title: RNA-IPS-Fibr_F_Y-fMG02

value: fibroblast-derived derived iPSCs fMG02


title: Methyl-IPS-Rod_M_Y-3302

status: Public on May 03 2017

type: SRA

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hosipital

library_source: genomic

data_processing:
Basecalls performed using CASAVA
Whole genome bisulfite sequencing (WGBS) data were mapped to mm9 (MGSCv37) by BSMAP2.74 with the following parameters: -z 33 -f 5 -g 3 -r 0 -m 17 -x 600 –u.
raw methylation status was called by Bis-SNP (Version 0.82.2).
Based on bis-SNP results, beta-value of non-abolished and non-estabilished CG have been extracted and converted to bigwig for visualization.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: retina

extract_protocol:
Genomic DNA was isolated from retinal tissues using the DNeasy Blood & Tissue Kit (QIAGEN #69504) according to the manufacturers protocol.
Typically, 2 µg of genomic DNA is used to make WGBS libraries.Whole genome bisulfite sequencing was conducted by the Hudson Alpha research institute for Biotechnology using the Cambridge Epigenetix TrumethylSeq kit (BS workflow) per manufacturer's instructions.

tag: strain

tag: cell type

value: mature retinal-derived iPSCs 3302


title: RNA-Adult-Rod_T_N-MDMX replicate 2

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA
Transcriptome sequencing data were mapped to the mouse genome mm9 (MGSCv37) using in-house software StrongArm.
We required > 30% of exon have > 30x depth. And then classic FPKM have been calculated by cufflink package( version 2.1.1 along with default parameters and “--frag-bias-correct --multi-read-correct“) based on GENCODE annotation vM7.
For Differential Expression analysis between f-iPSC and r-iPSC, we counted reads by HTSEQ(version 0.6.1p1) and used Voom packge(R 3.23, edgeR 3.12.1, limma 3.26.9) for statical tests. CPM(counts per million) have been provided for iPSC RNA-seq
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: tab-delimited text files include FPKM or CPM values for each Sample

molecule: total RNA

extract_protocol:
RNA was extracted from freshly isolated retinas using RNeasy Plus Mini kit (Qiagen #74134). Technologies #Q33120)
Libraries were prepared from ~ 500 ng total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 2500 sequencers according to the manufacturer’s directions (Illumina.)

tag: genotype/variation

tag: age

value: adult


title: RNA-IPS-Rod_I_Y-8601

value: immature retinal-derived iPSCs 8601


title: RNA-IPS-Fibr_F_Y-fG140.03

source_name: fibroblast-derived iPSCs fG140.03

value: fibroblast-derived iPSCs fG140.03


title: RNA-Adult-Rod_T_N-MDMX replicate 1


title: RNA-Adult-Rod_M_N-P21 replicate 2

value: Wild-type

value: postnatal day 21


title: RNA-Adult-Rod_M_N-P21 replicate 1


title: RNA-Adult-Rod_M_N-P14 replicate 2

value: postnatal day 14


title: RNA-Adult-Rod_M_N-P10 replicate 2

value: postnatal day 10


title: mel_rep5

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: single-cell transcriptomics

data_processing:
Cell and molecular barcodes were extracted from read1 and added as tags using Drop-seq tools v1.12.  Sequenced reads were trimmed for polyA stretches, SMART adaptor sequences and low quality filtering using Drop-seq tools v1.12.  Trimmed sequenced reads were mapped to hg38 and mm10 using STAR_2.4.0j.  Mapped reads were sorted using samtools v1.2 and merged with cell and molecular barcodes using Drop-seq tools v1.12.  Gene annotation tags were added and bead synthesis errors were detected and corrected using Drop-seq tools v1.12.  Cumulative fraction of reads per cell was computed using Drop-seq tools v1.12, inflection point was computed using dropbead v.0.2.  The digital gene expression matrices were computed using Drop-seq tools v1.12.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: *txt: Tab-separated text files containing UMI counts per gene and per cell of each sample.
clusters*.txt files generated using Seurat.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Drop-seq of whole embryo

growth_protocol: Egg lays occurred in 2 hour intervals after 3x 1 hour pre-lays; embryos were aged for 6 hours (D. melanogaster) at room temperature.

extract_protocol: Methanol-fixation was adapted from Stöckius et al. 2009 (Nat. Methods). To avoid cell clumping, 8 volumes (800 µl) of methanol p. a. (pre-chilled to -20˚C) were added drop-wise, while gently mixing or vortexing the cell suspension.  Macosko et al. 2015 Cell; Online-Dropseq-Protocol-v.3.1.

tag: developmental stage

value: mixture stage 10 to 17 batch1

tag: fixation

value: 80% methanol/PBS

value: dissociated cells


title: RNA-Adult-Rod_M_N-P10 replicate 1


title: RNA-NRL-Rod_M_N-P7

value: Nrl-GFP

value: postnatal day 7


title: RNA-Adult-Rod_M_N-P14 replicate 1


title: RNA-Adult-Rod_M_N-P7 replicate 2


title: RNA-Adult-Rod_I_N-P3 replicate 2

value: postnatal day 3


title: RNA-Adult-Rod_I_N-P3 replicate 1


title: Methyl-Adult-Rod_E_N-E17.5

value: embryonic day 17.5


title: RNA-Adult-Rod_M_N-P7 replicate 1


title: RNA-Adult-Rod_I_N-P0 replicate 2

value: postnatal day 0


title: RNA-Adult-Rod_I_N-P0 replicate 1


title: RNA-Adult-Rod_E_N-E17.5 replicate 1


title: RNA-Adult-Rod_E_N-E17.5 replicate 2


title: INPUT-IPS-Rod_M_Y-3302

data_processing:
Basecalls performed using CASAVA
BWA (version 0.5.9-r26-dev, default parameter) to align the ChIP-Seq reads to mouse genome mm9(MGSCv37 from Sanger), Picard(version 1.65(1160)) then have been used for marking duplicated reads. Then only non-duplicated reads with have been kept by samtools (parameter “-q 1 -F 1024” version 0.1.18 (r982:295)). We followed the ENCODE criterion to quality control (QC) the data that non-duplicated version of SPP (version 1.11) have been used to draw cross-correlation and calculated relative strand correlation value (RSC) under support of R (version 2.14.0) with packages caTools(version 1.17) and bitops(version 1.0-6) and estimated the fragment size.
We required > 10M unique mapped reads for point-source factor (H3K4me2/3, H3K9/14Ac, H3K27Ac, CTCF, RNAPolII, BRD4) and RSC > 1. We required 20M unique mapped reads for broad markers (H3K9me3, H3K27me3, H3K36me3). We required 10M unique mapped reads for INPUTs and RSC < 1. We noticed H3K4me1 is point-source factor in some stages while broad in other stages so we QC H3K4me1 as broad markers. Then upon manually inspection, the cross-correlation plot generated by SPP, the best fragment size estimated (the smallest fragment size estimated by SPP in all our cases) were used to extend each reads and generate bigwig file to view on IGV (version 2.3.40).
All profiles were manually inspected for clear peaks and good signal to noise separation. For mouse data, all data broad markers with RSC < 0.8 have biological replicates except several samples with one of antibody for H3K9me3(due to availability of outsourcing), we think the quality of those H3K9me3 are good since they show clear peaks and RSC are bigger than most of the H3K9me3 data available in ENCODE or Epigenomics Roadmap.
To estimate the consistence between biological replicates, for point-source factors, MACS2 (version 2.0.9 20111102, option “nomodel” with “extsize” defined as fragment size estimated above) have been used to call peaks with FDR corrected p-value cutoff 0.05(strong peak set) and 0.5(weak peak set) separately, peaks within 100bp have been merged by bedtools (version 2.17.0). We required > 80% of strong peak set from either one replicate overlapping the weak peak set from the other replicate (median percentage 96.8%). For broad peaks, SICER (version 1.1 redundancy threshold 1, window size 200bp, effective genome fraction 0.86, gap size 600bp, FDR 0.00001 with fragment size defined above) has been used for domain calling and we required > 70% of domains called overlapping the domains called from the other replicate(median percentage 89.9%). After confirmed the consistency between replicates, we pool extended reads and generate the final bigwig track for visualization.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigwig

extract_protocol:
ChIP with iDeal ChIP-seq kit (Diagenode # C01010051), MinElute PCR-purification kit (QIAGEN #28006), quantified using the Quant-iT PicoGreen ds DNA assay (Life Technologies #Q33120)
Libraries were prepared from 5-10 ng DNA using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext High-Fidelity 2x PCR Master Mix according to the manufacturer’s instructions (New England Biolabs, Ipswich, MA) with the following modifications: A 1:1 Ampure cleanup was added after adaptor ligation a total of 2 times.

tag: chip antibody


title: RNA-mESC-Eb5_E_Y-Eb5

source_name: mouse embryonic stem cell

value: mouse embryonic stem cell


title: INPUT-IPS-Rod_I_Y-8601


title: INPUT-mESC-Eb5_E_Y-Eb5


title: INPUT-Adult-Rod_M_N-WTM11 replicate 2

value: adult 11 month


title: INPUT-Adult-Rod_T_N-MDMX replicate 1

value: p107 minus minus MDMXTg


title: INPUT-Adult-Rod_M_N-P21 replicate 4


title: INPUT-IPS-Fibr_F_Y-fG140.03


title: INPUT-IPS-Fibr_F_Y-fG140.04

source_name: fibroblast-derived iPSCs fG140.04

value: fibroblast-derived iPSCs fG140.04


title: INPUT-IPS-Fibr_F_Y-fMG02

source_name: fibroblast-derived iPSCs fMG02

value: derived iPSCs fMG02


title: INPUT-Adult-Rod_M_N-WTM11 replicate 1


title: INPUT-Adult-Rod_M_N-P14 replicate 1


title: INPUT-IPS-Fibr_F_Y-fMG03

source_name: fibroblast-derived iPSCs fMG03

value: derived iPSCs fMG03


title: INPUT-Adult-Rod_M_N-P14 replicate 2


title: INPUT-Adult-Rod_M_N-P21 replicate 2

value: postnatal day 21


title: INPUT-Adult-Rod_M_N-P10 replicate 1


title: INPUT-Adult-Rod_M_N-P7 replicate 2


title: INPUT-Adult-Rod_M_N-P10 replicate 2


title: INPUT-Adult-Rod_M_N-P7 replicate 3


title: INPUT-Adult-Rod_M_N-P7 replicate 1


title: INPUT-IPS-Rod_M_Y-7602

value: mature retinal-derived iPSCs 7602


title: INPUT-Adult-Rod_M_N-P21 replicate 1


title: INPUT-Adult-Rod_I_N-P0 replicate 1


title: INPUT-Adult-Rod_E_N-E14.5 replicate 5

value: embryonic day 14.5


title: INPUT-Adult-Rod_E_N-E14.5 replicate 1


title: INPUT-Adult-Rod_I_N-P3 replicate 1


title: RNAPolII-AB1-IPS-Rod_M_Y-7602


title: INPUT-Adult-Rod_I_N-P0 replicate 2


title: RNAPolII-AB1-IPS-Rod_M_Y-3302

value: mature retinal-derived iPSCs 3302


title: INPUT-Adult-Rod_E_N-E17.5 replicate 1


title: INPUT-Adult-Rod_I_N-P0 replicate 4


title: RNAPolII-AB1-IPS-Rod_I_Y-8601

value: immature retinal-derived iPSCs 8601


title: INPUT-Adult-Rod_M_N-P10 replicate 3

value: postnatal day 10


title: RNAPolII-AB1-IPS-Fibr_F_Y-fMG03


title: RNAPolII-AB1-Adult-Rod_M_N-WTM11 replicate 1


title: INPUT-Adult-Rod_I_N-P3 replicate 2


title: RNAPolII-AB1-mESC-Eb5_E_Y-Eb5


title: RNAPolII-AB1-Adult-Rod_M_N-P21 replicate 1


title: RNAPolII-AB1-Adult-Rod_M_N-P14 replicate 1

value: postnatal day 14


title: RNAPolII-AB1-Adult-Rod_T_N-MDMX replicate 2


title: RNAPolII-AB1-IPS-Fibr_F_Y-fG140.04


title: RNAPolII-AB1-IPS-Fibr_F_Y-fG140.03

value: fibroblast-derived iPSCs fG140.03


title: RNAPolII-AB1-Adult-Rod_I_N-P0 replicate 1


title: RNAPolII-AB1-Adult-Rod_I_N-P3 replicate 1

value: postnatal day 3


title: RNAPolII-AB1-Adult-Rod_M_N-P7 replicate 1

value: postnatal day 7


title: RNAseq_RA-d6-3

city: Stanford

first: Zhana

last: Duren

state: CA

address: 318 Campus Drive

institute: Stanford university

description:
Retinoic-acid induction
RNA-seq.txt

data_processing:
RNA-seq: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie.
RNA-seq: Fregments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks.
ATAC-seq: Reads are mapped to mm9 by ATAC-seq pipeline described in https://www.encodeproject.org/atac-seq/.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Bed file for open peak region

growth_protocol: mESC cells R1 were grown in mESC medium supplemented with 15% Knockout Serum Replacement and 1,000 U/ml of LIF. mESCs were differentiated using the handing drop method for 48 hours. Then, embryoid bodies (EBs) were collected for further treatment.

