung-16


title: Blood_Platelets_Lung-12


title: Blood_Platelets_Lung-08


title: Blood_Platelets_Lung-14


title: Blood_Platelets_Lung-17


title: Blood_Platelets_Lung-06


title: Blood_Platelets_Lung-07


title: Blood_Platelets_Lung-0119


title: ILC2s IL-33 + IL-27 #2

city: Yokohama, Tsurumi-ku

first: Hiroki

last: Kabata

state: Kanagawa

address: Suehirocho 1-7-22

country: Japan

institute: RIKEN-IMS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the reference genome (mm9) using Bowtie2 v2.1.0 and TopHat2 v2.0.8.
The transcript abundances were estimated as FPKM (fragments per kilobase of exon million fragments mapped) value using Cufflinks v2.1.1.
Genome_build: mm9
Supplementary_files_format_and_content: Text files include FPKM values for each Sample.

source_name: Group 2 innate lymphoid cells

growth_protocol: ILC2s were isolated from fat-asociated lymphoid clusters (FALC) of wild-type mice.

extract_protocol:
RNA was isolated by Allprep DNA/RNA Micro Kit (QIAGEN)
cDNA libraries were prepared by TruSeq RNA Sample Preparation kits v2 (Illumina) according to the manufacturer’s low sample protocol

treatment_protocol: ILC2s were cultured with IL-33 (10ng/ml), IL-33 + IFN-g (10ng/ml), or IL-33 + IL-27 (10ng/ml) for 48hrs.

value: fat-asociated lymphoid cells

tag: strain

value: wild-type


title: Blood_Platelets_Lung-15


title: Blood_Platelets_Lung-0110


title: Blood_Platelets_Lung-04


title: ILC2s IL-33 + IL-27 #3


title: Blood_Platelets_Lung-0104


title: Blood_Platelets_Lung-0112


title: Blood_Platelets_Lung-0101


title: Blood_Platelets_Lung-0102


title: ILC2s IL-33 + IFNg #2


title: ILC2s IL-33 + IFNg #3


title: Blood_Platelets_Lung-01


title: Blood_Platelets_Lung-0100


title: Blood_Platelets_Lung-0096


title: ILC2s IL-33 + IFNg #1


title: ILC2s IL-33 #3


title: mES-control

city: Seoul

first: Boyoun

last: Park

address: 50 Yonsei-ro, Seodaemun-gu

department: Systems biology

country: South Korea

institute: Yonsei University

data_processing:
Basecalls performed using bl2fastq version 2.16.0.10
RNA-seq reads were aligned to the mm10 genome using STAR version 2.4.1c using default parameters.
Read counts were obtained with featureCounts using respective gene annotation data.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: embronic stem cell

growth_protocol: mES cells were routinely generated by re-plating 3-4 days onto fresh MEF-seed dishes in mESC growth medium that consisted of DMEM with high glucose (Hyclone) supplemented with 20% Knockout serum replacement and 1000 U/ml LIF.

extract_protocol:
Total RNA was isolated using TRIzol® RNA Isolation Reagents (Life technologies, Carlsbad, CA)
The isolated total RNA was processed for preparing mRNA sequencing library using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA) according to manufacturer’s instruction.

value: embronic stem cell

tag: passages


title: Blood_Platelets_Lung-0082

value: MET


title: mES-Pc4-OE


title: Blood_Platelets_Liver-366


title: ILC2s IL-33 #2


title: Blood_Platelets_Liver-297


title: ILC2s IL-33 + IL-27 #1


title: Blood_Platelets_HC-55

value: HC


title: Blood_Platelets_Liver-274

value: wt


title: Blood_Platelets_HC-51


title: Blood_Platelets_HC-52


title: WT_mono_nucleosomes

description: MNase-protected DNA

data_processing:
Paired reads were aligned to the ASM294v1.17 reference genome using Bowtie 0.12.7 with command line flags: -n 0 --trim3 64 --maxins 5000 --fr -k 1 --sam. Reads in the .bam files are therefore trimmed to 36bp.
Aligned read pairs for each fission yeast strain were combined (bash cat) from the two HiSeq lane data sets and  then  sorted according to chromosome using grep, and into a range of size classes based on the SAM format ISIZE value (difference between 5’ end of the mate read and the 5’ end of the first mapped read) plus or minus 20% using scripts described in Kent et al., (2011,Nucleic Acids Res. 39:e26) . E.g. Mono-nucleosome-sized reads are, therefore, represented as 150bp ± 30bp.
To define the genomic position of MNase-resistant chromatin entities we mapped the mid-point position of the read pairs in a particular size class. Frequency distributions of the mid-point positions, were then calculated using 10bp bins, and the distributions lightly smoothed to a 3 bin moving average using scripts decribed in Kent et al., (2011,Nucleic Acids Res. 39:e26).
Note: WT_7 is a re-analysis of wild-type S. pombe MNase-seq data previously published in Gal C., Moore K.M., Paszkiewicz K., Kent N.A., Whitehall S.K. (2015) The impact of the HIRA histone chaperone upon global nucleosome architecture. Cell Cycle 14:123-134. Raw paired-end sequence (rather than .bam alignment) available under SRA: SRS712792
Genome_build: ASM294v1.17
Supplementary_files_format_and_content: After unzipping, the files describe nucleosome and di-nucleosome mid point position frequency distributions as zero-referenced, chromosome base, three-column tab-delimited text files. The three columns are: chromosome number; bin position; 3MA mid-point frequency value. By adding the file extension .sgr these files can be rendered directly using the Integrated Genome Browser.
Supplementary_files_format_and_content: WT_7_Part150chr_10.txt: Genomic mono-nucleosome map: frequency distribution of 150bp CPSA size class paired-read mid-point positions, in 10bp bins, 3-bin moving average.
Supplementary_files_format_and_content: WT_7_Part300chr_10.txt: Genomic di-nucleosome map: frequency distribution of 300bp CPSA size class paired-read mid-point positions, in 10bp bins, 3-bin moving average.
Supplementary_files_format_and_content: abo1_7_Part150chr_10.txt: Genomic mono-nucleosome map: frequency distribution of 150bp CPSA size class paired-read mid-point positions, in 10bp bins, 3-bin moving average.
Supplementary_files_format_and_content: abo1_7_Part300chr_10.txt: Genomic di-nucleosome map: frequency distribution of 300bp CPSA size class paired-read mid-point positions, in 10bp bins, 3-bin moving average.

growth_protocol: Cells (100 ml) were grown to OD595= 0.75-8.0  in YE5S at 30°C

treatment_protocol: Cells were crosslinked for 20 min at 30°C using 1% formaldehyde and quenched by the addition of glycine to 125 mM. Cells were washed once in CES buffer (50 mM citric acid/50 mM Na2HPO4 [pH 5.6], 40 mM EDTA [pH 8.0], 1.2 M sorbitol and 10 mM β-mercaptoethanol) and resuspended in 500 μl of CES buffer with 0.5mg Zymolase 100-T. Cells were spheroplasted at 30°C for up to 1 h and then washed twice with ice cold 1.2M sorbitol. Spheroplasts were then resuspended in 800 μl NP-S buffer (1.2 M sorbitol, 10 mM CaCl2, 100 mM NaCl, 1 mM EDTA pH 8.0, 14 mM β-mercaptoethanol, 50 mM Tris pH 8.0, 0.075% NP-40, 5 mM spermidine, 0.1 mM PMSF, 1% Sigma Protease inhibitors cocktail [Sigma P8215]). Spheroplasts were then divided into four 200 μl aliquots and each aliquot was mixed with 300 μl of NP-S buffer. Three aliquots were digested with between 75-187.5 units of MNase (USB) for 10 min at 37°C. The fourth was retained as an undigested control. MNase digestion was terminated by adding EDTA [pH 8.0] to a final concentration of 50 mM and SDS to 0.2%.

value: h-


title: Blood_Platelets_HC-54


title: Blood_Platelets_HC-53

description: Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.


title: Blood_Platelets_HC-50


title: Blood_Platelets_HC-49


title: abo1_mono_nucleosomes

description: MNase-protected DNA

value: h-, abo1::KanMX


title: Blood_Platelets_HC-47

value: Thrombocytes


title: Blood_Platelets_HC-48


title: Blood_Platelets_HC-46


title: SCL-seq naive B cells from blood

data_processing:
Library strategy: SCL-Seq
SCL-seq fastq files were mapped to human hg19 genome assembly using Bowtie with parameters l=32 bp, n=1, m=1, strata, best, and Samtools.
The bam files were then processed to generate .wig files using MACS 1.4.0.
Genome_build: hg19
Supplementary_files_format_and_content: wig files

source_name: primary B cells from blood

value: naive B cells

value: NBC from buffy coat (healthy donor)


title: SCL-seq naive B cells from lymph node

source_name: primary B cells from lymph node

value: NBC from reactive (non tumoral) lymph node


title: Blood_Platelets_HC-44


title: Blood_Platelets_HC-43


title: SCL-seq P1 cells

value: plasmablasts

value: differentiation of NBC from buffy coat (healthy donor)


title: Mitotic_HCT116_nascentRNA

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description:
nuclear RNA
Nascent RNA-seq

data_processing:
Base-calling and quality filtering, default settings, Illumina Casava 1.8 for reads generated with Illumina HiSeq 2000
ChIP-seq: Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to two mismatches in the entire read length. Alignments were extended to a total fragment length of 150 bases toward the interior of the sequenced fragment. UCSC bigWig files were created with 1bp resolution coverage across the genome and normalized to total reads per million (r.p.m).
Nascent RNA-seq: Reads were aligned to the human genome (UCSC hg19) and Ensembl 72 GTF human annotations  using the Tophat aligner version 2.0.10, with the - g1 option. Alignments were not extended. UCSC bigWig files were created with 1bp resolution coverage across the genome and normalized to total reads per million (r.p.m).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: bigwig http://genome.ucsc.edu/goldenPath/help/bigWig.html

growth_protocol: HeLa and HCT116 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, catalog No. 11995, Gibco) supplemented with 10% fetal bovine serum (FBS, catalog No. F6178, Sigma).