extract_protocol:
Total RNA were extracted using Qiagen RNeasy mini kit.
RNA-seq library were constructed using the NEBNext Ultra RNA Library Prep kit for Illumina. ATAC-seq library were constructed using Tn5 transposase, followed by PCR amplification.

treatment_protocol: EBs were placed in the well of a 6-well ultra-low attachment plate with fresh differentiation medium containing 0.5 mM retinoic acid (RA) for up to 6 days, with the medium being changed daily.

tag: cell line

tag: induced with


title: ATACseq_RA-d6_1

description:
Retinoic-acid induction
RAd6_sorted.bed

value: 0.5 mM retinoic acid (RA) for up to 6 days


title: ATACseq_RA-d6_2

description:
Retinoic-acid induction
RAd6_sorted.bed

value: mouse embryonic stem cell


title: RNAseq_RA-d6-2

description:
Retinoic-acid induction
RNA-seq.txt


title: ATACseq_RA-d6_3

description:
Retinoic-acid induction
RAd6_sorted.bed


title: RNAseq_RA-d6-1

description:
processed data file:
RNA-seq.txt


title: RNA-Adult-Rod_E_N-E14.5 replicate 2

value: Wild-type


title: RNAPolII-AB1-Adult-Rod_E_N-E14.5 replicate 1


title: RNAPolII-AB1-IPS-Fibr_F_Y-fMG02


title: H3K9me3-AB1-mESC-Eb5_E_Y-Eb5


title: RNAPolII-AB1-Adult-Rod_M_N-P10 replicate 1


title: RNAPolII-AB1-Adult-Rod_E_N-E17.5 replicate 1

value: embryonic day 17.5


title: H3K9me3-AB1-IPS-Rod_M_Y-7602


title: H3K9me3-AB1-IPS-Fibr_F_Y-fG140.04

value: fibroblast-derived iPSCs fG140.04


title: H3K9me3-AB1-IPS-Fibr_F_Y-fMG03


title: H3K9me3-AB1-IPS-Fibr_F_Y-fG140.03


title: H3K9me3-AB1-IPS-Fibr_F_Y-fMG02

value: derived iPSCs fMG02


title: H3K9me3-AB1-Adult-Rod_M_N-P14 replicate 1


title: H3K9me3-AB1-Adult-Rod_M_N-WTM11 replicate 1

value: adult 11 month


title: H3K9me3-AB1-Adult-Rod_M_N-P21 replicate 1

value: postnatal day 21


title: H3K9me3-AB1-Adult-Rod_T_N-MDMX replicate 2

value: p107 minus minus MDMXTg


title: H3K9me3-AB1-Adult-Rod_M_N-P7 replicate 1


title: H3K9me3-AB1-Adult-Rod_I_N-P3 replicate 1


title: H3K9me3-AB1-Adult-Rod_I_N-P0 replicate 1

value: postnatal day 0


title: H3K9me3-AB1-Adult-Rod_E_N-E17.5 replicate 1


title: H3K9me3-AB1-Adult-Rod_E_N-E14.5 replicate 1

value: embryonic day 14.5


title: H3K9-14Ac-AB3-IPS-Rod_M_Y-7602

value: mature retinal-derived iPSCs 7602


title: H3K9-14Ac-AB3-IPS-Fibr_F_Y-fMG02


title: H3K9-14Ac-AB3-IPS-Rod_M_Y-3302

value: mature retinal-derived iPSCs 3302


title: H3K9-14Ac-AB3-IPS-Rod_I_Y-8601

value: immature retinal-derived iPSCs 8601


title: H3K9-14Ac-AB3-mESC-Eb5_E_Y-Eb5


title: H3K9-14Ac-AB3-IPS-Fibr_F_Y-fMG03

value: derived iPSCs fMG03


title: H3K9me3-AB1-IPS-Rod_I_Y-8601


title: H3K9me3-AB1-IPS-Rod_M_Y-3302


title: H3K9-14Ac-AB3-IPS-Fibr_F_Y-fG140.04


title: H3K9-14Ac-AB3-IPS-Fibr_F_Y-fG140.03

value: fibroblast-derived iPSCs fG140.03


title: CAP-H +dox rep3

city: Melbourne

first: Tao

last: Zhang

state: Vic

address: Flemington Road, Parkville

department: Chromosome Research

country: Australia

institute: Murdoch childrens research institute

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were aligned to the Ensembl 73 (galGal4) version of the chicken genome with TopHat version 2.0.8b with options --read-realign-edit-dist 0 -o tophat2_RNASEQ_WT_out --mate-std-dev 50 --solexa1.3-quals -p 10 --bowtie-n.
Following quality test using FASTQC. Differential expression of genes was analyzed using the Bioconductor v2.3 package edgeR v3.2.3 (Robinson, McCarthy et al., 2010). Tag enrichment in NCBI RefSeq genes was calculated (Pruitt, Tatusova et al., 2012) between dox-treated (CAP-H OFF) and untreated cells (CAP-H ON) using edgeR exact test with tag-wise dispersion estimation. p-values were calculated and corrected using the Benjamini-Hochberg method.
Genome_build: galGal4
Supplementary_files_format_and_content: tab-delimited text files including read counts for each sample. logFC, logCPM and FDR values between CAP-H ON and CAP-H OFF cells from EdgeR are available in the file CAP-H DE.txt.

organism: Gallus gallus

growth_protocol: Chicken lymphoma B DT40 cell culture was performed as described previously (Buerstedde & Takeda, 1991).

extract_protocol:
Total RNA samples were extracted using a mirVanaTM miRNA Isolation Kit (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols, which were performed by Macrogen (South Korea).

treatment_protocol: Chicken DT40 CAP-H KO cells were treated with or without dox (100 ng/ml) for 36 h.

value: lymphoma B cell line

tag: genotype

value: CAP-H off


title: CAP-H -dox rep3

value: CAP-H on


title: CAP-H -dox rep2


title: CAP-H +dox rep1


title: H3K9-14Ac-AB3-Adult-Rod_M_N-WTM11 replicate 1


title: CAP-H -dox rep1


title: H3K9-14Ac-AB3-Adult-Rod_M_N-P21 replicate 2


title: Fc_rep1

city: Durham

first: Gregory

last: Crawford

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

data_processing:
Single-end basecalls were done by using Illumina CASAVA 1.3 software.
First 20 bp of Dnase-seq raw reads were mapped to hg19 with bowtie-0.12.9, with 2 mismatches allowed, to generate bam files, then bam files were converted to bed file by bedtools. After removing PCR artifacts bigWig files were created by using MACS2(version 2.1.0) .
Genome_build: hg19
Supplementary_files_format_and_content: peak calls

organism: Homo sapiens

source_name: Fibroblast cells transfected with vectors carrying MyoD gene

growth_protocol: Primary human dermal fibroblasts (Catalog ID: GM03348) were obtained from Coriell Institute (Camden, New Jersey) and were maintained in DMEM supplemented with 10% FBS and 1% penicillin streptomycin. All cells were cultured at 37 °C with 5% CO2. Three biological replicates of both the parental fibroblast cells and transduced fibroblast cells were were harvested on different days. Four replicates of Myoblasts were originally sampled and grown from four different patients, as described and published previously (PMID: 26041816).

extract_protocol:
Cells were Lysed and nuclei were digested according to the publication PMID: 20150147.
Libraries were prepared according to the publication PMID: 20150147.

treatment_protocol: Fibroblasts cells were transfected with 20 µg of transfer vector(Tet-ON lentivirus that expresses a 3xFlag-tagged full-length MYOD1 cDNA ), 6 µg of pMD2G, and 10 µg psPAX2 using a calcium phosphate transfection. The media was changed 12-14 hours post transfection. The viral supernatant was collected 24 and 48 hours after this media change and pooled. For transduction, the cell medium was replaced with viral supernatant supplemented with 4 μg/mL polybrene. The viral supernatant was changed 24-48 hours later.

tag: transduced gene

value: human MyoD

value: Fibroblast cells


title: Fc_rep2


title: WaplKO_rep2

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Library strategy: ESS
Insertion sites were mapped by aligning the deep sequencing reads to the human genome (hg19) using bowtie (Langmead et al., 2009) allowing for a single mismatch.
Reads from the HiSeq 2500 (65bp) were cropped to 50 bp similar to the output for the HiSeq 2000 runs
Unique aligned reads were subsequently assigned to Refseq gene coordinates using Bedtools (Quinlan and Hall, 2010).
Overlapping gene regions on opposite strands were disregarded (since orientation bias in that region is not readily interpretable), while genes with overlapping regions on the same strand the names were concatenated.
For each replicate a binomial test for the distribution of sense and antisense orientation insertions was performed.
Genome_build: hg19
Supplementary_files_format_and_content: Screen-results. Columns are Gene-name, Fwd Integrations, Rev Integrations, P-value, and FDR-corrected P-value.

source_name: HAP1 cells

growth_protocol: One day prior to infection, ∆WAPL cells were seeded with 40 million cells in a single T175 flask.

extract_protocol:
Genomic DNA was isolated from 30 million sorted cells using a DNA mini kit (Qiagen) with the lysis step occurring overnight at 56 o C for decrosslinking.The gene trap insertion sites were amplified using a LAM-PCR procedure as described (Blomen et al., 2015).
Using a biotinylated primer in the gene trap cassette, single-stranded DNA (ssDNA) products were generated for 120 cycles, captured on magnetic beads, a pre-adenylated ssDNA linker ligated to the 3’ end, and a final round of exponential amplificationusing a primer containing Illumina sequencing compatible overhangs at the end of the LTR andin the ssDNA linker.

treatment_protocol: Infection occurred over the consecutive days using the pelleted gene trap retrovirus in the presence of 8 ug/ml protamine sulfate. The mutagenized ∆WAPL cells were passaged for 10-12 days following the last infection with the mutagen, collected following dissociation using trypsin-EDTA by pelleting, and fixed using fix buffer I (BD biosciences).

value: WaplKO


title: H3K9-14Ac-AB3-Adult-Rod_T_N-MDMX replicate 1


title: input DNA

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

data_processing:
Illumina HiSeq sequencing pipeline Basecalling RTA version 1.12
The reads were aligned to the human reference genome (hg19) using Bowtie software.
Only uniquely mapped reads were retained.
STAT3 binding sites in Th17 relative to input DNA were identified using MACS tool with the default parameter settings.
Genome_build: hg19
Supplementary_files_format_and_content: The locations of the detected STAT3 binding sites in Th17.

source_name: Th17 cells

growth_protocol: Umbilical cord blood was collected from healthy neonates born in Turku University Hospital, Hospital District of Southwest Finland. Mononuclear cells were isolated with Ficoll-Paque (Amersham Biosciences) gradient centrifugation, and CD4+ cell population was purified using magnetic beads (Dynal CD4 Positive Isolation Kit, Invitrogen) according to manufacturers instructions.

extract_protocol:
Cells were fixed using formaldehyde solution, lysed and sonicated to obtain chromatin fragments of 100-500bp size. The sonicated chromatin was then subjected to immunoprecipitation with polyclonal anti-STAT3 antibody (rabbit polyclonal αSTAT3 3291L, Cell Signaling Technology). The STAT3 bound chromatin was isolated using Dynal magnetic beads coated with secondary antibody anti-rabbit IgG (Dynal Biotech). The immunoprecipitated DNA was eluted, reverse crosslinked and purified using Qiagen minielute columns. The sample preparation for Solexa sequencing was performed according to Illumina's recommendations by Illumina service provider, Fasteris Life Sciences, Switzerland. Briefly, the ChIP DNA was end-repaired with T4 DNA polymerase, Klenow and PNK, and after purification with Qiagen minielute columns, a 3-´A was added using Klenow (exo-). The -A tailed DNA samples were purified and ligated with Illumina paired ends adaptors. After adapter ligation, fragments of size range of 200-300bp were purified from agarose gel and subjected to PCR amplification using Phusion polymerase with paired ends primers for 18 cycles. The libraries were quantified using PicoGreen Assay (Q-bit Invitrogen) before in situ amplification on the Illumina Cluster Station to generate DNA colonies according to the manufacturer's standard recommended protocol. Sequencing was performed on an Illumina Genome Analyzer “GAII” for 36 cycles using sequencing kit V-1.0 with scanning buffers V-2.0 and GA data analysis pipeline 1.0rc4. Each library was sequenced in a single read channel that produced between 10 to15 million reads.
The sample preparation for Solexa sequencing was performed according to Illumina's recommendations by Illumina service provider, Fasteris Life Sciences, Switzerland. Briefly, the ChIP DNA was end-repaired with T4 DNA polymerase, Klenow and PNK, and after purification with Qiagen minielute columns, a 3-´A was added using Klenow (exo-). The -A tailed DNA samples were purified and ligated with Illumina paired ends adaptors. After adapter ligation, fragments of size range of 200-300bp were purified from agarose gel and subjected to PCR amplification using Phusion polymerase with paired ends primers for 18 cycles. The libraries were quantified using PicoGreen Assay (Q-bit Invitrogen) before in situ amplification on the Illumina Cluster Station to generate DNA colonies according to the manufacturer's standard recommended protocol. Sequencing was performed on an Illumina Genome Analyzer “GAII” for 36 cycles using sequencing kit V-1.0 with scanning buffers V-2.0 and GA data analysis pipeline 1.0rc4. Each library was sequenced in a single read channel that produced between 10 to15 million reads.

treatment_protocol: Isolated CD4+ T cells were activated with plate-bound anti-CD3 (750 ng/24well culture plate and 3.75ug/ 6 well culture plate, Immunotech, Marseille, France) and soluble anti-CD28 (1 μg/ml, Immunotech) in X-vivo 20 serum free medium (Lonza, Basel, Switzerland) supplemented with 2 mM L-Glutamine (#G7513, Sigma, St. Louis, MO, USA), and 50 U/ml Penicillin and cultured at 37°C in 5 % CO2. IL-6 (20 ng/ml, Roche, Basel, Switzerland), IL-1β (10 ng/ml) and TGFβ (10 ng/ml) in the presence of neutralizing anti-IFNγ (1 μg/ml) and anti-IL4 (1 μg/ml) were used to initiate Th17 polarization. Control Th0 cells were cultured in a medium containing only the neutralizing antibodies. All cytokines and neutralizing antibodies were purchased from R&D Systems (Minneapolis, MN, USA) unless otherwise stated.

tag: antibody


title: WaplKO_rep3


title: WaplKO_rep1


title: wt_Dam-Lamin_Rep2

description: wt Hap1 cell expressing Dam:Lamin fusion protein

data_processing:
Library strategy: DamID
All reads were processed by removing the adapter sequences: "GGTCGCGGCCGAG" or "CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAG" using cutadapt version 1.9.1
Reads were mapped against the reference human genome hg19 using bowtie2 with default parameters (except for --local and -k 3)
Reads that mapped in multiple locations were discarded
We calculated the coverage of reads per GATC fragment using the program htseq-count. GATC fragments were obtained by digesting in-vitro the reference genome with in-house scripts. We excluded un-mappable regions bigger than 5Kb
We concatenated GATC fragments in 50Kb windows (each window starting and finishing in a "GATC").
The DamID profiles were calculated as the log2 ratio of the coverage of reads in the 50Kb-extended GATC fragments between Lamin-Dam and Dam-only
Genome_build: hg19
Supplementary_files_format_and_content: *.GATCcounts.txt contains total read count per GATC: Format is as followed:  "GATC ID": "Chr" : "Start Position" : "End Position" : "Total read count at the GATC"

growth_protocol: HAP1 cells (Carette et al., 2011) were cultured in IMDM (Invitrogen) supplemented with 10% FCS (Clontech), 1% Penicillin-Streptomycin (Invitrogen) and 1% Ultraglutamin (Lonza).

extract_protocol:
DNA isolation was performed using the Isolate II Genomic DNA isolation kit
DNA was digested for 4 hours at 37˚C by DpnI. Adapters were ligated overnight at 16˚C and products were amplified by PCR. DNA was isolated using a QIAquick PCR Purification kit and sheared using the Covaris S2 instrument. Library was prepared using a KAPA HTP Library preparation kit

treatment_protocol: 300.000 cells were plated per 6 well and transduced with virus encoding either Dam only or Lamin-Dam

value: WT

tag: dam

value: LaminB - Dam protein fusion

tag: replicate


title: deltaWapl-mut3_Dam-Lamin_Rep2

description: WAPL KO Hap1 cell expressing Dam:Lamin fusion protein


title: H3K9-14Ac-AB3-Adult-Rod_M_N-P21 replicate 1

value: postnatal day 21


title: deltaWapl-mut1_Dam-Lamin_Rep2


title: H3K9-14Ac-AB3-Adult-Rod_M_N-P14 replicate 2

value: postnatal day 14


title: deltaWapl-mut3_Dam-Only_Rep2

description: WAPL KO Hap1 cell expressing soluble Dam

value: Dam


title: deltaWapl-mut1_Dam-Only_Rep2


title: H3K9-14Ac-AB3-Adult-Rod_M_N-P14 replicate 1


title: H3K9-14Ac-AB3-Adult-Rod_M_N-P10 replicate 2

value: postnatal day 10


title: wt_Dam-Only_Rep2

description: wt Hap1 cell expressing soluble Dam


title: deltaWapl-mut3_Dam-Lamin_Rep1


title: H3K9-14Ac-AB3-Adult-Rod_M_N-WTM11 replicate 2

value: adult 11 month


title: deltaWapl-mut1_Dam-Lamin_Rep1


title: Fc_rep3


title: H3K9-14Ac-AB3-Adult-Rod_M_N-P7 replicate 2

value: postnatal day 7


title: STAT3 ChIP-seq

tag: catalog#/vendor

value: rabbit polyclonal αSTAT3 3291L, Cell Signaling Technology


title: wt_Dam-Lamin_Rep1


title: deltaWapl-mut3_Dam-Only_Rep1


title: H3K9-14Ac-AB3-Adult-Rod_M_N-P10 replicate 1


title: deltaWapl-mut1_Dam-Only_Rep1


title: H3K9-14Ac-AB3-Adult-Rod_T_N-MDMX replicate 2

value: p107 minus minus MDMXTg


title: H3K9-14Ac-AB3-Adult-Rod_M_N-P7 replicate 1


title: HOK16B_VLV #3 (mRNA)

city: los angeles

first: Danyang

last: Gong

address: 650 Charles Young Dr. So.

department: pharmacology

institute: UCLA

description:
A13
cell.xlsx

data_processing:
TopHat under default parameter
Genome_build: hg38, KSHV JSC-1 clone BAC16
Supplementary_files_format_and_content: counts

source_name: HOK16B cells

growth_protocol: HOK16B cells

extract_protocol:
Trizol for total RNA, and then oligodT beads for polyA RNA
method based on ScriptSeq mRNA-Seq library preparation kit (Epicentre)

treatment_protocol: Treat with or without KSHV VLV for one days

value: Oral epithelial cell

tag: virus

value: no


title: HOK16B_VLV #2 (mRNA)

description:
A4
cell.xlsx


title: HOK16B_VLV #4 (mRNA)

description:
A14
cell.xlsx


title: HOK16B_VLV #1 (mRNA)

description:
A3
cell.xlsx


title: H3K9-14Ac-AB3-Adult-Rod_I_N-P3 replicate 2

value: postnatal day 3


title: HOK16B_Ctl #4 (mRNA)

description:
A12
cell.xlsx


title: H3K9-14Ac-AB3-Adult-Rod_I_N-P0 replicate 2

value: postnatal day 0


title: HOK16B_Ctl #1 (mRNA)

description:
A1
cell.xlsx


title: HOK16B_Ctl #2 (mRNA)

description:
A2
cell.xlsx


title: HOK16B_Ctl #3 (mRNA)

description:
A11
cell.xlsx


title: H3K9me3-AB1-Adult-Rod_M_N-P10 replicate 1


title: H3K9-14Ac-AB3-Adult-Rod_I_N-P0 replicate 1


title: SP140_4h_WCE

city: Boston

first: Shannan

last: Ho Sui

state: Massachusetts

address: 401 Park Drive, Level 3 East

department: Biostatistics

institute: Harvard T.H. Chan School of Public Health

data_processing:
Illumina Casava1.7 software used for basecalling. Bcbio-nextgen was used for the analysis.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie2 v2.2.7. Alignments were sorted and filtered to retain only uniquely mapping reads using sambamba v0.5.9
ChIP peaks were called using MACS2 v2.1.0 using the --broadpeak option.
Peaks were filtered such that only peaks with fold enrichment > 3.5 were retained.
Genome_build: hg19
Supplementary_files_format_and_content: All coordinates are based on hg19. BED Format: chromosome,chromstart,chromend,peak name,macs2 integer score

source_name: primary human macrophages

growth_protocol: PBMCs were re-suspended in X-VIVO medium (Lonza) containing 1% penicillin/streptomycin (Gibco) and incubated at 37oC, 5% CO2 for 1 h to adhere to the tissue culture dish. After 1 h, adherent cells were washed 3 times with PBS and differentiated in complete X-VIVO medium containing 100ng/mL human M-CSF (Peprotech) for 7 days at 37oC, 5% CO2. On day 4, cultures were supplemented with one volume of complete X-VIVO medium containing 100ng/mL human M-CSF.

extract_protocol:
Mononuclear cells were isolated by density gradient centrifugation of PBS-diluted buffy coat/blood (1:2) over Lymphoprep (Stemcell Tech). Following RBC lysis with red blood cell lysis buffer (Sigma) and 3 washes in PBS, mononuclear cells were collected as PBMC.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: On day 7, cells were re-plated and polarized with of IFNγ (100ng/mL,Peprotech) for 24 h, followed by a 4h stimulation by LPS (100ng/mL)

value: macrophage

tag: lps treatment

value: LPS treated, 100ng/mL, 4h


title: H3K9-14Ac-AB3-Adult-Rod_E_N-E17.5 replicate 2

tag: strain

value: embryonic day 17.5


title: SP140_0h_IP

tag: cell type

value: no LPS treatment


title: SP140_0h_WCE


title: wt_Dam-Only_Rep1

description: wt Hap1 cell expressing soluble Dam

value: WT


title: H3K9-14Ac-AB3-Adult-Rod_E_N-E14.5 replicate 2

value: embryonic day 14.5


title: H3K9-14Ac-AB3-Adult-Rod_E_N-E17.5 replicate 1


title: Donor 2 SP140 KD 4h LPS

first: Lorena

last: Pantano

state: MA

address: 655 Huntington Ave

institute: Harvard Chan School of Public Health

description: LPS treated, 100ng/mL, 4h

data_processing:
Illumina Casava1.7 software used for basecalling. Bcbio-nextgen was used for the analysis.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR and to the transcriptome with sailfish
Gene counts were produced by featureCounts and sailfish
Differential expression analysis was done by DESeq2
All commands used in this analysis is stored at gihub: https://github.com/hbc/kjeffrey_CD_RNAseq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample.