extract_protocol:
For ChIP-seq, HeLa cells were crosslinked with 1% paraformaldehyde for 10 minutes and were quenched by glycine for 5 minutes at room temperature. Fixed chromatin was sonicated with a Misionix sonicator 3000 and immunoprecipitated with a specific antibody.
ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit using standard protocols. Nascent RNA-seq libraries were prepared with Illumina’s Ribo-Zero Gold and TruSeq RNA sample Prep Kit  using standard protocols.

tag: cell stage

value: Mitotic

tag: drug treatment

value: Nocodazole

value: no antibody


title: Asynchronous_STLCneg_nascentRNA

description:
nuclear RNA
Nascent RNA-seq

source_name: Hela

value: HeLa

value: Asynchronous

value: no drug


title: Blood_Platelets_HC-42

value: blood


title: Mitotic_STLC_nascentRNA

description:
nuclear RNA
Nascent RNA-seq

value: STLC


title: Asynchronous_HCT116_nascentRNA

description:
nuclear RNA
Nascent RNA-seq


title: Blood_Platelets_HC-41

value: HC

value: wt


title: Blood_Platelets_HC-40


title: Blood_Platelets_HC-39


title: Mitotic_nascentRNA_rep2

description:
nuclear RNA
Nascent RNA-seq


title: Blood_Platelets_HC-38


title: ILC2s IL-33 #1

value: fat-asociated lymphoid cells

tag: genotype

value: wild-type


title: Blood_Platelets_HC-37

value: Thrombocytes


title: SCL_input_DNA


title: Blood_Platelets_HC-45


title: Mitotic_nascentRNA_rep1

description:
nuclear RNA
Nascent RNA-seq

tag: chip antibody


title: Asynchronous_nascentRNA_rep2

description:
nuclear RNA
Nascent RNA-seq


title: Asynchronous_nascentRNA_rep1

description:
nuclear RNA
Nascent RNA-seq


title: G2M_TFIIB_3

description: ChIPseq of TFIIB

value: TFIIB(Santa Cruz, sc-225)


title: G2M_N20_2

description: ChIP of Total Pol II

value: Pol II (Santa Cruz, sc-899)


title: Blood_Platelets_HC-36


title: Blood_Platelets_HC-34


title: Blood_Platelets_HC-35


title: G2M_S5P_2

description: ChIP-seq of Ser5 Phosphorylated Pol II


title: Blood_Platelets_HC-32


title: Blood_Platelets_HC-30


title: Asynchronous_TFIIB_3

description: ChIPseq of TFIIB


title: Blood_Platelets_HC-31


title: G2M_H3K4me3_3

description: ChIPseq of H3K4me3


title: Blood_Platelets_HC-29


title: Asynchronous_N20_3

description: ChIP of Total Pol II


title: Blood_Platelets_HC-27


title: Asynchronous_H3K4me3_3

description: ChIPseq of H3K4me3


title: G2M_N20_1

description: ChIP of Total Pol II


title: Asynchronous_S5P_3

description: ChIP-seq of Ser5 Phosphorylated Pol II


title: Blood_Platelets_HC-26


title: Asynchronous_Flavo_N20_2

description: ChIP of Total Pol II

value: Nocodazole + Flavopiridol


title: Blood_Platelets_HC-33


title: Blood_Platelets_HC-28


title: G2M_S5P_1

description: ChIP-seq of Ser5 Phosphorylated Pol II


title: Blood_Platelets_HC-24


title: Mitotic_DMSO_N20_2

description: ChIP of Total Pol II


title: Mitotic_Flavo_N20_2

description: ChIP of Total Pol II


title: Mitotic_DMSO_N20_1

description: ChIP of Total Pol II


title: Mitotic_Flavo_N20_1

description: ChIP of Total Pol II


title: Asynchronous_N20_1

description: ChIP of Total Pol II


title: Asynchronous_input_2

description: Input DNA


title: Blood_Platelets_HC-18


title: Blood_Platelets_HC-19


title: Blood_Platelets_HC-22


title: Blood_Platelets_HC-15


title: Blood_Platelets_HC-17


title: Blood_Platelets_HC-20


title: Blood_Platelets_HC-16


title: Blood_Platelets_HC-21


title: Asynchronous_input_1

description: Input DNA


title: Blood_Platelets_HC-23


title: Blood_Platelets_HC-14


title: Blood_Platelets_HC-12


title: Blood_Platelets_HC-13


title: Mitotic_TFIIB_1

description: ChIPseq of TFIIB


title: Mitotic_TFIIB_2

description: ChIPseq of TFIIB


title: Mitotic_H3K4me3_2

description: ChIPseq of H3K4me3


title: Asynchronous_TFIIB_2

description: ChIPseq of TFIIB


title: Blood_Platelets_HC-11


title: Blood_Platelets_HC-10


title: Asynchronous_S5P_1

description: ChIP-seq of Ser5 Phosphorylated Pol II


title: Blood_Platelets_HC-09


title: Blood_Platelets_HC-08


title: Mitotic_H3K4me3_1

description: ChIPseq of H3K4me3


title: Asynchronous_Flavo_N20_1

description: ChIP of Total Pol II


title: Blood_Platelets_HC-07


title: Asynchronous_H3K4me3_1

description: ChIPseq of H3K4me3


title: Kdm1a mutant eggs rep 3

city: Bethesda

first: Todd

last: Macfarlan

address: 6 Center Drive, Building 6B, Room 2B-211

institute: NIH

data_processing:
For expression analysis, only first mate pair was used and reads were trimmed from 3' end to 50bp
Trimmed reads were filtered to a minimum average base quality of 15. We combined the knownGene, ensGene and refGene annotations for mm10 (downloaded from UCSC Genome Browser) with the full RepeatMasker annotation, also from UCSC Genome Browser, to build a single gene annotation.  Redundant transcripts were filtered out using the gffread utility packaged with Cufflinks.  The annotation was modified to include a common gene_id value for same-name repeat elements resulting in a total of 875 repeats.  Sequences for all annotated features were extracted from the mouse genome and RNA-Seq reads were aligned to them using BBMap with 95% identity, up to a single INDEL and up to 2000 equally best alignments per read.
Alignments to features were quantified by counting hits to gene loci and down-weighting read alignments that mapped to multiple gene loci by 1/N^2 where N is equal to the number of gene loci.  Reads aligned to repeat elements were counted in the same way but instead of using gene loci the repeat name was used for binning hits. If a read mapped to multiple repeat features all of the same name then it was counted as 1 hit to that repeat name.
Raw read counts were loaded into R and median normalized for differential expression analysis. For each pair-wise test genes with raw counts less than 10 in all conditions were not tested. Differential expression was performed by testing the null hypothesis that a gene's fold change between conditions is zero. The observed dispersion-mean relationship was fit using a method similar to that of DESeq and the predicted dispersions were used as the minimum dispersion per gene. Fold-changes between conditions were tested by monte-carlo simulation using the observed and estimated means and dispersions to generate random negative binomial distributed count values (the rnbinom method in R).  In each monte-carlo iteration N samples were simulated per condition (N = to the number of samples in each condition), averaged into conditions and the log fold-change was calculated. The resulting simulated log fold-change distributions are normally distributed. Z-scores were computed for each observed log fold-change compared to its corresponding monte-carlo simulated fold-change distribution and translated to two-tail p-values against the normal probability distribution. Raw p-values were adjusted using the Benjamini & Hochberg correction.  Genes and repeats were tested together and marked significant if the adjusted p-value was less than 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: .xls files, chrom: chromosome name/number in Ensembl language  gene_id: custom gene id value for the merged annotation  gene_name: gene symbol / repeat name  isRepeat: binary value. 1 = repeat element, 0 = gene  repClass, repFarmily: additional information for repeats or '-' for genes  a: average normalized count for condition a (second condition name in the file name)  b: average normalized count for condition b (first condition name in the file name)  fc: log2 fold change of b / a  tested: binary field indicating if the gene/repeat was tested in DE analysis. based on raw count level (see analysis description)  fc_prob: non-parametric probability derived from monte-carlo log fold-change distribution  pval: p-value from normal distribution  qval: Benjamini & Hochberg adjusted p-values (calculated over those with tested == 1)  significant: yes/no based on qval < 0.05

source_name: ovulated egg

growth_protocol: LSD1 FL/FL mice (From Wang et al, Nature 446, 2007 ) were crossed with ZP3::Cre mice (Jax labs strain 003651) and backcrossed again to generate LSD1 FL/FL, ZP3Cre+ females.