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted with a Qiagen Rneasy Mini Kit (including DNAse treatment and elution in 40ul EB)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1.5x106 differentiated macrophage cells were transfected with a final siRNA concentration of 200nM using the HiPerfect (Qiagen) fast forward protocol in medium containing 100ng/mL M-CSF and 100ng/ML IFNg (peprotech). Cells were incubated at 37oC for an additional 48h and were subsequently stimulated (or not) with LPS (Sigma, 100 ng/mL).

tag: disease status

value: unknown

value: PBMC derived macrophage

tag: sirna


title: H3K9-14Ac-AB3-Adult-Rod_E_N-E14.5 replicate 1

tag: age


title: Donor 2 control 4h LPS

description: LPS treated, 100ng/mL, 4h


title: Donor 1 SP140 KD 4h LPS

description: LPS treated, 100ng/mL, 4h


title: Donor 1 control 4h LPS

description: LPS treated, 100ng/mL, 4h


title: Donor 1 SP140 KD 0h

description: no LPS treatment


title: Donor 2 SP140 KD 0h

description: no LPS treatment


title: H3K9-14Ac-AB3-Adult-Rod_I_N-P3 replicate 1


title: Methyl-FW21

data_processing:
Basecalls performed using CASAVA
Whole genome bisulfite sequencing (WGBS) data were mapped to hg19(GRCh37) by BSMAP2.74 with the following parameters: -z 33 -f 5 -g 3 -r 0 -m 17 -x 600 –u.
raw methylation status was called by Bis-SNP (Version 0.82.2).
Based on bis-SNP results, beta-value of non-abolished and non-established CG have been extracted and converted to bigwig for visualization.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig

extract_protocol:
Genomic DNA was isolated from retinal tissues using the DNeasy Blood & Tissue Kit (QIAGEN #69504) according to the manufacturer's protocol.
Typically, 2 µg of genomic DNA is used to make WGBS libraries.Whole genome bisulfite sequencing was conducted by the Hudson Alpha research institute for Biotechnology using the Cambridge Epigenetix TrumethylSeq kit (BS workflow) per manufacturer's instructions.

value: fetal week 21


title: Donor 1 control 0h

description: no LPS treatment


title: H3K4me3-AB2-IPS-Rod_I_Y-8601

value: immature retinal-derived iPSCs 8601


title: Methyl-FW20

value: fetal week 20


title: Methyl-FW23

value: fetal week 23


title: SP140_4h_IP


title: Methyl-FW17

value: fetal week 17


title: H3K4me3-AB2-mESC-Eb5_E_Y-Eb5

value: mouse embryonic stem cell


title: H3K4me3-AB2-IPS-Rod_M_Y-3302

value: mature retinal-derived iPSCs 3302


title: Methyl-FW14

value: fetal week 14


title: Methyl-FW18

value: fetal week 18


title: Methyl-FW19

value: fetal week 19


title: H3K4me3-AB2-IPS-Fibr_F_Y-fMG03

value: derived iPSCs fMG03


title: Methyl-FW10

value: fetal week 10


title: Donor 2 control 0h

description: no LPS treatment


title: H3K4me3-AB2-IPS-Fibr_F_Y-fMG02

value: derived iPSCs fMG02


title: Methyl-RB-X2

tag: disease state

value: retinoblastoma xenograft


title: RNA-WT-FW20

data_processing:
Basecalls performed using CASAVA
Transcriptome sequencing data were mapped to the human genome hg19(GRCh37) using in-house software StrongArm developed from PCGP project.
We required > 30% of exon have > 30x depth. And then classic FPKM have been calculated by cufflink package( version 2.1.1 along with default parameters and “--frag-bias-correct --multi-read-correct“) based on GENCODE annotation v23.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample


title: H3K4me3-AB2-IPS-Rod_M_Y-7602

value: mature retinal-derived iPSCs 7602

tag: chip antibody


title: RNA-WT-FW23


title: Methyl-RB-X1


title: Methyl-RB-D1

value: retinoblastoma diagnosis


title: RNA-WT-FW17


title: Methyl-RB-D2


title: H3K4me3-AB2-IPS-Fibr_F_Y-fG140.03

value: fibroblast-derived iPSCs fG140.03


title: H3K4me3-AB2-Adult-Rod_M_N-WTM11 replicate 2

value: adult 11 month


title: RNA-WT-FW18


title: H3K4me3-AB2-IPS-Fibr_F_Y-fG140.04

value: fibroblast-derived iPSCs fG140.04


title: RNA-WT-FW14


title: RNA-WT-FW10


title: RNA-WT-FW19


title: RNA-RB-X4


title: RNA-RB-X3


title: RNA-RB-X2


title: RNA-RB-X1


title: H3K4me3-AB2-Adult-Rod_M_N-P21 replicate 2

value: postnatal day 21


title: H3K4me3-AB2-Adult-Rod_T_N-MDMX replicate 1

tag: genotype/variation

value: p107 minus minus MDMXTg


title: H3K4me3-AB2-Adult-Rod_M_N-WTM11 replicate 1


title: RNA-RB-D

description: RB-D


title: INPUT-RB replicate 2

description: RB-INPUT.bw

data_processing:
Basecalls performed using CASAVA
BWA (version 0.5.9-r26-dev, default parameter) to align the ChIP-Seq reads to human genome hg19(GRCh37), Picard(version 1.65(1160)) then have been used for marking duplicated reads. Then only non-duplicated reads with have been kept by samtools (parameter “-q 1 -F 1024” version 0.1.18 (r982:295)). We followed the ENCODE criterion to quality control (QC) the data that non-duplicated version of SPP (version 1.11) have been used to draw cross-correlation and calculated relative strand correlation value (RSC) under support of R (version 2.14.0) with packages caTools(version 1.17) and bitops(version 1.0-6) and estimated the fragment size.
We required > 10M unique mapped reads for point-source factor (H3K4me2/3, H3K9/14Ac, H3K27Ac, CTCF, RNAPolII, BRD4) and RSC > 1. We required 20M unique mapped reads for broad markers (H3K9me3, H3K27me3, H3K36me3). We required 10M unique mapped reads for INPUTs and RSC < 1. We noticed H3K4me1 is point-source factor in some stages while broad in other stages so we QC H3K4me1 as broad markers. Then upon manually inspection, the cross-correlation plot generated by SPP, the best fragment size estimated (the smallest fragment size estimated by SPP in all our cases) were used to extend each reads and generate bigwig file to view on IGV (version 2.3.40).
All profiles were manually inspected for clear peaks and good signal to noise separation. For mouse data, all data broad markers with RSC < 0.8 have biological replicates except several samples with one of antibody for H3K9me3(due to availability of outsourcing), we think the quality of those H3K9me3 are good since they show clear peaks and RSC are bigger than most of the H3K9me3 data available in ENCODE or Epigenomics Roadmap.
To estimate the consistence between biological replicates, for point-source factors, MACS2 (version 2.0.9 20111102, option “nomodel” with “extsize” defined as fragment size estimated above) have been used to call peaks with FDR corrected p-value cutoff 0.05(strong peak set) and 0.5(weak peak set) separately, peaks within 100bp have been merged by bedtools (version 2.17.0). We required > 80% of strong peak set from either one replicate overlapping the weak peak set from the other replicate (median percentage 96.8%). For broad peaks, SICER (version 1.1 redundancy threshold 1, window size 200bp, effective genome fraction 0.86, gap size 600bp, FDR 0.00001 with fragment size defined above) has been used for domain calling and we required > 70% of domains called overlapping the domains called from the other replicate(median percentage 89.9%). After confirmed the consistency between replicates, we pool extended reads and generate the final bigwig track for visualization.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig


title: INPUT-RB replicate 3

description: RB-INPUT.bw


title: INPUT-FW24

value: fetal week 24


title: INPUT-RB replicate 1

description: RB-INPUT.bw


title: H3K4me3-AB2-Adult-Rod_M_N-P14 replicate 2

value: postnatal day 14


title: INPUT-FW23

value: fetal week 23


title: INPUT-FW20

value: fetal week 20


title: H3K4me3-AB2-Adult-Rod_M_N-P14 replicate 1


title: H3K4me3-AB2-Adult-Rod_M_N-P10 replicate 2

value: postnatal day 10


title: H3K4me3-AB2-Adult-Rod_M_N-P10 replicate 1


title: INPUT-FW13

value: fetal week 13


title: INPUT-FW16

value: fetal week 16


title: INPUT-FW14

value: fetal week 14


title: H3K4me3-AB2-Adult-Rod_M_N-P21 replicate 1


title: RNAPolII-AB1-RB replicate 1

value: RNAPolII (Abcam,ab5095)


title: H3K4me3-AB2-Adult-Rod_I_N-P3 replicate 2

value: postnatal day 3


title: RNAPolII-AB1-FW13


title: RNAPolII-AB1-FW20


title: H3K9me3-AB1-RB replicate 1

value: retinoblastoma xenograft

value: H3K9me3 (ActiveMotif,39161)


title: INPUT-FW18

value: fetal week 18


title: RNAPolII-AB1-FW15

value: fetal week 15


title: INPUT-FW15


title: H3K4me3-AB2-Adult-Rod_M_N-P7 replicate 1

value: postnatal day 7


title: H3K4me3-AB2-Adult-Rod_M_N-P7 replicate 2


title: H3K4me3-AB2-Adult-Rod_I_N-P3 replicate 1


title: H3K9me3-AB1-FW20


title: H3K4me3-AB2-Adult-Rod_M_N-P14 replicate 3


title: H3K4me3-AB2-Adult-Rod_I_N-P0 replicate 2

value: postnatal day 0


title: H3K9me3-AB1-FW23


title: H3K4me3-AB2-Adult-Rod_I_N-P0 replicate 1


title: H3K9me3-AB1-FW13


title: H3K9-14Ac-AB3-RB replicate 1


title: H3K4me3-AB2-Adult-Rod_E_N-E17.5 replicate 2

value: embryonic day 17.5


title: H3K9-14Ac-AB3-RB replicate 2


title: H3K9-14Ac-AB3-FW24

value: fetal week 24


title: H3K9-14Ac-AB3-FW18


title: H3K4me3-AB2-Adult-Rod_E_N-E17.5 replicate 1


title: RNAPolII-AB1-FW23


title: H3K9-14Ac-AB3-FW16


title: H3K4me3-AB2-Adult-Rod_E_N-E14.5 replicate 2

value: embryonic day 14.5


title: H3K4me3-AB2-Adult-Rod_E_N-E14.5 replicate 1


title: H3K4me3-AB2-FW24


title: H3K4me3-AB2-FW16


title: H3K4me3-AB2-FW18


title: H3K4me3-AB2-RB replicate 1


title: H3K9-14Ac-AB3-FW14


title: H3K4me2-AB2-IPS-Rod_M_Y-7602

value: mature retinal-derived iPSCs 7602


title: H3K4me2-AB2-RB replicate 2

value: H3K4me2 (Abcam,ab7766)


title: H3K4me2-AB2-RB replicate 3


title: H3K9me3-AB1-FW15


title: H3K4me2-AB2-RB replicate 1


title: H3K4me2-AB2-IPS-Rod_I_Y-8601

value: immature retinal-derived iPSCs 8601


title: H3K4me2-AB2-IPS-Rod_M_Y-3302

value: mature retinal-derived iPSCs 3302


title: H3K4me2-AB2-FW18


title: H3K4me2-AB2-FW15


title: H3K4me2-AB2-mESC-Eb5_E_Y-Eb5

value: mouse embryonic stem cell


title: H3K4me2-AB2-FW14

value: fetal week 14


title: H3K4me2-AB2-IPS-Fibr_F_Y-fMG03

value: derived iPSCs fMG03


title: H3K4me2-AB2-FW24


title: H3K4me1-AB2-RB replicate 1

value: H3K4me1 (Abcam,ab8895)


title: H3K4me1-AB2-FW23

value: fetal week 23


title: H3K4me1-AB2-FW16

value: fetal week 16


title: H3K4me2-AB2-IPS-Fibr_F_Y-fMG02

value: derived iPSCs fMG02


title: H3K4me2-AB2-IPS-Fibr_F_Y-fG140.03

value: fibroblast-derived iPSCs fG140.03


title: H3K36me3-AB1-RB replicate 3

value: retinoblastoma xenograft

value: H3K36me3 (ActiveMotif,61101)


title: H3K4me1-AB2-FW14


title: H3K4me2-AB2-IPS-Fibr_F_Y-fG140.04

value: fibroblast-derived iPSCs fG140.04


title: H3K4me3-AB2-FW14


title: H3K4me2-AB2-Adult-Rod_M_N-WTM11 replicate 2

value: adult 11 month


title: H3K4me2-AB2-Adult-Rod_M_N-WTM11 replicate 1


title: H3K36me3-AB1-RB replicate 2


title: H3K36me3-AB1-RB replicate 1


title: H3K36me3-AB1-FW15

value: fetal week 15


title: H3K36me3-AB1-FW18

value: fetal week 18


title: H3K27me3-AB1-RB replicate 1

value: H3K27me3 (Millipore,07-449)


title: H3K27me3-AB1-FW24

value: fetal week 24


title: H3K27me3-AB1-FW18


title: H3K4me2-AB2-Adult-Rod_M_N-P21 replicate 2

value: postnatal day 21


title: H3K4me2-AB2-Adult-Rod_T_N-MDMX replicate 1

value: p107 minus minus MDMXTg


title: H3K4me2-AB2-Adult-Rod_T_N-MDMX replicate 2


title: H3K27me3-AB1-FW14

value: fetal week 14


title: H3K27me3-AB1-FW16


title: H3K4me2-AB2-Adult-Rod_M_N-P21 replicate 1


title: H3K27Ac-AB2-FW18

value: H3K27Ac (Abcam,ab4729)


title: H3K27Ac-AB2-FW24


title: H3K27Ac-AB2-FW15


title: H3K4me2-AB2-Adult-Rod_M_N-P14 replicate 3

value: postnatal day 14


title: H3K4me1-AB2-FW18

value: H3K4me1 (Abcam,ab8895)


title: H3K27Ac-AB2-RB replicate 1


title: H3K27Ac-AB2-FW14


title: CTCF-AB1-RB replicate 2

description: RB-CTCF.bw

value: CTCF (ActiveMotif,61311)


title: Fixed2 (1 week)

description:
Drop-seq
Unique lab identifier: NR_CK_043 (ds019_50fix)

data_processing:
Cell and molecular barcodes were extracted from read1 and added as tags using Drop-seq tools v1.12.
Sequenced reads were trimmed for polyA stretches, SMART adaptor sequences and low quality filtering using Drop-seq tools v1.12.
Trimmed sequenced reads were mapped to hg38 and mm10 using STAR_2.4.0j.
Mapped reads were sorted using samtools v1.2 and merged with cell and molecular barcodes using Drop-seq tools v1.12.
Gene annotation tags were added and bead synthesis errors were detected and corrected using Drop-seq tools v1.12.
Cumulative fraction of reads per cell was computed using Drop-seq tools v1.12, inflection point was computed using dropbead v.0.2.
The digital gene expression matrices were computed using Drop-seq tools v1.12.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: *txt: Tab-separated text files containing UMI counts per gene and per cell of each sample.
clusters*.txt files generated using Seurat.

organism:
Homo sapiens
Mus musculus

source_name: Cell culture cells, fixed for 1 wk

growth_protocol: Cells were grown in DMEM (Invitrogen 61965-026) without antibiotics containing 10% fetal bovine serum, and confirmed to be mycoplasma-free (LookOut Mycoplasma PCR detection kit, Sigma Aldrich).

extract_protocol:
Methanol-fixation was adapted from Stöckius et al. 2009 (Nat. Methods). To avoid cell clumping, 8 volumes (800 µl) of methanol p. a. (pre-chilled to -20˚C) were added drop-wise, while gently mixing or vortexing the cell suspension.
Macosko et al. 2015 Cell; Online-Dropseq-Protocol-v.3.1.

treatment_protocol: Cells were grown to 30 to 60% confluence, dissociated with 0.05% bovine trypsin-EDTA (Invitrogen 25300062), quenched with growth medium, and further processed as described previously (Macosko et al. 2015 Cell; Online-Dropseq-Protocol-v.3.1).

tag: human cell line

value: Flp-In T-Rex 293 HEK

tag: mouse cell line

value: NIH-3T3 (ACC 59)

tag: condition

value: fixed, stored for 1 wk


title: Fixed2 (3 weeks)

description:
Drop-seq
Unique lab identifier: NR_CK_048 (ds021_50fix)

source_name: Cell culture cells, fixed for 3 wk

value: fixed, stored for 3 wk


title: H3K36me3-AB1-FW23

value: fetal week 23

value: H3K36me3 (ActiveMotif,61101)


title: H3K36me3-AB1-FW14


title: Fixed

description:
Drop-seq
Unique lab identifier: NR_CK_028 (ds013_50fix)

source_name: Cell culture cells, fixed

value: fixed


title: H3K4me2-AB2-Adult-Rod_M_N-P14 replicate 2


title: CTCF-AB1-RB replicate 1

description: RB-CTCF.bw

value: retinoblastoma xenograft


title: Live

description:
Drop-seq
Unique lab identifier: NR_CK_027 (ds013_50)

source_name: Cell culture cells, live

value: live


title: H3K4me2-AB2-Adult-Rod_M_N-P10 replicate 2

source_name: retina

value: postnatal day 10


title: H3K4me2-AB2-Adult-Rod_M_N-P7 replicate 2

value: postnatal day 7


title: CTCF-AB1-FW18

value: fetal week 18


title: H3K4me2-AB2-Adult-Rod_M_N-P10 replicate 1


title: H3K4me2-AB2-Adult-Rod_M_N-P7 replicate 1


title: C59_CTCF_ChIPSeq

city: Berkeley

first: Robert

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

description: Homozygote cell line with endogenously tagged CTCF and Rad21 loci

data_processing:
Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley
Reads quality control performed with FastQC (version 0.10.1)
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie (version 0.12.8) with the following configurations: -n 2 -m 1
ChIP-Seq peaks were called using MACS2 (version 2.1.0.20140616) with the following configurations: -t <sample.bam>  -c <input.bam> -f BAM -g mm --nomodel --extsize 250
bigWig coverage files were generated with deepTools (version 2.0) with the following configurations: bamCoverage -of bigwig --binSize 50 --normalizeTo1x 2150570000 --extendReads 250 --ignoreDuplicates
Genome_build: mm10
Supplementary_files_format_and_content: text files containing ChIP-Seq peak genomic coordinates (mm10), length, summit, pileup, pvalue, qvalue and fold enrichment over input as determined by MACS2
Supplementary_files_format_and_content: bigWig files containing the number of reads per 50 bp bins normalized to 1x sequencing depth (Reads Per Genomic Content)

source_name: embryonic stem cells

growth_protocol: JM8.N4 mouse embryonic stem cells were grown on plates pre-coated with a 0.1% autoclaved gelatin solution (Sigma-Aldrich, G9391) under feeder free condition in knock-out DMEM with 15% FBS and LIF (full recipe: 500 mL DMEM (ThermoFisher#10829018), 6 mL MEM NEAA (ThermoFisher #11140050), 6 mL GlutaMax (ThermoFisher#35050061), 5 mL Penicillin-streptomycin (ThermoFisher #15140122), 4.6 μL 2-mercapoethanol (Sigma-Aldrich M3148), 90 mL fetal bovine serum (HyClone FBS SH30910.03 lot #AXJ47554)). mES cells were fed by replacing half the medium with fresh medium daily and passaged every two days by trypsinization.

extract_protocol:
Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10 min at 4000 rpm, resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) and incubated for 10 min on ice.  During the incubation, the lysates were repeatedly pipetted up and down every 5 minutes. Lysates were then centrifuged for 10 min at 4000 rpm.  Nuclear pellets were resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS), incubated on ice for 10 min, and sonicated to obtain DNA fragments below 2000 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 100 peak incident power, 50 cycles of 30" on and 30" off).  Sonicated lysates were cleared by centrifugation and 400-1600 μg of chromatin was diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) to a final concentration of 0.8 μg/μl, precleared with Protein A sepharose (GE Healthcare) for 2 hours at 4°C and immunoprecipitated overnight with 8-16 μg of normal rabbit IgGs, anti-Rad21 or anti-CTCF antibodies.  About 15% of the precleared chromatin was saved as input.  Immunoprecipitated DNA was purified with the Qiagen QIAquick PCR Purification Kit, eluted in 60 μl of water and analyzed by qPCR together with 2% of the input chromatin prior to ChIP-Seq library preparation.
ChIP-seq libraries were prepared independently from two ChIP biological replicates using the Illumina TruSeq™ DNA sample preparation kit according to manufacturer instructions with few modifications. We used 100 ng of ChIP input DNA (as measured by Fragment analyzer™) and 50 μl of immunoprecipitated DNA as a starting material; Illumina adapters were diluted 1:50, and library samples were enriched through 18 cycles of PCR amplification.  We assessed library quality and fragment size by qPCR and Fragment analyzer™, and when necessary we performed an additional size selection step on agarose gel after PCR amplification to enrich for fragments between 150 and 500 bp.  We sequenced 4 to 8 multiplexed libraries per lane on the Illumina HiSeq4000 sequencing platform (single end-reads, 50 bp long) at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant.

treatment_protocol: Cells were cross-linked for 5 minutes at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final).

tag: cell line

tag: genotype

value: FLAG-Halo-CTCF/Rad21-SNAPf-V5 Knock-in

value: CTCF (Abcam ab128873)


title: H3K4me2-AB2-Adult-Rod_I_N-P3 replicate 2

value: postnatal day 3


title: CTCF-AB1-FW14

value: fetal week 14


title: C59_IgG_ChIPSeq

value: Rabbit normal IgG (Jackson ImmunoResearch 011-000-002)


title: C59_input


title: C59_Rad21_ChIPSeq

value: Rad21 (Abcam ab154769)


title: H3K4me2-AB2-Adult-Rod_M_N-P10 replicate 3


title: BRD4-AB1-RB replicate 1

value: BRD4 (Bethyl,A301-985A)


title: BRD4-AB1-FW23


title: H3K4me2-AB2-Adult-Rod_I_N-P0 replicate 2

value: postnatal day 0


title: WT_CTCF_ChIPSeq

value: wild type


title: H3K4me2-AB2-Adult-Rod_I_N-P3 replicate 1


title: WT_Rad21_ChIPSeq


title: H3K4me2-AB2-Adult-Rod_E_N-E17.5 replicate 1

value: embryonic day 17.5


title: WT_IgG_ChIPSeq

value: Rabbit gamma globulin (Jackson ImmunoResearch 011-000-002)


title: H3K4me2-AB2-Adult-Rod_I_N-P0 replicate 1


title: BRD4-AB1-FW15

value: fetal week 15


title: CTCF-AB1-FW23

value: fetal week 23

value: CTCF (ActiveMotif,61311)


title: BRD4-AB1-FW20

value: fetal week 20


title: WT_input


title: H3K4me2-AB2-Adult-Rod_E_N-E14.5 replicate 2

value: embryonic day 14.5


title: BRD4-AB1-FW13

value: fetal week 13


title: H3K4me2-AB2-Adult-Rod_E_N-E14.5 replicate 1


title: WT C/C LPS rep2

description:
LPS treated, 100ng/mL, 4h
WT2-4h

data_processing:
Illumina Casava1.7 software used for basecalling. Bcbio-nextgen was used for the analysis.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR
Gene counts were produced by featureCounts
Differential expression analysis was done by DESeq2
All commands used in this analysis is stored at gihub: https://github.com/hbc/kjeffrey_CD_RNAseq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample ...