extract_protocol:
NugenPrelude  Direct Lysis buffer, followed by Ovation RNA-seq V2 for cDNA creation, and amplfication, using random hexamer and polydt priming
mRNA-seq sample prep kit (Illumina)

treatment_protocol: Litters of eggs were collected in Prelude direct lysis buffer

value: ovulated egg

value: Kdm1a mutant


title: Blood_Platelets_HC-25


title: Asynchronous_TFIIB_1

description: ChIPseq of TFIIB


title: Blood_Platelets_HC-03


title: Blood_Platelets_HC-04


title: Kdm1a mutant eggs rep 1


title: Kdm1a mutant eggs rep 2


title: Blood_Platelets_HC-06


title: Blood_Platelets_GBM-505

value: GBM


title: Blood_Platelets_HC-01


title: Blood_Platelets_GBM-499


title: Blood_Platelets_GBM-486


title: Asynchronous_H3K4me3_2

description: ChIPseq of H3K4me3


title: Blood_Platelets_GBM-471


title: Blood_Platelets_GBM-475


title: Blood_Platelets_GBM-476


title: Blood_Platelets_GBM-484


title: Blood_Platelets_GBM-480


title: Blood_Platelets_GBM-468


title: Blood_Platelets_GBM-456


title: Blood_Platelets_HC-05


title: Blood_Platelets_GBM-454


title: Blood_Platelets_HC-02


title: Blood_Platelets_GBM-445


title: Blood_Platelets_GBM-439


title: Blood_Platelets_GBM-440


title: Blood_Platelets_GBM-438


title: Blood_Platelets_GBM-436


title: Blood_Platelets_GBM-431


title: Blood_Platelets_GBM-429


title: Blood_Platelets_GBM-422


title: Blood_Platelets_GBM-421


title: Asynchronous_N20_2

description: ChIP of Total Pol II


title: Blood_Platelets_GBM-418


title: Blood_Platelets_GBM-485


title: Blood_Platelets_GBM-417


title: Blood_Platelets_GBM-408


title: Blood_Platelets_GBM-406


title: Blood_Platelets_GBM-398

description: Please note this sample did not yield sufficient number of total mapped intron-spanning reads and was thus excluded from analyses.


title: Blood_Platelets_GBM-443


title: Blood_Platelets_GBM-393


title: Blood_Platelets_GBM-372


title: Blood_Platelets_GBM-378


title: Blood_Platelets_GBM-402


title: Blood_Platelets_GBM-280


title: Blood_Platelets_GBM-306


title: Blood_Platelets_GBM-430


title: Blood_Platelets_GBM-425


title: Blood_Platelets_GBM-360


title: Blood_Platelets_CRC-576

value: CRC


title: Blood_Platelets_CRC-565


title: Blood_Platelets_GBM-383


title: Blood_Platelets_CRC-556


title: Blood_Platelets_GBM-419


title: Blood_Platelets_GBM-284


title: Blood_Platelets_GBM-394


title: Blood_Platelets_CRC-504


title: Blood_Platelets_CRC-543

value: KRAS


title: Blood_Platelets_CRC-523


title: Blood_Platelets_CRC-546


title: Blood_Platelets_CRC-552


title: Blood_Platelets_CRC-511


title: Blood_Platelets_CRC-531


title: Blood_Platelets_CRC-497


title: Blood_Platelets_CRC-548


title: Blood_Platelets_CRC-524


title: Blood_Platelets_CRC-496


title: Blood_Platelets_CRC-487


title: Blood_Platelets_CRC-466


title: Blood_Platelets_CRC-462


title: Blood_Platelets_CRC-474


title: Blood_Platelets_CRC-459


title: Blood_Platelets_CRC-450


title: Blood_Platelets_CRC-429


title: Blood_Platelets_CRC-374


title: Blood_Platelets_CRC-453


title: Blood_Platelets_CRC-378


title: Blood_Platelets_CRC-357


title: Blood_Platelets_CRC-420


title: Blood_Platelets_CRC-527


title: Blood_Platelets_CRC-351


title: Blood_Platelets_CRC-342


title: Blood_Platelets_CRC-329


title: Blood_Platelets_CRC-463


title: Blood_Platelets_CRC-272


title: Blood_Platelets_CRC-276


title: Blood_Platelets_CRC-258


title: Blood_Platelets_CRC-304


title: Blood_Platelets_CRC-356


title: Blood_Platelets_Chol-341

value: Hepatobiliary


title: Blood_Platelets_Chol-ALK-28


title: Blood_Platelets_Chol-379


title: Blood_Platelets_Chol-292


title: Blood_Platelets_Chol-376


title: Blood_Platelets_CRC-354


title: Blood_Platelets_Chol-410


title: Blood_Platelets_Chol-611


title: Blood_Platelets_Chol-316


title: Blood_Platelets_Chol-442


title: Blood_Platelets_Breast-97

value: Breast

value: HER2+, PIK3CA


title: Blood_Platelets_Breast-ALK-82

value: blood


title: Blood_Platelets_Breast-86


title: Blood_Platelets_Breast-85

value: Triple Negative


title: Blood_Platelets_Breast-61


title: Blood_Platelets_Breast-59


title: Blood_Platelets_Breast-603

value: wt


title: Blood_Platelets_Breast-564


title: Blood_Platelets_Breast-590


title: Blood_Platelets_Breast-60


title: Blood_Platelets_Breast-56


title: Blood_Platelets_Breast-55


title: Blood_Platelets_Chol-460


title: Blood_Platelets_CRC-256


title: Blood_Platelets_Breast-50


title: Blood_Platelets_Breast-48


title: Blood_Platelets_Breast-21


title: Blood_Platelets_Breast-42


title: Blood_Platelets_Breast-33


title: Blood_Platelets_Breast-03


title: Blood_Platelets_Breast-15


title: Blood_Platelets_Breast-08


title: Blood_Platelets_Breast-10


title: Blood_Platelets_Breast-16


title: 22_Control_5hmc_input_rep2

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description: Input control.

data_processing:
Basecalls performed using CASAVA version 1.4.
Aligned with hg19 genome using Bowtie.
Enriched regions identified with spp at low confidence levels, yielding tagAlign files.
High-confidence contrasting bed files generated using the IDR procedure (https://sites.google.com/site/anshulkundaje/projects/idr). Resulting bam files, based on thresholds established by IDR, come from pooled replicates.
Overlapping intervals generated using Bedtools.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: tagAlign files from spp show low-confidence genomic intervals compared with input control.
Supplementary_files_format_and_content: bed files from IDR show high-confidence contrasting genomic intervals enriched as indicated.

source_name: Cerebellar cortex, normal control, input

growth_protocol: Human frozen tissue was obtained from the NICHD Brain and Tissue Bank of Developmental Disorders at the University of Maryland, Baltimore, MD.

extract_protocol:
Genomic DNA was extracted with a DNeasy kit from Qiagen, Inc. Immunoprecipitations were performed on sonicated DNA using the Active Motif MeDIP Kit. 5mC MeDIP was performed with Active Motif mAB #39649 and 5hmC MeDIP was performed with Active Motife mAB #39999 antibodies.
Illumina TruSeq DNA Sample kit, run on an Illumina HiSeq 2500 instrument.

treatment_protocol: Frozen samples were not treated.

value: cerebellar cortex

tag: diagnosis

value: control

tag: age

value: average age 25 yrs

tag: antibody


title: 4A_Control_5hmc_IP_rep3

description: Immunoprecipitated with anti-5hmC.

source_name: Cerebellar cortex, normal control, anti-5hmC antibody


title: 11_Control_5hmc_IP_rep1

description: Immunoprecipitated with anti-5hmC.


title: 4B_Control_5mc_IP_rep1

description: Immunoprecipitated with anti-5mC.

source_name: Cerebellar cortex, normal control, anti-5mC antibody


title: 8B_AT_5mc_IP_rep1

description: Immunoprecipitated with anti-5mC.

source_name: Cerebellar cortex, A-T, anti-5mC antibody

value: ataxia-telangiectasia

value: average age 21 yrs


title: 8A_AT_5hmc_IP_rep3

description: Immunoprecipitated with anti-5hmC.

source_name: Cerebellar cortex, A-T, anti-5hmC antibody


title: wt_ache_2

city: Eggenstein-Leopoldshafen

first: olivier

last: ARMANT

address: Hermann-von-Helmholtz-Platz 1

department: ITG

country: Germany

institute: Karlsruhe Institute of Technology

description: Wild type siblings ache 72hpf

data_processing:
Base calling with RTA v1.13
Alignment with tophat v1.4.1
Quantification made with HTSeq v0.5.3p3
Normalisation and differential expression with DESeq2
Genome_build: zv9
Supplementary_files_format_and_content: Quantification from HTSeq

organism: Danio rerio

source_name: whole larvae

growth_protocol: Zebrafish mutants and wild type siblings grown in standard conditions and medium

extract_protocol:
Trizol total RNA extraction
Stranded TruSeq mRNAseq Illumina

tag: genotype/variation

value: ache WT


title: 21_Control_5hmc_input_rep1

description: Input control.


title: wt_ache_1

description: Wild type siblings ache 72hpf


title: 16_AT_5hmc_IP_rep2

description: Immunoprecipitated with anti-5hmC.


title: 15_AT_5hmc_IP_rep1

description: Immunoprecipitated with anti-5hmC.


title: 24_AT_5hmc_input_rep2

description: Input control.

source_name: Cerebellar cortex, A-T, input


title: ache_mut_2

description: ache mutant 72hpf

value: ache -/-


title: Blood_Platelets_Breast-454

tag: cell type

value: Thrombocytes

tag: patient id

tag: cancer type


title: wt_para_3

description: Wild type siblings paralytico 72hpf

value: hsp90a WT


title: wt_para_2

description: Wild type siblings paralytico 72hpf


title: Blood_Platelets_Breast-100

tag: tissue

tag: batch

tag: mutational subclass


title: 23_AT_5hmc_input_rep1

description: Input control.


title: wt_para_1

description: Wild type siblings paralytico 72hpf


title: para_mut_1

description: paralytico mutant 72hpf


title: 12_Control_5hmc_IP_rep2

description: Immunoprecipitated with anti-5hmC.