source_name: Peripheral blood derived mononuclear cells

growth_protocol: PBMCs were isolated from heparin collected whole blood by density-gradient centrifugation using lymphoprep

extract_protocol:
Total RNA was extracted from PBMCs using the Qiagen RNAeasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PBMCs were placed in RPMI medium with 10% FBS and 1% Penicillin-Streptomycin and left untreated or stimulated with 100ng/mL of LPS for 4h

value: non-disease


title: H3K4me1-AB2-IPS-Rod_M_Y-7602

value: mature retinal-derived iPSCs 7602


title: CTCF-AB1-FW16

value: fetal week 16


title: WT C/C LPS rep1

description:
LPS treated, 100ng/mL, 4h
WT1-4h

value: Peripheral blood derived mononuclear cells


title: H3K4me1-AB2-IPS-Rod_M_Y-3302

value: mature retinal-derived iPSCs 3302


title: H3K4me1-AB2-IPS-Rod_I_Y-8601

value: immature retinal-derived iPSCs 8601


title: WT C/C rep1

description:
no LPS treatment
WT1-0h


title: H3K4me1-AB2-mESC-Eb5_E_Y-Eb5

source_name: mouse embryonic stem cell

value: mouse embryonic stem cell


title: H3K4me1-AB2-IPS-Fibr_F_Y-fMG02

value: derived iPSCs fMG02


title: CD C/C LPS+ rep2

description:
LPS treated, 100ng/mL, 4h
SNP2-4h

value: Crohn's disease


title: H3K4me1-AB2-IPS-Fibr_F_Y-fG140.04

source_name: fibroblast-derived iPSCs fG140.04

value: fibroblast-derived iPSCs fG140.04


title: H3K4me1-AB2-IPS-Fibr_F_Y-fG140.03

source_name: fibroblast-derived iPSCs fG140.03

value: fibroblast-derived iPSCs fG140.03


title: H3K4me1-AB2-Adult-Rod_M_N-WTM11 replicate 2

value: adult 11 month


title: H3K4me1-AB2-Adult-Rod_M_N-WTM11 replicate 1


title: CD T/T LPS+ rep1

description:
LPS treated, 100ng/mL, 4h
SNP1+4h


title: CD C/C rep1

description:
no LPS treatment
SNP1-0h


title: CD C/C rep2

description:
no LPS treatment
SNP2-0h


title: CD C/C LPS+ rep1

description:
LPS treated, 100ng/mL, 4h
SNP1-4h


title: CD T/T rep2

description:
no LPS treatment
SNP2+0h


title: H3K4me1-AB2-Adult-Rod_T_N-MDMX replicate 2

value: p107 minus minus MDMXTg


title: CD T/T rep1

description:
no LPS treatment
SNP1+0h


title: H3K4me1-AB2-Adult-Rod_T_N-MDMX replicate 1


title: H3K4me1-AB2-Adult-Rod_M_N-P21 replicate 2

value: postnatal day 21


title: AM con-3

city: Birmingham

first: Huachun

last: Cui

state: Alabama

institute: University of Alabama at Birmingham

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used to convert bcl files to fastq files
Sequenced reads were mapped to mm10 whole genome using STAR version 2.5.2b with parameters --outReadsUnmappedFastx --runThreadN 4 --outSAMtype BAM SortedByCoordinate -c --twopassMode Basic
Counts were calculated using htseq-count version 0.6.0 with parameters -r pos -t exon -i gene_id -a 10 -s no -f bam
Differential expression was performed using DESeq2 version 2.1.14.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file which includes normalized count values

source_name: BALF, AM control

growth_protocol: Bronchoalveolar lavage fluids (BALFs) were collected from mice that were treated intratracheally with saline or bleomycin for 2 weeks. BAL cells were ontained by centrifuge. After red blood cell lysis, BAL cells were re-suspended in RPMI-1640 medium containing 10% FBS and plated in 48 wells plates for 30min at 37℃. Cells were then washed five times and macrophage on the plates were lysed in Trizol reagent. Total RNA was purified with Qiagen RNAeasy column.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: control

value: Alveolar macrophages


title: PV_in_HD

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

data_processing:
Adapter removal step was conducted using the UEA sRNA workbench [Stocks et al, 2012]. The 3' adapter sequence was identified using the first 6 nt. Adapter guessing strategy was also used to double check the adapter removal procedure.
Quality checks including size class distribution, nucleotide composition analysis, complexity analysis and Jaccard similarity were done before genome matching.
Reads were mapped full length, no mis-matches or gaps allowed to the host Aspergillus fumigatus genome and also viral genomes using PatMan [Prueffer et al, 2008]
Differentially expressed virus-derived small RNAs were determined and mapped to the fungal genome to identify the potential targets.
The miRNAs were identified using the miRCat and miRprof tool within the UEA workbench.
The sRNA loci were identfied using CoLIde [Mohorianu et al, 2013]
Genome_build: A_fumigatus_Af293 genome version_s03_m04_r22
Supplementary_files_format_and_content: csv file containing the sRNA expression levels.

organism: Aspergillus fumigatus

source_name: Partitivirus infected isolate

growth_protocol: All A. fumigatus strains of interest were inoculated onto 25 ml of solid Aspergillus Complete Media (ACM) from 50% glycerol stocks which were kept at -20 °C.Plates were incubated at 37°C for 5 days and spores were harvested with 15 ml of sterile distilled water. Spore suspensions were used to inoculate 500 ml of ACM broth. Inoculated bottles were incubated at 37°C with shaking at 130 rpm. After 5 days, mycelia were harvested.

extract_protocol:
Total RNAs were extracted using Trizol and small RNAs were isolated using PEG8000 precipitation.
Libraries were constructed using Scriptminer kit with high definition Illumina adapters.

treatment_protocol: No special treatment

tag: tissue

value: Fungal mycelia


title: NK_in_HD

source_name: NK virus infected isolate


title: CV_in_HD

source_name: Chrysovirus infected isolate


title: WT C/C rep2

description:
no LPS treatment
WT2-0h

value: non-disease


title: H3K4me1-AB2-Adult-Rod_M_N-P21 replicate 1

data_processing:
Basecalls performed using CASAVA
BWA (version 0.5.9-r26-dev, default parameter) to align the ChIP-Seq reads to mouse genome mm9(MGSCv37 from Sanger), Picard(version 1.65(1160)) then have been used for marking duplicated reads. Then only non-duplicated reads with have been kept by samtools (parameter “-q 1 -F 1024” version 0.1.18 (r982:295)). We followed the ENCODE criterion to quality control (QC) the data that non-duplicated version of SPP (version 1.11) have been used to draw cross-correlation and calculated relative strand correlation value (RSC) under support of R (version 2.14.0) with packages caTools(version 1.17) and bitops(version 1.0-6) and estimated the fragment size.
We required > 10M unique mapped reads for point-source factor (H3K4me2/3, H3K9/14Ac, H3K27Ac, CTCF, RNAPolII, BRD4) and RSC > 1. We required 20M unique mapped reads for broad markers (H3K9me3, H3K27me3, H3K36me3). We required 10M unique mapped reads for INPUTs and RSC < 1. We noticed H3K4me1 is point-source factor in some stages while broad in other stages so we QC H3K4me1 as broad markers. Then upon manually inspection, the cross-correlation plot generated by SPP, the best fragment size estimated (the smallest fragment size estimated by SPP in all our cases) were used to extend each reads and generate bigwig file to view on IGV (version 2.3.40).
All profiles were manually inspected for clear peaks and good signal to noise separation. For mouse data, all data broad markers with RSC < 0.8 have biological replicates except several samples with one of antibody for H3K9me3(due to availability of outsourcing), we think the quality of those H3K9me3 are good since they show clear peaks and RSC are bigger than most of the H3K9me3 data available in ENCODE or Epigenomics Roadmap.
To estimate the consistence between biological replicates, for point-source factors, MACS2 (version 2.0.9 20111102, option “nomodel” with “extsize” defined as fragment size estimated above) have been used to call peaks with FDR corrected p-value cutoff 0.05(strong peak set) and 0.5(weak peak set) separately, peaks within 100bp have been merged by bedtools (version 2.17.0). We required > 80% of strong peak set from either one replicate overlapping the weak peak set from the other replicate (median percentage 96.8%). For broad peaks, SICER (version 1.1 redundancy threshold 1, window size 200bp, effective genome fraction 0.86, gap size 600bp, FDR 0.00001 with fragment size defined above) has been used for domain calling and we required > 70% of domains called overlapping the domains called from the other replicate(median percentage 89.9%). After confirmed the consistency between replicates, we pool extended reads and generate the final bigwig track for visualization.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigwig


title: H3K4me1-AB2-Adult-Rod_M_N-P14 replicate 2

value: postnatal day 14


title: AM con-2


title: AM BLM-5

source_name: BALF, AM BLM

value: bleomycin model of pulmonary fibrosis


title: H3K4me1-AB2-IPS-Fibr_F_Y-fMG03

source_name: fibroblast-derived iPSCs fMG03

value: derived iPSCs fMG03


title: H3K4me1-AB2-Adult-Rod_M_N-P14 replicate 1


title: CD T/T LPS+ rep2

description:
LPS treated, 100ng/mL, 4h
SNP2+4h

value: Peripheral blood derived mononuclear cells


title: AM con-1


title: H3K4me1-AB2-Adult-Rod_M_N-P10 replicate 2

value: postnatal day 10


title: AM BLM-1


title: H3K4me1-AB2-Adult-Rod_M_N-P7 replicate 2

value: postnatal day 7


title: bulk_3t3

description: bulk transcriptomics

data_processing:
Cell and molecular barcodes were extracted from read1 and added as tags using Drop-seq tools v1.12.  Sequenced reads were trimmed for polyA stretches, SMART adaptor sequences and low quality filtering using Drop-seq tools v1.12.  Trimmed sequenced reads were mapped to hg38 and mm10 using STAR_2.4.0j.  Mapped reads were sorted using samtools v1.2 and merged with cell and molecular barcodes using Drop-seq tools v1.12.  Gene annotation tags were added and bead synthesis errors were detected and corrected using Drop-seq tools v1.12.  Cumulative fraction of reads per cell was computed using Drop-seq tools v1.12, inflection point was computed using dropbead v.0.2.  The digital gene expression matrices were computed using Drop-seq tools v1.12.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: gene counts
clusters*.txt files generated using Seurat.

source_name: mRNAseq of cell culture cells

extract_protocol: Methanol-fixation was adapted from Stöckius et al. 2009 (Nat. Methods). To avoid cell clumping, 8 volumes (800 µl) of methanol p. a. (pre-chilled to -20˚C) were added drop-wise, while gently mixing or vortexing the cell suspension.  Macosko et al. 2015 Cell; Online-Dropseq-Protocol-v.3.1.

value: NIH 3T3

tag: developmental stage

value: not applicable

tag: fixation

value: live, not fixed


title: mm_rep1

description: single-cell transcriptomics

data_processing:
Cell and molecular barcodes were extracted from read1 and added as tags using Drop-seq tools v1.12.  Sequenced reads were trimmed for polyA stretches, SMART adaptor sequences and low quality filtering using Drop-seq tools v1.12.  Trimmed sequenced reads were mapped to hg38 and mm10 using STAR_2.4.0j.  Mapped reads were sorted using samtools v1.2 and merged with cell and molecular barcodes using Drop-seq tools v1.12.  Gene annotation tags were added and bead synthesis errors were detected and corrected using Drop-seq tools v1.12.  Cumulative fraction of reads per cell was computed using Drop-seq tools v1.12, inflection point was computed using dropbead v.0.2.  The digital gene expression matrices were computed using Drop-seq tools v1.12.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: *txt: Tab-separated text files containing UMI counts per gene and per cell of each sample.
clusters*.txt files generated using Seurat.