title: BD patient, Li-non-responder + Lithium (N2 Li)

data_processing:
Paired end reads from all libraries were mapped to the human reference genome (GRCh37) using STAR version 2.3.0. The assignment of reads to gene regions was performed by htseq-count, version 0.5.4 p5. The raw counts are taken as input for edgeR pacakage for differential gene expression analysis.
Genome_build: GRCh37
Supplementary_files_format_and_content: edgeR.txt: tab-delimitted text file containg cpm of genes in different samples and p-values, logFC for multiple comparisons

source_name: iPSC-derived hippocampal dentate gyrus granule neurons

growth_protocol: Hippocampal dentate gyrus (DG) granule neurons were derived according to Yu et al, Stem Cell Reports 2014

extract_protocol:
total RNA by RNAbee extraction
total RNA, ribosomal depletion, stranded, according to Illumina protocol

treatment_protocol: Lithium Cloride was added to the culture media as described in the manuscript

tag: lithium treated

value: yes

tag: bd patient


title: BD patient, Li-responder + Lithium (R2 Li)

value: Hippocampal dentate gyrus (DG) granule neurons


title: BD patient, Li-non-responder + Lithium (N3 Li)


title: S2_24hpf

description: steif mutant 24hpf


title: BD patient, Li-responder + Lithium (R3 Li)


title: S1_24hpf

description: steif mutant 24hpf


title: BD patient, Li-responder + Lithium (R1 Li)


title: C1_24hpf

description: Wild type siblings steif 24hpf

value: unc45b WT


title: BD patient, Li-non-responder (N2)

value: no


title: C2_24hpf

description: Wild type siblings steif 24hpf


title: WGBS_WT_cerebral_hemisphere

city: hackensack

first: Benjamin

last: Tycko

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

description: WT mouse

data_processing:
Basecalls was performed using illumina CASAVA
Trimming of adaptors, low quality base calls (quality score <30), and exclusion of short reads (<40 bp) using TrimGalore
Alignment against mouse reference genome (Mm10) was performed using Bismark Aligner
Read deduplication was performed using Samtools
Methylation calling was performed using Bismark Methyl Extractor
CpGs with less than 20X coverage were filtered out
Copy numbers were assessed using the ratio between the coverage of each CpG  normalized by the total coverage in DS and WT mice
Differential methylation was assessed using the difference in fractional methylation between DS  and WT mice
For the comparison with human data, only CpGs within a 1kb window of a CpG queried by Illumina 450K BeadChips were considered. For this purpose, Illumina queried CpGs coordinates were converted to mouse genome (mm10) using the LiftOver tool.
Genome_build: Mm10
Supplementary_files_format_and_content: The coverage BigWig files were generated using Bismark Methyl Extractor outputs which provides the read counts for each CpGs, the values  represent total reads count, CpGs with less than 20X coverage were filtered out; the methylation percentage  BigWig files were generated using Bismark Methyl Extractor outputs,   the values  represent the percentage of methylation, CpGs with less than 20X coverage were filtered out;  the copy number BedGraphs were generated using Bismark Methyl Extractor outputs, the values represent the ratio between the coverage normalized by the total coverage in DS and WT mice, CpGs with less than 20X coverage were filtered out ; the differential methylation BedGraphs were generated using Bismark Methyl Extractor outputs,  the values represent the difference in fractional methylation in DS versus WT mice, two differential methylation BedGraphs were generated per DS mouse, one file including all CpGs with more than 20X coverage and one file including only CpGs with more than 20X coverage within a 1kb window of a CpG queried by Illumina 450K BeadChips.

source_name: Bisulfite DNA from whole cerebral hemisphere

extract_protocol:
Genomic DNA (500 ng) was extracted from whole cerebral hemispheres and bisulfite-converted using the EpiTect Bisulfite Kit (Qiagen)
Libraries were prepared according to Illumina's instructions accompanying EpiGnome/TruSeq DNA Methylation kit

value: Whole cerebral hemispheres (with meninges removed)

tag: strain

tag: duplication

tag: phenotype

value: Normal


title: WGBS_Dp(16)1Yey_cerebral_hemisphere

description: Chromosome-engineered mouse model of Down syndrome with sub-chromosomal duplication of the Hsa21 syntenic region on chromosome 16

value: Sub-chromosomal duplication of chr16 (Lipi-Zbtb21)

value: Down syndrome


title: BD patient, Li-non-responder (N1)


title: ache_mut_1

description: ache mutant 72hpf


title: WGBS_Dp(10)1Yey_cerebral_hemisphere

description: Chromosome-engineered mouse model of Down syndrome with sub-chromosomal duplication of the Hsa21 syntenic region on chromosome 10

value: Sub-chromosomal duplication of chr10 (Prmt2-Pdxk)


title: S2_72hpf

description: steif mutant 72hpf


title: BD patient, Li-responder (R2)


title: S1_72hpf

description: steif mutant 72hpf


title: C2_72hpf

description: Wild type siblings steif 72hpf


title: BD patient, Li-responder (R3)


title: BD patient, Li-responder (R1)


title: S2_48hpf

description: steif mutant 48hpf


title: S1_48hpf

description: steif mutant 48hpf


title: Control iPS neurons (C4)


title: C1_72hpf

description: Wild type siblings steif 72hpf


title: para_mut_2

description: paralytico mutant 72hpf


title: BD patient, Li-non-responder + Lithium (N1 Li)


title: C2_48hpf

description: Wild type siblings steif 48hpf


title: Control iPS neurons (C2)


title: BD patient, Li-non-responder (N3)


title: Control iPS neurons (C3)


title: C1_48hpf

description: Wild type siblings steif 48hpf


title: Control iPS neurons (C1)


title: CTCF_ChIPseq_E14_ESC

status: Public on Oct 29 2015

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
SOLiD sequence tags were mapped to the mm9 genome with the MAQ package (V0.7.1, options: -c -n 3, -e 170).
MACS was used to call peaks from the SOLiD data (V1.4.2, options: bw 300, -p 1e-10).
Genome_build: mm9
Supplementary_files_format_and_content: bed

source_name: E14 ESC

growth_protocol: E14Tg2A (E14) ES cells (IB10 cells) were cultured in BRL-conditioned Dulbecco’s Modified Eagle Medium (DMEM with High Glucose, GlutaMAX™, Pyruvate; Life technologies) supplemented with 10% fetal calf serum (FCS), non-essential amino acids (NEAA) (Life technologies), 1000 U/ml leukemia inhibitory factor (LIF) and 2-mercaptoethanol. NPCs were derived from E14 ESCs as described in Peric-Hupkes et al. (2010) and were cultured on gelatin (0.1%) coated plates in DMEM/F12 medium (GIBCO-BRL) with addition of N2-supplement (life technologies), human basic FGF (20ng/ml; peprotech), murine EGF (20ng/ml; peprotech) and penicillin-streptomycin (P/S) (50U/ml - 50ug/ml) (Life technologies).

extract_protocol: Library preparation and SOLiD sequencing were done as described in Mokry et al. (2010)

value: E14 ESC

value: anti-CTCF (Millipore #07-729)


title: CTCF_ChIPseq_E14_NPC

source_name: E14 NPC

value: E14 NPC


title: BRD1-L_ChIPseq_HA

city: Aarhus

first: Tue

last: Fryland

state: Aarhus

address: Bartholins Allé 6

department: Biomedicine

country: Denmark

institute: Aarhus University

data_processing:
fastq files - chastity filtered (low quality reads removed)
filtered reads were trimmed for adapters, groomed for sanger format and aligned to the human genome (hg19) with bowtie for Illumina through the Galaxy portal (https://usegalaxy.org/)
peak calling was performed using the Model-based Analysis of ChIP-Seq v1.4 (MACS), (Zhang et al. 2008) through the Galaxy portal. Settings: distance = 100, and otherwise standard settings
Genome_build: hg19
Supplementary_files_format_and_content: wiggle files were obtained through the Galaxy portal (https://usegalaxy.org/)

extract_protocol:
Chromatin immunoprecipitations of V5 epitope proteins were carried out as described in (Kolodziej et al. 2009) with a few adjustments
DNA libraries were prepared using the ChIP-seq DNA Sample Prep kit (Illumina; IP-102-1001)

tag: cell line

value: HEK293T stably expressing BRD1-L-V5-His6

tag: beads/antibody

value: Anti-HA antibody conjugated agarose beads (Sigma A2095)


title: BRD1-S_ChIPseq_HA

value: HEK293T stably expressing BRD1-S-V5-His6

value: Anti-V5 antibody conjugated agarose beads (Sigma A7345)


title: BRD1-L_ChIPseq_V5


title: OCT4 CLIP-Seq

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Cutadapt was used to trim the sequence TGGAATTCTCGGGTGCCAAGG off of the 3’ end of CLIP-Seq reads with parameter –m 18.  First, bowtie was used to map trimmed reads to the mm9 mouse genome with parameters –best –strata –m1 –n 2 -5 5 –p 50 –S.  Bowtie2  was used to map those reads bowtie failed to map (accounting for deletions caused by UV crosslinking) with parameters -5 5 –sensitive –p 50.  The resulting bowtie and bowtie2 mappings were combined and used for downstream analysis.
Multiple reads were collapsed to one if they had the same chromosome, start, end, and first four nucleotides (barcode) to account for PCR duplicates.  RepeatMasker regions for mm9 were downloaded from the UCSC Genome Browser and subsetted for rRNA repeats.  Reads contacting these regions were discarded.  Remaining reads were separated into + and – strand reads using samtools view.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files represent the denity of strand-separated mapped reads in 50bp bins using MACS with parameters –w –S –space=50 –nomodel –shiftsize=40 –keep-dup=1.

source_name: Embryonic stem cells

growth_protocol: Bio-Oct4 and BirA -expressing murine embryonic stem cells (mESCs) and control mESCs expressing only biotin ligase BirA were grown on irradiated murine embryonic fibroblasts (MEFs). Cells were grown on 0.2% gelatinized (Sigma, G1890) tissue culture plates in ESC media; DMEMKO (Invitrogen, 10829-018) supplemented with 15% fetal bovine serum (Sigma, F4135-500), 1000 U/mL LIF (ESGRO, ESG1106), 100 μM nonessential amino acids (Invitrogen, 11140-050), 2 mM L-glutamine (Invitrogen, 25030-081), 100 U/mL penicillin, 100 μg/mL streptomycin (Invitrogen, 15140-122), and 8 nL/mL of 2-mercaptoethanol (Sigma, M7522).

extract_protocol:
RNA was UV crosslinked to protein using 254nm light, nuclei were purfied and lysed
RNA crosslinked with Bio-Oct4 protein was purified using streptavidin beads (Dynabeads MyOne T1 magnetic beads, Life Technologies 65601) and reverse transcribed into cDNA.

value: BirA


title: BRD1-S_ChIPseq_V5


title: mES_shExosc3

data_processing:
Reads were aligned to a reference genome containing ERCC probes as additional chromosomes using tophat with Refseq genes provided for the -G parameter
Genome_build: mm9 with ERCC probes
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins calculated by MACS 1.4 with shiftsize=40

growth_protocol: Cells were grown on irradiated MEFs and split onto gelatin coated dishes for 2 passages in mES media

extract_protocol:
Total RNA was extracted using mirVana kit (Life Technologies) and ERCC spike-in controls were added to RNA isolated from the same number of control cells and for cells targeted with the shRNA
Total RNA was depleted of ribosomal RNA fraction and recerse-transribed into cDNA  using Illumina TruSeq protocol

value: BirA BioYY1


title: Control CLIP-Seq for OCT4


title: FL_chr8_87495179

description: 4C PCR product

data_processing:
The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank DpnII or NlaIII sites (fragment ends) depending on the first restriction enzyme used, using custom perl scripts. Due to their ambiguous nature in reporting contacts, repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse mm9.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated from the 4C mapping procedure using custom perl scripts. Scores represent the number of reads mapping to a DpnII restriction fragment end.

source_name: fetal liver

growth_protocol: E14Tg2A (E14) ES cells (IB10 cells) were cultured in BRL-conditioned Dulbecco’s Modified Eagle Medium (DMEM with High Glucose, GlutaMAX™, Pyruvate; Life technologies) supplemented with 10% fetal calf serum (FCS), non-essential amino acids (NEAA) (Life technologies), 1000 U/ml leukemia inhibitory factor (LIF) and 2-mercaptoethanol. NPCs were derived from E14 ESCs as described in Peric-Hupkes et al. (2010) and were cultured on gelatin (0.1%) coated plates in DMEM/F12 medium (GIBCO-BRL) with addition of N2-supplement (life technologies), human basic FGF (20ng/ml; peprotech), murine EGF (20ng/ml; peprotech) and penicillin-streptomycin (P/S) (50U/ml - 50ug/ml) (Life technologies). Fetal livers (FL) were isolated from e14.5 embryos by dissection. Single cell suspensions for FL were obtained by filtration through a cell strainer (BD biosciences).

extract_protocol: The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics), remain unchanged. Cells are cross linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS, nuclei are isolated, after which chromatin is digested with DpnII or NlaIII and subsequently ligated. After reversal of the cross links the DNA is purified and treated with the second restriction enzyme treatment (Csp6I or NlaIII, respectively). After a second re-ligation step the sample is purified and a 4C PCR is performed.

treatment_protocol: cells are cross linked using 2% formaldehyde for 10minutes at room temperature in 10%FCS/PBS