source_name: Drop-seq of hindbrain P0 cells

value: newborn P0

value: 80% methanol/PBS

value: FACS-sorted cells


title: H3K4me1-AB2-Adult-Rod_M_N-P7 replicate 1

extract_protocol:
ChIP with iDeal ChIP-seq kit (Diagenode # C01010051), MinElute PCR-purification kit (QIAGEN #28006), quantified using the Quant-iT PicoGreen ds DNA assay (Life Technologies #Q33120)
Libraries were prepared from 5-10 ng DNA using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext High-Fidelity 2x PCR Master Mix according to the manufacturer’s instructions (New England Biolabs, Ipswich, MA) with the following modifications: A 1:1 Ampure cleanup was added after adaptor ligation a total of 2 times.


title: mm_rep2

description: single-cell transcriptomics


title: H3K4me1-AB2-Adult-Rod_I_N-P3 replicate 1

value: postnatal day 3


title: H3K4me1-AB2-Adult-Rod_I_N-P0 replicate 2

value: postnatal day 0


title: H3K4me1-AB2-Adult-Rod_I_N-P3 replicate 2


title: common acquired nevus (JC302)

city: NEW YORK

first: Julide

middle: Tok

last: Celebi

state: New York

address: 1470 Madison Avenue

department: Tisch Cancer Institute

institute: Mount Sinai School of Medicine

description: Barcode: CAGATC

data_processing:
Illumina Casava1.8+ software used for basecalling.
Raw reads were quality filtered by trimming the read ends; bases with quality <20 were removed. We then computed the quality at the 20th percentile. The entire read was discarded if the quality at the 20th percentile was less than 15. Reads shorter than 40 bases after trimming were discarded as well. If one or more reads in the pair failed the quality check both reads were discarded.
Reads were mapped to the genome and to repbase sequences using STAR
Counts for genes and repeat elements were obtained using featureCounts application from subread package
Expression as log(counts per million) was computed using edgeR/limma packages
Genome_build: hg19, Ensembl annotation
Supplementary_files_format_and_content: tab-delimited text files include raw counts and expression for each sample

source_name: skin tumor

growth_protocol: human skin biopsy

extract_protocol:
Total RNA was extracted from samples using the miRNeasy Mini Kit (Qiagen). The RNA Integrity Number of each sample was determined using the 2100 Bioanalyzer instrument (Agilent Technologies). Samples were selected with stringent criteria based on RNA Integrity Number of 7.0 or greater, and a minimum of 500 ng of total RNA.
Unstranded, total RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina TruSeq Total RNA library preparation kit)

treatment_protocol: Treatment naïve

tag: gender

value: Female

value: common acquired nevus

tag: primary tumor thickness (breslow’s depth)

tag: primary tumor (t) category (tnm classification)

tag: regional nodes (n) category (tnm classification)

tag: distant metastasis (m) category (tnm classification)

tag: tumor stage (ajcc classification)

tag: ulceration

tag: time to death/last followup, months

tag: survival status (1=dead, 0=alive)


title: common acquired nevus (JC303)

description: Barcode: ATCACG


title: H3K4me1-AB2-Adult-Rod_E_N-E17.5 replicate 2

tag: strain

tag: age

value: embryonic day 17.5

tag: chip antibody


title: H3K4me1-AB2-Adult-Rod_I_N-P0 replicate 1


title: H3K4me1-AB2-Adult-Rod_E_N-E17.5 replicate 1


title: H3K4me1-AB2-Adult-Rod_E_N-E14.5 replicate 2

value: embryonic day 14.5


title: common acquired nevus (JC301)

description: Barcode: ATTCCT


title: H3K4me1-AB2-Adult-Rod_E_N-E14.5 replicate 1


title: H3K36me3-AB1-IPS-Rod_M_Y-3302

tag: cell type

value: mature retinal-derived iPSCs 3302


title: AM BLM-2

tag: disease state

value: bleomycin model of pulmonary fibrosis

value: Alveolar macrophages


title: primary melanoma (JC292)

description: Barcode: ATGAGC

tag: tissue

value: primary melanoma


title: common acquired nevus (JC286)

description: Barcode: TGACCA


title: primary melanoma (JC294)

description: Barcode: GTTTCG

value: Male


title: H3K36me3-AB1-IPS-Rod_M_Y-7602

value: mature retinal-derived iPSCs 7602


title: primary melanoma (JC296)

description: Barcode: TGACCA


title: primary melanoma (JC295)

description: Barcode: CTCAGA


title: H3K4me1-AB2-Adult-Rod_M_N-P10 replicate 1

value: postnatal day 10


title: common acquired nevus (JC282)

description: Barcode: TCCCGA


title: bulk_mm

description: bulk transcriptomics

source_name: mRNAseq of hindbrain P0 cells

tag: developmental stage


title: H3K36me3-AB1-IPS-Rod_I_Y-8601

value: immature retinal-derived iPSCs 8601


title: H3K36me3-AB1-mESC-Eb5_E_Y-Eb5

value: mouse embryonic stem cell


title: H3K36me3-AB1-IPS-Fibr_F_Y-fMG03

value: derived iPSCs fMG03


title: common acquired nevus (JC273)

description: Barcode: GGTAGC


title: common acquired nevus (JC272)

description: Barcode: CAACTA


title: H3K36me3-AB1-IPS-Fibr_F_Y-fG140.04

value: fibroblast-derived iPSCs fG140.04


title: H3K36me3-AB1-Adult-Rod_M_N-WTM11 replicate 2

value: adult 11 month


title: H3K36me3-AB1-IPS-Fibr_F_Y-fG140.03

value: fibroblast-derived iPSCs fG140.03


title: H3K36me3-AB1-IPS-Fibr_F_Y-fMG02

source_name: fibroblast-derived iPSCs fMG02

value: derived iPSCs fMG02


title: primary melanoma (JC293)

description: Barcode: CATGGC

value: Female


title: common acquired nevus (JC248)

description: Barcode: AGTCAA

value: common acquired nevus


title: H3K36me3-AB1-Adult-Rod_M_N-WTM11 replicate 1

source_name: retina


title: common acquired nevus (JC271)

description: Barcode: TCGAAG


title: H3K36me3-AB1-Adult-Rod_T_N-MDMX replicate 1

tag: genotype/variation

value: p107 minus minus MDMXTg


title: primary melanoma (JC235)

description: Barcode: GATCAG

tag: gender


title: H3K36me3-AB1-Adult-Rod_T_N-MDMX replicate 2


title: common acquired nevus (JC262)

description: Barcode: GGCTAC

tag: primary tumor thickness (breslow’s depth)


title: H3K36me3-AB1-Adult-Rod_M_N-P21 replicate 2

value: postnatal day 21


title: primary melanoma (JC224)

description: Barcode: GACGAC

tag: primary tumor (t) category (tnm classification)


title: H3K36me3-AB1-Adult-Rod_M_N-P14 replicate 2

value: postnatal day 14


title: primary melanoma (JC197)

description: Barcode: CTAGCT

tag: regional nodes (n) category (tnm classification)

value: Ia

value: No


title: H3K36me3-AB1-Adult-Rod_M_N-P21 replicate 1


title: primary melanoma (JC198)

description: Barcode: ATCACG

value: primary melanoma

tag: distant metastasis (m) category (tnm classification)


title: H3K36me3-AB1-Adult-Rod_M_N-P14 replicate 1


title: primary melanoma (JC194)

description: Barcode: GTAGAG

value: Nx

tag: tumor stage (ajcc classification)


title: primary melanoma (JC195)

description: Barcode: CAGATC

tag: ulceration


title: H3K36me3-AB1-Adult-Rod_M_N-P10 replicate 2

value: postnatal day 10


title: H3K36me3-AB1-Adult-Rod_M_N-P10 replicate 1


title: primary melanoma (JC189)

description: Barcode: ATGTCA

value: Male

tag: time to death/last followup, months


title: common acquired nevus (JC281)

description: Barcode: CCGTCC

tag: survival status (1=dead, 0=alive)


title: H3K36me3-AB1-Adult-Rod_M_N-P7 replicate 2

tag: strain

value: postnatal day 7


title: common acquired nevus (JC274)

description: Barcode: CACGAT


title: H3K36me3-AB1-Adult-Rod_M_N-P7 replicate 1

tag: age


title: primary melanoma (JC181)

description: Barcode: ACAGTG

value: IIa


title: H3K36me3-AB1-Adult-Rod_I_N-P3 replicate 2

value: postnatal day 3

tag: chip antibody


title: primary melanoma (JC182)

description: Barcode: GTGAAA


title: common acquired nevus (JC247)

description: Barcode: CACGAT


title: primary melanoma (JC180)

description: Barcode: CTTGTA

value: Yes


title: primary melanoma (JC179)

description: Barcode: GCCAAT

value: Ib


title: H3K36me3-AB1-Adult-Rod_I_N-P3 replicate 1


title: H3K36me3-AB1-Adult-Rod_I_N-P0 replicate 1

value: postnatal day 0


title: H3K36me3-AB1-Adult-Rod_I_N-P0 replicate 2


title: H3K36me3-AB1-Adult-Rod_E_N-E17.5 replicate 2

value: embryonic day 17.5


title: primary melanoma (JC169)

description: Barcode: TAGCTT

value: IIIb


title: H3K36me3-AB1-Adult-Rod_E_N-E17.5 replicate 1


title: primary melanoma (JC171)

description: Barcode: GGTAGC


title: primary melanoma (JC161)

description: Barcode: CTAGCT


title: primary melanoma (JC164)

description: Barcode: ATCACG

value: Female


title: H3K36me3-AB1-Adult-Rod_E_N-E14.5 replicate 2

value: embryonic day 14.5


title: H3K36me3-AB1-Adult-Rod_E_N-E14.5 replicate 1


title: H3K27me3-AB3-IPS-Rod_M_Y-7602

tag: cell type

value: mature retinal-derived iPSCs 7602


title: primary melanoma (JC153)

description: Barcode: CAACTA


title: H3K27me3-AB3-IPS-Rod_M_Y-3302

value: mature retinal-derived iPSCs 3302


title: primary melanoma (JC155)

description: Barcode: GTAGAG

value: No


title: primary melanoma (JC149)

description: Barcode: TCGAAG

value: primary melanoma

value: IIb


title: H3K27me3-AB3-IPS-Fibr_F_Y-fMG03

value: derived iPSCs fMG03


title: primary melanoma (JC146)

description: Barcode: GACGAC


title: primary melanoma (JC145)

description: Barcode: CTCAGA

value: Male


title: primary melanoma (JC144)

description: Barcode: ACTTGA


title: primary melanoma (JC143)

description: Barcode: TATAAT

value: IIIa


title: primary melanoma (JC178)

description: Barcode: TGACCA

value: Ia


title: H3K27me3-AB3-IPS-Fibr_F_Y-fG140.04

value: fibroblast-derived iPSCs fG140.04


title: H3K27me3-AB3-IPS-Fibr_F_Y-fG140.03

value: fibroblast-derived iPSCs fG140.03


title: primary melanoma (JC175)

description: Barcode: GATCAG

value: IIa


title: H3K27me3-AB3-Adult-Rod_M_N-WTM11 replicate 1

value: adult 11 month


title: primary melanoma (JC135)

description: Barcode: GTGGCC

value: Ib


title: primary melanoma (JC136)

description: Barcode: ATGTCA


title: primary melanoma (JC133)

description: Barcode: TCATTC

value: IIIb

value: Yes


title: H3K27me3-AB3-Adult-Rod_T_N-MDMX replicate 1

value: p107 minus minus MDMXTg


title: H3K27me3-AB3-Adult-Rod_M_N-WTM11 replicate 2


title: primary melanoma (JC132)

description: Barcode: CATTTT

value: IIc


title: primary melanoma (JC158)

description: Barcode: GGTAGC


title: H3K27me3-AB1-Adult-Rod_M_N-WTM11 replicate 1


title: primary melanoma (JC130)