value: fetal liver

tag: barcode

value: TCTCTCTCACCTTCAGGATC

tag: bait


title: FL_chr8_87500039

description: 4C PCR product

value: TGCTACTTGCTGTTGGGATC


title: FL_chr8_87436702

description: 4C PCR product

value: TCCGAAAGGACTTCCATG


title: FL_chr8_125946511

description: 4C PCR product

value: CCCTGTACTGGCTCCATG


title: FL_chr7_16880636_TC

description: 4C PCR product

value: TCGGAAGGAAAGGAGAGACATG


title: FL_chr7_16880636_AC

description: 4C PCR product

value: ACGGAAGGAAAGGAGAGACATG


title: FL_chr8_87499257

description: 4C PCR product

value: GTAGCCAAAGAAGCAAGATC


title: FL_chr8_87425935

description: 4C PCR product

value: GTCTCAGCTGAGGCCATG


title: FL_chr7_111348322_AC

description: 4C PCR product

value: ACTTTACATTTGTCCTGACATG


title: FL_chr7_127337731

description: 4C PCR product

value: AATCATACCCAACACCCATG


title: FL_chr7_111060513

description: 4C PCR product

value: CATTCCCCACAGTGTTCATG


title: FL_chr7_111091383

description: 4C PCR product

value: GAGGACAATCAAGATAGATC


title: FL_chr7_127364978

description: 4C PCR product

value: TGCACAAACCACTACACATG


title: FL_chr7_111061651

description: 4C PCR product

value: CTATGCTGCCATGTGATC


title: FL_chr7_110941674

description: 4C PCR product

value: CCCTTATTCAAAGATGCATG


title: FL_chr7_110658856

description: 4C PCR product

value: AGCTGCATGAGGACCTGATC


title: FL_chr7_109639896

description: 4C PCR product

value: fetal liver

value: TGAAAAACTACTGAGGGATC


title: FL_chr6_140738153

description: 4C PCR product

value: AAATGAAATTACAGTGGATC


title: FL_chr6_140749064

description: 4C PCR product

value: CCACATCCCAGGTGCTGATC


title: FL_chr7_110268777

description: 4C PCR product

value: AGCAATCACTTTTACTGATC


title: FL_chr6_83177116

description: 4C PCR product

value: GTAGGTATCTTGTTTCCATG


title: FL_chr6_83165563

description: 4C PCR product

value: CCACCAATCCAGGACATG


title: mES_shLuc

treatment_protocol: shLuc

value: BirA BioYY1


title: FL_chr6_122842449_CG

description: 4C PCR product

value: CGGATGAATGAGACAAAACATG


title: FL_chr6_124854582_TT

description: 4C PCR product

value: TTGGAAATGGCTGAATCCCATG


title: FL_chr6_124366508

description: 4C PCR product

value: GAATTTACCATGCCAAGATC


title: FL_chr6_124399179

description: 4C PCR product

value: ATAGGCCAAATGAGCAGATC


title: FL_chr6_122670095

description: 4C PCR product

value: AATCCTGAAATCTGGATC


title: FL_chr6_122209397

description: 4C PCR product

value: GGCTAATACCTTACTGGATC


title: FL_chr6_122583758

description: 4C PCR product

value: GCGCATACAGTGGGCATG


title: FL_chr4_55664746_TG

description: 4C PCR product

value: TGGGCGAGATGCTTTAGACATG


title: FL_chr4_55543823

description: 4C PCR product

value: GGGGGAAGTCGCTTCATG


title: FL_chr4_129974613_CG

description: 4C PCR product

value: fetal liver

value: CGGAGGAAGCATTGCACCCATG


title: FL_chr4_134519199_GA

description: 4C PCR product

value: GATGCTGCTTCAGAGGATCATG


title: FL_chr4_129974613_GC

description: 4C PCR product

value: GCGAGGAAGCATTGCACCCATG


title: FL_chr4_134435814

description: 4C PCR product

value: CATCCAGATAGCTACCATG


title: FL_chr6_112988569_TC

description: 4C PCR product

value: TCTGAACCTTAACCTAAAGATC


title: FL_chr3_80776364

description: 4C PCR product

value: GATGAAACATTTAATAGATC


title: FL_chr3_36037678

description: 4C PCR product

value: CTCCTCTGGTAGGCTAGATC


title: FL_chr4_134502243

description: 4C PCR product

value: TTTGAAGCCTTCCTGTGATC


title: FL_chr3_35587071

description: 4C PCR product

value: TAACTAACTTGTGCAAGATC


title: FL_chr3_80763070

description: 4C PCR product

value: ATAATTTGTTCAGAATGATC


title: FL_chr3_34670292

description: 4C PCR product

value: GGTCAGGGAGGAAGCTCATG


title: FL_chr3_34580073

description: 4C PCR product

value: AGGATGGTTGTGCACCCATG


title: FL_chr3_146658343

description: 4C PCR product

value: ACACGAACCTGTGGCATG


title: FL_chr3_34548270

description: 4C PCR product

value: GCTCTACAGTCAGCTACATG


title: FL_chr3_113810999

description: 4C PCR product

value: TTGCAAGTGTAATATAGATC


title: FL_chr3_146666992

description: 4C PCR product

value: GCAGGTAGCAGGTTAACATG


title: FL_chr2_151854960_AA

description: 4C PCR product

value: fetal liver

value: AAGTGCAGACAACGGAGATC


title: FL_chr2_131036039_AA

description: 4C PCR product

value: AAGGGTTTGTAGTTCAGCCATG


title: FL_chr3_113822502

description: 4C PCR product

value: TTTATTTAAAGGCACTGATC


title: FL_chr6_122618964

description: 4C PCR product

value: CTTACACATCTACCCTGATC


title: FL_chr1_67202421

description: 4C PCR product

value: TGCCACTTGTTTTTATCATG


title: FL_chr4_55527980

description: 4C PCR product

value: CTCACTGGGTCGCGCATG


title: FL_chr1_67191715

description: 4C PCR product

value: TGATTTCAACCTGCCTCATG


title: FL_chr2_116946594_GT

description: 4C PCR product

value: GTTTGTTATGCTGCCCACGATC


title: FL_chr1_163617684

description: 4C PCR product

value: CCTTCTTCCAGAGGCATG


title: FL_chr1_163330215_AC

description: 4C PCR product

value: ACATAGCAAATCATCCAACATG


title: FL_chr1_163342008_AG

description: 4C PCR product

value: AGCTGCTCAGAGACATTCCATG


title: FL_chr1_163313640_AT

description: 4C PCR product

value: ATCATACCACTCAGTCCTCATG


title: FL_chr19_5850247

description: 4C PCR product

value: AAGCCCTACTCAAGAACATG


title: FL_chr19_5862877

description: 4C PCR product

value: TCCAGTTCCTGGCCTCATG


title: FL_chr19_44637971

description: 4C PCR product

value: GGAGGAAATTAAATTTCATG


title: FL_chr19_44649508

description: 4C PCR product

value: TGACCAGTTTTTCCTACATG


title: FL_chr19_5862688

description: 4C PCR product

value: fetal liver


title: FL_chr18_68634562

description: 4C PCR product

value: CTTCTTAAGAGGAGCTGATC


title: FL_chr18_68634563

description: 4C PCR product


title: FL_chr19_10341018_TA

description: 4C PCR product

value: TATGAAGGCCCTGTTGGATC


title: FL_chr18_67090059

description: 4C PCR product

value: CACACAACTTAGCGCTGATC


title: FL_chr19_10993768

description: 4C PCR product

value: GGTAGGTGACGGGTTAGATC


title: FL_chr3_33724320

description: 4C PCR product

value: TTACATGGAGCTTCTTGATC


title: FL_chr18_66751774

description: 4C PCR product

value: AGTGGTGTCTACTTGGGATC


title: FL_chr18_66123148

description: 4C PCR product

value: AGATGAATGCAGAAACCATG


title: FL_chr18_66084401

description: 4C PCR product

value: TTCTCTTGTCCTAGGTGATC


title: FL_chr18_66084400

description: 4C PCR product


title: FL_chr18_64638642_AA

description: 4C PCR product

value: AAGTCAATCTTGAACAAAGATC


title: FL_chr18_65650559

description: 4C PCR product

value: CCCTCTTCCCAAGATGGATC


title: FL_chr18_65650564

description: 4C PCR product


title: FL_chr18_64910288

description: 4C PCR product

value: TACAAAATCCAGTGGAGATC


title: FL_chr18_64627519

description: 4C PCR product

value: TTTAGTAGATGCACTTGATC


title: FL_chr18_64616255_AT

description: 4C PCR product

value: ATATTTGAAAGTCTTTGGGATC


title: FL_chr1_163629235

description: 4C PCR product

value: TCAGCAACCTAGCATCCATG


title: FL_chr18_63811088

description: 4C PCR product

value: AAGAGATGGAGATTATGATC


title: FL_chr18_63811083

description: 4C PCR product


title: FL_chr18_63651530

description: 4C PCR product

value: GGGACTCAGCTCTATTCATG


title: FL_chr18_61650211

description: 4C PCR product

value: fetal liver

value: TTTTTCAGCAACTTCAGATC


title: FL_chr18_60871192

description: 4C PCR product

value: GGTGCTCTGTGAAAGAGATC


title: FL_chr18_60946693

description: 4C PCR product

value: TGTGTTCATAGTCATGGATC


title: FL_chr18_61650210

description: 4C PCR product


title: FL_chr18_57559968

description: 4C PCR product

value: TTCCTCTCACAAACCAGATC


title: FL_chr18_12394357_TT

description: 4C PCR product

value: TTGCTAAGTAAATGTGTGCATG


title: FL_chr18_58138077

description: 4C PCR product

value: TTACTATGTATATGGCGATC


title: FL_chr18_58138076

description: 4C PCR product


title: FL_chr18_57923652

description: 4C PCR product

value: AGAAGAAATGTTGCAAGATC


title: FL_chr18_56522429

description: 4C PCR product

value: CCAATTCCCTTCACAGGATC


title: FL_chr17_50376256

description: 4C PCR product

value: CCCTAGGGTTCTGCCATG


title: FL_chr18_60622875

description: 4C PCR product

value: AAGTGTAACCTTGCCTCATG


title: FL_chr17_50328697

description: 4C PCR product

value: AAAAGAATCTGGCACAGATC


title: FL_chr18_58857120_AC

description: 4C PCR product

value: ACAAAACACTCCTTCTCCCATG


title: FL_chr16_91646441_TC

description: 4C PCR product

value: TCCGTGGGCACAAACATACATG


title: FL_chr17_49607837

description: 4C PCR product

value: AGAAAGCAGTGTTTGGCATG


title: FL_chr17_50768048

description: 4C PCR product

value: AACAGTGCAGCTTGGAGATC


title: FL_chr17_50430446

description: 4C PCR product

value: AGTTGAAATGCATCCATG


title: FL_chr17_50089370

description: 4C PCR product

value: fetal liver

value: CTTATTGCACAGTTATGATC


title: FL_chr18_61682530_TC

description: 4C PCR product

value: TCTCTTAAGCATTCCTTCCATG


title: FL_chr15_38403138_TG

description: 4C PCR product

value: TGTGGACTAGATGGACTTCATG


title: FL_chr15_8564527_CC

description: 4C PCR product

value: CCAACACTTAGCCCATAACATG


title: FL_chr15_8577349

description: 4C PCR product

value: GAGAAACTGGAAGTCTCATG


title: FL_chr16_91224690

description: 4C PCR product

value: AAGCTGAGAAACTGGATC


title: FL_chr13_100123261_AG

description: 4C PCR product

value: AGCAATCACGACGCTCCACATG


title: FL_chr11_33049124

description: 4C PCR product

value: GTTGAGAGAATTGTTGCATG


title: FL_chr11_77487588_AG

description: 4C PCR product

value: AGAATCCCCGTAACCATACATG


title: FL_chr18_60946694

description: 4C PCR product

value: TGTGTTCATAGTCATGGATC


title: FL_chr18_60871191

description: 4C PCR product

value: GGTGCTCTGTGAAAGAGATC


title: FL_chr11_32609632

description: 4C PCR product

value: GGGAGATATATAAGGGGATC


title: FL_chr11_32224410

description: 4C PCR product

value: GTGGGTTGTAAGGACATG


title: FL_chr11_103194723

description: 4C PCR product

value: GAAGAGCTTCAGGGCACC


title: FL_chr11_32138087

description: 4C PCR product

value: TAGGTCTTGACTGGGATC


title: FL_chr11_31537749

description: 4C PCR product

value: AGCGTTCCCATTACGATC


title: FL_chr11_32149201_AG

description: 4C PCR product

value: fetal liver

value: AGTGGAAAATTAGGTGGGCATG


title: FL_chr11_102755095

description: 4C PCR product

value: CCAGACTGTCACTGCATG


title: FL_chr11_102552165

description: 4C PCR product

value: AACTGCAGCTTGGTGGGATC


title: FL_chr11_102282204_GC

description: 4C PCR product

value: GCGTTGCCTGTAAGTTGTGATC


title: FL_chr11_102762586

description: 4C PCR product

value: CAAGCCACTGCGTCCATG


title: FL_chr11_102295886

description: 4C PCR product

value: CTCCAAGCACTGGGCTGATC


title: FL_chr11_102864574

description: 4C PCR product

value: ACTTCCCATGTGTCTTGATC


title: FL_chr11_102160656

description: 4C PCR product

value: CATCTATGACCTTGTCATG


title: FL_chr10_57473250_AC

description: 4C PCR product

value: ACCCTTGTCCCTCACTTACATG


title: FL_chr11_102273033

description: 4C PCR product

value: CTCCCACAGTGGGTGATC


title: FL_chr10_57463988_AT

description: 4C PCR product

value: ATAATTGAGACTTATTTGGATC


title: FL_chr10_57454886_CG

description: 4C PCR product

value: CGATTACTAAGCTAAGGACATG


title: NPC_chr8_87500025

description: 4C PCR product

source_name: NPC

value: NPC

value: TGCTACTTGCTGTTGGGATC


title: FL_chr10_57568589

description: 4C PCR product

value: GCCCTAGAAAAAATTTCATG


title: FL_chr10_57473241

description: 4C PCR product

value: CCTTGTCCCTCACTTACATG


title: NPC_chr8_125946511

description: 4C PCR product

value: CCCTGTACTGGCTCCATG


title: NPC_chr8_87425935

description: 4C PCR product

value: GTCTCAGCTGAGGCCATG


title: NPC_chr7_143563042_AA

description: 4C PCR product

value: AACCCCACTCTTATCTTCCATG


title: NPC_chr7_111091383_CA

description: 4C PCR product

value: CAGAGGACAATCAAGATAGATC


title: NPC_chr7_110268777_CT

description: 4C PCR product

value: CTAGCAATCACTTTTACTGATC


title: NPC_chr7_110658856_CA

description: 4C PCR product

value: CAAGCTGCATGAGGACCTGATC


title: FL_chr11_102263652_CC

description: 4C PCR product

value: fetal liver

value: CCGGACACCCAGATTACAGATC


title: NPC_chr6_83165563

description: 4C PCR product

value: CCACCAATCCAGGACATG


title: NPC_chr6_124366508

description: 4C PCR product

value: GAATTTACCATGCCAAGATC


title: NPC_chr6_122670095

description: 4C PCR product

value: AATCCTGAAATCTGGATC


title: NPC_chr6_6063986

description: 4C PCR product

value: TCCTCTAGAGGGGCGATC


title: FL_chr10_57515889

description: 4C PCR product

value: AGAAGGAGAGTCACATGATC


title: NPC_chr6_140709308

description: 4C PCR product

value: NPC

value: CAGGAAGAGTAAGCTTGATC


title: NPC_chr6_140715040

description: 4C PCR product

value: CTAGCCAGAAGGTGGCGATC


title: NPC_chr7_111061651

description: 4C PCR product

value: CTATGCTGCCATGTGATC


title: NPC_chr6_122209397_CT

description: 4C PCR product

value: CTGGCTAATACCTTACTGGATC


title: NPC_chr4_134502243

description: 4C PCR product

value: TTTGAAGCCTTCCTGTGATC


title: NPC_chr6_122618964

description: 4C PCR product

value: CTTACACATCTACCCTGATC


title: NPC_chr6_122842449

description: 4C PCR product

value: GATGAATGAGACAAAACATG


title: NPC_chr6_124399179

description: 4C PCR product

value: ATAGGCCAAATGAGCAGATC


title: NPC_chr6_122583758

description: 4C PCR product

value: GCGCATACAGTGGGCATG


title: NPC_chr6_121506642

description: 4C PCR product

value: TTCTGGGAAAACTGACCATG


title: NPC_chr3_35873314_CA

description: 4C PCR product

value: CATCACGTGCAGAAAGGCGATC


title: NPC_chr6_122784770_AG

description: 4C PCR product

value: AGAAGGATGACTTTGAATGATC


title: NPC_chr3_35472989_CA

description: 4C PCR product

value: CAAGTGGCCTCTAACCTCGATC


title: NPC_chr3_36081587_GA

description: 4C PCR product

value: GACCTCTATGAGAAAGAACATG


title: NPC_chr6_100112933

description: 4C PCR product

value: ACGGGATATTGGGGAGCATG


title: NPC_chr4_119634899

description: 4C PCR product

value: TTCTGGCTCAGGAGAGCATG


title: NPC_chr3_33855757_AC

description: 4C PCR product

value: NPC

value: ACAAAGACCAAGTAATTGCATG


title: NPC_chr3_36037678_GA

description: 4C PCR product

value: GACTCCTCTGGTAGGCTAGATC


title: NPC_chr3_33724320_TC

description: 4C PCR product

value: TCTTACATGGAGCTTCTTGATC


title: NPC_chr3_34533727

description: 4C PCR product

value: AGCAGTAGCAGGAGGCCATG


title: NPC_chr3_33691481_GT

description: 4C PCR product

value: GTTCATAGCCTGCCAAGATC


title: NPC_chr7_109639896_AG

description: 4C PCR product

value: AGTGAAAAACTACTGAGGGATC


title: NPC_chr3_146666992

description: 4C PCR product

value: GCAGGTAGCAGGTTAACATG


title: NPC_chr4_101760689

description: 4C PCR product

value: GGGCGAACCTCGGAGATC


title: NPC_chr3_51239266

description: 4C PCR product

value: GAGTCCATTCAGTGTTGATC


title: NPC_chr2_59360368

description: 4C PCR product

value: AGCGTTAGCCAACATGGATC


title: NPC_chr3_146658343

description: 4C PCR product

value: ACACGAACCTGTGGCATG


title: NPC_chr2_59584273_AC

description: 4C PCR product

value: ACCTGAGGAGGTTGCAGTGATC


title: NPC_chr2_58311565

description: 4C PCR product

value: AATTTAAAACAGCCCCGATC


title: NPC_chr2_56970173

description: 4C PCR product

value: GGCCCCCTACTGACAAGATC


title: NPC_chr2_53939033_TC

description: 4C PCR product

value: TCACTCCAGAAGATACAGGATC


title: NPC_chr2_169186200

description: 4C PCR product

value: CGTGATTCTGAGCCCACATG


title: NPC_chr1_71235263

description: 4C PCR product

value: NPC

value: CTGTGAAGGACCATATGATC


title: NPC_chr1_71255030_GA

description: 4C PCR product

value: GAAGAAGCTCACTGGGGGCATG


title: NPC_chr1_74009781

description: 4C PCR product

value: TGTAGGAAGCCTGTGGGATC


title: NPC_chr1_71219536_CT

description: 4C PCR product

value: CTTCTCAGGGACTGAAGACATG


title: NPC_chr1_163629235

description: 4C PCR product

value: TCAGCAACCTAGCATCCATG


title: NPC_chr1_186013204

description: 4C PCR product

value: GATGCTAAGGTATATAGATC


title: NPC_chr19_5862877

description: 4C PCR product

value: TCCAGTTCCTGGCCTCATG


title: NPC_chr19_5862688

description: 4C PCR product


title: NPC_chr19_10993768

description: 4C PCR product

value: GGTAGGTGACGGGTTAGATC


title: NPC_chr19_44649508

description: 4C PCR product

value: TGACCAGTTTTTCCTACATG


title: NPC_chr19_5850247

description: 4C PCR product

value: AAGCCCTACTCAAGAACATG


title: NPC_chr19_22958563

description: 4C PCR product

value: CCGCCCAAATTTCTGATC


title: NPC_chr19_44637971

description: 4C PCR product

value: GGAGGAAATTAAATTTCATG


title: NPC_chr19_22970173

description: 4C PCR product

value: CTCAAGTTCGTGTTGGGATC


title: NPC_chr1_163617684

description: 4C PCR product

value: CCTTCTTCCAGAGGCATG


title: NPC_chr2_55961628

description: 4C PCR product

value: CTCTGTAGCTGGGAAGGATC


title: NPC_chr18_67090059_GT

description: 4C PCR product

value: GTCACACAACTTAGCGCTGATC


title: NPC_chr1_74033465_CT

description: 4C PCR product

value: NPC

value: CTACGTGAGAGAGATACTCATG


title: NPC_chr2_166747949

description: 4C PCR product

value: TGATGAAATTGTCCTTCATG


title: NPC_chr2_53939033

description: 4C PCR product

value: ACTCCAGAAGATACAGGATC


title: NPC_chr18_65650559_GA

description: 4C PCR product

value: GACCCTCTTCCCAAGATGGATC


title: NPC_chr18_66084401_GA

description: 4C PCR product

value: GATTCTCTTGTCCTAGGTGATC


title: NPC_chr18_64627519_AT

description: 4C PCR product

value: ATTTTAGTAGATGCACTTGATC


title: NPC_chr18_64910288_AT

description: 4C PCR product

value: ATTACAAAATCCAGTGGAGATC


title: NPC_chr18_66123148_GA

description: 4C PCR product

value: GAAGATGAATGCAGAAACCATG


title: NPC_chr18_63811083_TG

description: 4C PCR product

value: TGAAGAGATGGAGATTATGATC


title: NPC_chr18_60622875_TA

description: 4C PCR product

value: TAAAGTGTAACCTTGCCTCATG


title: NPC_chr19_10983266

description: 4C PCR product

value: CACTCAGTGGTAGGCAGATC


title: NPC_chr18_58138077_TA

description: 4C PCR product

value: TATTACTATGTATATGGCGATC


title: NPC_chr18_57488404_TA

description: 4C PCR product

value: TAAGTGACTTTATGACTGGATC


title: NPC_chr18_58857120

description: 4C PCR product

value: AAAACACTCCTTCTCCCATG


title: NPC_chr18_56522429_GA

description: 4C PCR product

value: GACCAATTCCCTTCACAGGATC


title: NPC_chr18_37121212

description: 4C PCR product

value: TCTGATTAGCGTGTCAGATC


title: NPC_chr18_37126634

description: 4C PCR product

value: NPC

value: CTGTGCATCTCAGGATGATC


title: NPC_chr17_50768048_TA

description: 4C PCR product

value: TAAACAGTGCAGCTTGGAGATC


title: NPC_chr18_37377867

description: 4C PCR product

value: GTATTGTAAAGTGGTCGATC


title: NPC_chr17_50430446

description: 4C PCR product

value: AGTTGAAATGCATCCATG


title: NPC_chr18_60871192_CT

description: 4C PCR product

value: CTGGTGCTCTGTGAAAGAGATC


title: NPC_chr17_50934747_GC

description: 4C PCR product

value: GCGACGAATTTGTTGTAAGATC


title: NPC_chr18_68634563_TA

description: 4C PCR product

value: TACTTCTTAAGAGGAGCTGATC


title: NPC_chr18_60946694_GA

description: 4C PCR product

value: GATGTGTTCATAGTCATGGATC


title: NPC_chr17_50376256

description: 4C PCR product

value: CCCTAGGGTTCTGCCATG


title: NPC_chr16_91937007_TT

description: 4C PCR product

value: TTGGTCTTGCTTCACTGGCATG


title: NPC_chr17_49607837_CT

description: 4C PCR product

value: CTAGAAAGCAGTGTTTGGCATG


title: NPC_chr17_50328697_CT

description: 4C PCR product

value: CTAAAAGAATCTGGCACAGATC


title: NPC_chr16_91646441

description: 4C PCR product

value: CGTGGGCACAAACATACATG


title: NPC_chr18_61650211_CT

description: 4C PCR product

value: CTTTTTTCAGCAACTTCAGATC


title: NPC_chr16_91314856

description: 4C PCR product

value: TTCTGGGATACTGCCAGATC


title: NPC_chr18_57923652_CT

description: 4C PCR product

value: CTAGAAGAAATGTTGCAAGATC


title: NPC_chr16_91298749

description: 4C PCR product

value: NPC

value: TAAGGAATTCAGCCCAGATC


title: NPC_chr18_37164843

description: 4C PCR product

value: CAGCAGAAGAAAATCAGATC


title: NPC_chr16_91046624_CT

description: 4C PCR product

value: CTAGAGGCCAATGGTGTGGATC


title: NPC_chr12_74319439

description: 4C PCR product

value: CTGCAAACTGCTGTCACATG


title: NPC_chr13_72906854

description: 4C PCR product

value: CTGCAGCTGCAGCTGATC


title: NPC_chr14_77370919

description: 4C PCR product

value: ATGTTTTCTCTGAGAGCATG


title: NPC_chr16_91224690

description: 4C PCR product

value: AAGCTGAGAAACTGGATC


title: NPC_chr16_90323506

description: 4C PCR product

value: TCCAGTCAGTCCTGTGCATG


title: NPC_chr11_33049124_CA

description: 4C PCR product

value: CAGTTGAGAGAATTGTTGCATG


title: NPC_chr11_32041144_CT

description: 4C PCR product

value: CTACAGAGCCCTAGGGTAGATC


title: NPC_chr11_32609632_CG

description: 4C PCR product

value: CGGGGAGATATATAAGGGGATC


title: NPC_chr11_103194723

description: 4C PCR product

value: GAAGAGCTTCAGGGCACC


title: NPC_chr11_31537749_TA

description: 4C PCR product

value: TAAGCGTTCCCATTACGATC


title: NPC_chr11_32138087

description: 4C PCR product

value: TAGGTCTTGACTGGGATC


title: NPC_chr11_102854422

description: 4C PCR product

value: CACTCACTCAAGCCTGGATC


title: NPC_chr12_30481827

description: 4C PCR product

value: GCTGCCTGCCCTCAAAGATC


title: NPC_chr11_102864574

description: 4C PCR product

value: NPC

value: ACTTCCCATGTGTCTTGATC


title: NPC_chr11_102963921_AG

description: 4C PCR product

value: AGCTGGAAGGAATCAAGAGATC


title: NPC_chr11_102762586

description: 4C PCR product

value: CAAGCCACTGCGTCCATG


title: NPC_chr16_91322719

description: 4C PCR product

value: GGATGCTAACAGGGTGGATC


title: NPC_chr11_102552165_CC

description: 4C PCR product

value: CCAACTGCAGCTTGGTGGGATC


title: NPC_chr11_102160656

description: 4C PCR product

value: CATCTATGACCTTGTCATG


title: NPC_chr11_102273033

description: 4C PCR product

value: CTCCCACAGTGGGTGATC


title: NPC_chr11_102348013

description: 4C PCR product

value: CTACAACCTCCTAGCACATG


title: NPC_chr11_102295886_AA

description: 4C PCR product

value: AACTCCAAGCACTGGGCTGATC


title: NPC_chr16_90197456_TG

description: 4C PCR product

value: TGCAGCACTTTGCTTCTACATG


title: NPC_chr10_79638291

description: 4C PCR product

value: GAGCTGTAGCCCATAGGATC


title: NPC_chr10_57515889

description: 4C PCR product

value: AGAAGGAGAGTCACATGATC


title: NPC_chr10_57568589

description: 4C PCR product

value: GCCCTAGAAAAAATTTCATG


title: ESC_chr9_75446737

description: 4C PCR product

value: E14 ESC

value: CATCTTCGGAGCTCCAGATC


title: ESC_chr9_102030688

description: 4C PCR product

value: GCTGGGCCTTCACTAACATG


title: ESC_chr9_101358660

description: 4C PCR product

value: TGAGAACGTGACAAGACATG


title: ESC_chr9_101651911

description: 4C PCR product

value: TAAGTCCTGTGTGAGCCATG


title: NPC_chr10_57190786

description: 4C PCR product

value: NPC

value: GTGTCGGAGGGGCTATGATC


title: ESC_chr8_87509708

description: 4C PCR product

value: TGTGCTTTCCACTCCTGATC


title: NPC_chr10_57142766

description: 4C PCR product

value: AATTTGGTCCTTTTGTGATC


title: ESC_chr9_101269028

description: 4C PCR product

value: TGACACCTTTCAAGTTCATG


title: ESC_chr8_87495179

description: 4C PCR product

value: TCTCTCTCACCTTCAGGATC


title: ESC_chr8_87436702

description: 4C PCR product

value: TCCGAAAGGACTTCCATG


title: ESC_chr8_87425935

description: 4C PCR product

value: GTCTCAGCTGAGGCCATG


title: ESC_chr8_44337413

description: 4C PCR product

value: GATGGCATCCTAAAAGATC


title: ESC_chr8_87500029

description: 4C PCR product

value: TGCTACTTGCTGTTGGGATC


title: ESC_chr8_28391303

description: 4C PCR product

value: CTGTCTAGCCCAGTTTCATG


title: ESC_chr8_28374319

description: 4C PCR product

value: TGGTCCCCGTCTGACATG


title: ESC_chr8_28333424

description: 4C PCR product

value: E14 ESC

value: CATCCTAACACAGGCCATG


title: ESC_chr8_125946511

description: 4C PCR product

value: CCCTGTACTGGCTCCATG


title: ESC_chr7_28835655

description: 4C PCR product

value: GGCGAGGAGCCAATCAGATC


title: ESC_chr8_106812987

description: 4C PCR product

value: AGAGAGAGTTCCAGGAGATC


title: NPC_chr10_57463988

description: 4C PCR product

value: NPC

value: AATTGAGACTTATTTGGATC


title: ESC_chr7_127337731

description: 4C PCR product

value: AATCATACCCAACACCCATG


title: ESC_chr7_127364978

description: 4C PCR product

value: TGCACAAACCACTACACATG


title: NPC_chr10_57168805

description: 4C PCR product

value: GACGGCCATATCTAGGGATC


title: ESC_chr7_127221218

description: 4C PCR product

value: TGGCTGGTTGCAACATCATG


title: ESC_chr7_111348322

description: 4C PCR product

value: TTTACATTTGTCCTGACATG


title: ESC_chr7_16880636

description: 4C PCR product

value: GGAAGGAAAGGAGAGACATG


title: ESC_chr7_110658856

description: 4C PCR product

value: AGCTGCATGAGGACCTGATC


title: ESC_chr7_110941674

description: 4C PCR product

value: CCCTTATTCAAAGATGCATG


title: ESC_chr8_87499257

description: 4C PCR product

value: GTAGCCAAAGAAGCAAGATC


title: ESC_chr7_110268777

description: 4C PCR product

value: AGCAATCACTTTTACTGATC


title: ESC_chr6_140749064

description: 4C PCR product

value: E14 ESC

value: CCACATCCCAGGTGCTGATC


title: ESC_chr7_111060513

description: 4C PCR product

value: CATTCCCCACAGTGTTCATG


title: ESC_chr6_140738153

description: 4C PCR product

value: AAATGAAATTACAGTGGATC


title: ESC_chr7_109639896

description: 4C PCR product

value: TGAAAAACTACTGAGGGATC


title: ESC_chr6_140715040

description: 4C PCR product

value: CTAGCCAGAAGGTGGCGATC


title: ESC_chr7_109655935

description: 4C PCR product

value: ATGAGGTCATAGCTTGCATG


title: ESC_chr6_124854582

description: 4C PCR product

value: GGAAATGGCTGAATCCCATG


title: ESC_chr6_124388747

description: 4C PCR product

value: CCTTCTCTGGACCGGATC


title: ESC_chr6_140709308

description: 4C PCR product

value: CAGGAAGAGTAAGCTTGATC


title: ESC_chr6_124350483

description: 4C PCR product

value: CCTACAATGACTTTATGATC


title: ESC_chr6_122784770

description: 4C PCR product

value: AAGGATGACTTTGAATGATC


title: ESC_chr7_111091383

description: 4C PCR product

value: GAGGACAATCAAGATAGATC


title: ESC_chr6_122618964

description: 4C PCR product

value: CTTACACATCTACCCTGATC


title: ESC_chr6_122496643

description: 4C PCR product

value: GTAGTCTTGGGCCCTGGATC


title: ESC_chr8_28364142

description: 4C PCR product

value: TCAGGGGCTCAAAACATG


title: ESC_chr6_122670095

description: 4C PCR product

value: AATCCTGAAATCTGGATC


title: ESC_chr6_100238781

description: 4C PCR product

value: E14 ESC

value: ATAGCCAAGGAATGTGCATG


title: ESC_chr6_100112933

description: 4C PCR product

value: ACGGGATATTGGGGAGCATG


title: ESC_chr6_121506642

description: 4C PCR product

value: TTCTGGGAAAACTGACCATG


title: ESC_chr6_6063986

description: 4C PCR product

value: TCCTCTAGAGGGGCGATC


title: ESC_chr6_112988569

description: 4C PCR product

value: TGAACCTTAACCTAAAGATC


title: ESC_chr4_55664746

description: 4C PCR product

value: GGCGAGATGCTTTAGACATG


title: ESC_chr4_55671996

description: 4C PCR product

value: TGAGTCAGCTGGTGCTCATG


title: ESC_chr4_46214945

description: 4C PCR product

value: ATATGTTCAGGCCACAGATC


title: ESC_chr6_124399179

description: 4C PCR product

value: ATAGGCCAAATGAGCAGATC


title: ESC_chr4_134539378

description: 4C PCR product

value: AGAACTGAAAACTTGTGATC


title: ESC_chr6_124366508

description: 4C PCR product

value: GAATTTACCATGCCAAGATC


title: ESC_chr4_134435814

description: 4C PCR product

value: CATCCAGATAGCTACCATG


title: ESC_chr4_129974613

description: 4C PCR product

value: GAGGAAGCATTGCACCCATG


title: ESC_chr4_55653556

description: 4C PCR product

value: GAAAACTGCCTTATTTCATG


title: ESC_chr3_51239266

description: 4C PCR product

value: GAGTCCATTCAGTGTTGATC