description: Barcode: ATTCCT


title: primary melanoma (JC129)

description: Barcode: CGTACG


title: primary melanoma (JC127)

description: Barcode: GTGAAA


title: H3K27me3-AB3-mESC-Eb5_E_Y-Eb5

value: mouse embryonic stem cell


title: H3K27me3-AB1-Adult-Rod_M_N-WTM11 replicate 2


title: H3K27me3-AB1-Adult-Rod_M_N-P14 replicate 2

value: postnatal day 14


title: H3K27me3-AB1-Adult-Rod_M_N-P21 replicate 1

value: postnatal day 21


title: H3K27me3-AB1-Adult-Rod_M_N-P21 replicate 2


title: primary melanoma (JC126)

description: Barcode: ACAGTG

value: primary melanoma

value: No


title: H3K27me3-AB3-IPS-Fibr_F_Y-fMG02

value: derived iPSCs fMG02


title: H3K27me3-AB1-Adult-Rod_M_N-P14 replicate 1


title: primary melanoma (JC123)

description: Barcode: GCCAAT

value: Male


title: primary melanoma (JC121)

description: Barcode: CTATAC

value: Female


title: H3K27me3-AB1-Adult-Rod_M_N-P10 replicate 2

value: postnatal day 10


title: H3K27me3-AB3-Adult-Rod_T_N-MDMX replicate 2


title: primary melanoma (JC117)

description: Barcode: GTGGCC


title: H3K27me3-AB1-Adult-Rod_M_N-P10 replicate 1


title: H3K27me3-AB1-Adult-Rod_M_N-P7 replicate 2

value: postnatal day 7


title: H3K27me3-AB1-Adult-Rod_M_N-P7 replicate 1


title: primary melanoma (JC116)

description: Barcode: ACTGAT


title: primary melanoma (JC115)

description: Barcode: GTCCGC


title: primary melanoma (JC113)

description: Barcode: TAATCG

value: IIIc


title: H3K27me3-AB1-Adult-Rod_I_N-P3 replicate 1

value: postnatal day 3


title: primary melanoma (JC111)

description: Barcode: GTAGAG


title: H3K27me3-AB1-Adult-Rod_I_N-P0 replicate 2

value: postnatal day 0


title: primary melanoma (JC110)

description: Barcode: CCGTCC


title: H3K27me3-AB1-Adult-Rod_I_N-P0 replicate 1


title: H3K27me3-AB1-Adult-Rod_E_N-E17.5 replicate 1

value: embryonic day 17.5


title: primary melanoma (JC124)

description: Barcode: CTTGTA

value: IIb

value: Yes


title: primary melanoma (JC108)

description: Barcode: GACGAC

value: IIc


title: primary melanoma (JC109)

description: Barcode: ATGTCA

value: Nx


title: H3K27me3-AB1-Adult-Rod_E_N-E17.5 replicate 2


title: primary melanoma (JC107)

description: Barcode: CTCAGA

value: IIa


title: H3K27me3-AB1-Adult-Rod_E_N-E14.5 replicate 2

value: embryonic day 14.5


title: H3K27me3-AB1-Adult-Rod_E_N-E14.5 replicate 1


title: H3K27Ac-AB2-IPS-Rod_M_Y-7602

value: mature retinal-derived iPSCs 7602


title: common acquired nevus (JC077)

description: Barcode: CACCGG

value: common acquired nevus


title: primary melanoma (JC106)

description: Barcode: ACTTGA

value: primary melanoma

value: IIIa

value: No


title: H3K27Ac-AB2-IPS-Rod_M_Y-3302

value: mature retinal-derived iPSCs 3302


title: H3K27Ac-AB2-IPS-Rod_I_Y-8601

value: immature retinal-derived iPSCs 8601


title: common acquired nevus (JC069)

description: Barcode: CGTACG

value: Female


title: H3K27Ac-AB2-mESC-Eb5_E_Y-Eb5

value: mouse embryonic stem cell


title: common acquired nevus (JC066)

description: Barcode: GTGGCC


title: H3K27me3-AB3-IPS-Rod_I_Y-8601


title: H3K27Ac-AB2-IPS-Fibr_F_Y-fMG03

value: derived iPSCs fMG03


title: common acquired nevus (JC067)

description: Barcode: GTTTCG


title: H3K27me3-AB1-Adult-Rod_I_N-P3 replicate 2

value: postnatal day 3


title: common acquired nevus (JC060)

description: Barcode: GTAGAG


title: H3K27Ac-AB2-IPS-Fibr_F_Y-fMG02

value: derived iPSCs fMG02


title: common acquired nevus (JC059)

description: Barcode: CCGTCC


title: common acquired nevus (JC058)

description: Barcode: ATGTCA


title: H3K27Ac-AB2-IPS-Fibr_F_Y-fG140.03

value: fibroblast-derived iPSCs fG140.03


title: H3K27Ac-AB2-IPS-Fibr_F_Y-fG140.04

value: fibroblast-derived iPSCs fG140.04


title: common acquired nevus (JC055)

description: Barcode: AGTCAA


title: common acquired nevus (JC056)

description: Barcode: AGTTCC


title: H3K27Ac-AB2-Adult-Rod_M_N-WTM11 replicate 2

value: adult 11 month


title: common acquired nevus (JC053)

description: Barcode: GGCTAC


title: common acquired nevus (JC052)

description: Barcode: TAGCTT


title: H3K27Ac-AB2-Adult-Rod_M_N-WTM11 replicate 1


title: common acquired nevus (JC054)

description: Barcode: CTTGTA


title: H3K27Ac-AB2-Adult-Rod_T_N-MDMX replicate 2

value: p107 minus minus MDMXTg


title: common acquired nevus (JC072)

description: Barcode: ACTGAT


title: H3K27Ac-AB2-Adult-Rod_M_N-P21 replicate 2

value: postnatal day 21


title: H3K27Ac-AB2-Adult-Rod_T_N-MDMX replicate 1


title: H3K27Ac-AB2-Adult-Rod_M_N-P21 replicate 1


title: WAPL2_NCAM

description: Libraries prepared from 3C template

data_processing:
Reads for every sample were demultiplexed and trimmed based on the reading primer adding GATC to the start of the sequence. Trimmed reads were mapped to the genome using bwa bwasw (Li and Durbin, 2010). Reads that did not start at a DpnII restriction site were filtered out as they probably do not represent ligation events. Non-unique fragments and fragments created by the digestion of two DpnII sites (“blind” fragments) were also filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: Wiggle files of each experiment

source_name: Hap1 WaplKO_3.3

extract_protocol:
4C was performed essentially as previously described (van de Werken et al., 2012).
For every viewpoint we performed a two-step PCR reaction using viewpoint specific primers in the first round and universal index primers in de second round (see figure S4 for more details). The forward (‘reading’) primers contained the entire P5 sequencing primer. The reverse primer contained a viewpoint specific sequence and 30nt of the P7 sequencing primer in the initial PCR round. Per viewpoint 5 initial rounds of PCR of 20 cycles were performed on 100ng of 4C template. In a second round of PCR we combined 5 ul of the initial 5 PCR volumes and ran a PCR using the forward adapters from the initial round of PCR and barcoded universal adapters.

treatment_protocol: CRISPRs targeting WAPL (5’-CACCGCGTTCCATAGTATCCTGTA-3’) and SCC4 (5’-CACCGTACGGGCCTCGATGCGCTG-3’) were cloned into px330 (Addgene plasmid #42230). ∆WAPL and ∆SCC4 HAP1 clones were generated by insertion of a Blasticidine or Puromycin cassette respectively, as previously described (Blomen et al., 2015). ∆WAPL/∆SCC4 cells were generated by knocking out SCC4 in ∆WAPL cells.

tag: genotype


title: WAPL1_NCAM

description: Libraries prepared from 3C template


title: H3K27Ac-AB2-Adult-Rod_M_N-P14 replicate 2

value: postnatal day 14


title: DKO_3.3-A Hi-C

description:
TruSeq libraries prepared from 3C template
DKO_3.3.validPairs

data_processing:
Library strategy: HiC-Seq
Raw sequence data was mapped and processed using HiC-Pro v2.7.7 (Servant et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C summary files contain the genomic position and strand of the two pairs of a Hi-C ligation

source_name: Hap1 WaplKO_3.3/SCC4KO

extract_protocol:
Hi-C was performed essentially as previously described (Rao et al., 2014). Briefly, for each template roughly 10 million cells were crosslinked using 2% formaldehyde. In nucleus restriction was performed using MboI. Restriction overhangs were filled in with biotinylated nucleotides followed by blunt-end ligation. A streptavidin pull-down was performed to enrich for ligated sequences.
Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.

tag: cell line


title: WT1_NCAM

description: Libraries prepared from 3C template

source_name: Hap1 WT

value: WT


title: H3K27Ac-AB2-Adult-Rod_M_N-P10 replicate 1

value: postnatal day 10


title: H3K27Ac-AB2-Adult-Rod_M_N-P7 replicate 2

value: postnatal day 7


title: SCC4KO-A Hi-C

description:
TruSeq libraries prepared from 3C template
SCC4KO.validPairs

source_name: Hap1 SCC4KO


title: H3K27Ac-AB2-Adult-Rod_I_N-P3 replicate 1


title: H3K27Ac-AB2-Adult-Rod_M_N-P7 replicate 1


title: WaplKO_3.3-A Hi-C

description:
TruSeq libraries prepared from 3C template
WaplKO_3.3.validPairs


title: H3K27Ac-AB2-Adult-Rod_I_N-P3 replicate 2


title: H3K27Ac-AB2-Adult-Rod_I_N-P0 replicate 3

value: postnatal day 0


title: H3K27Ac-AB2-Adult-Rod_I_N-P0 replicate 2


title: WaplKO_1.14 rep 1 RNAseq

data_processing:
Reads were mapped to hg19 using TopHat 2.0.9 and HTSeq-count was used to generate transcript-counts.
DESeq2 1.10.1 was used to infer differentially expressed genes with basic settings.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq output

source_name: Hap1 WaplKO_1.14

extract_protocol:
Total RNA from cultured cells was extracted using TRIzol reagent (Invitrogen).
Strand-specific libraries were generated using the TruSeq PolyA Stranded mRNA sample preparation kit (iIlumina). In brief, polyadenylated RNA was purified using oligo-dT beads. Following purification, the RNA was fragmented, random-primed and reserve transcribed using SuperScript II Reverse Transcriptase (Invitrogen). The generated cDNA was 3’ end-adenylated and ligated to Illumina Paired-end sequencing adapters and amplified by PCR using HiSeq SR Cluster Kit v4 cBot (Illumina).


title: WaplKO_1.14 rep 3 RNAseq


title: common acquired nevus (JC050)

description: Barcode: ACTTGA

tag: tissue

value: common acquired nevus


title: Hap1 rep B3 RNAseq

tag: genotype/variation


title: H3K27Ac-AB2-Adult-Rod_E_N-E17.5 replicate 1

value: embryonic day 17.5


title: WaplKO_1.14 rep 2 RNAseq


title: Hap1 rep B2 RNAseq


title: Hap1 rep B1 RNAseq


title: H3K27Ac-AB2-Adult-Rod_E_N-E17.5 replicate 2


title: DKO_3.3 rep 3 RNAseq


title: H3K27Ac-AB2-Adult-Rod_E_N-E14.5 replicate 2

value: embryonic day 14.5


title: WT2_NCAM

description: Libraries prepared from 3C template


title: H3K27Ac-AB2-Adult-Rod_M_N-P10 replicate 2


title: DKO_3.3 rep 2 RNAseq


title: H3K27Ac-AB2-Adult-Rod_E_N-E14.5 replicate 1


title: CTCF-AB1-IPS-Rod_M_Y-7602

value: mature retinal-derived iPSCs 7602


title: DKO_3.3 rep 1 RNAseq


title: SCC4KO rep 3 RNAseq


title: CTCF-AB1-IPS-Rod_M_Y-3302

value: mature retinal-derived iPSCs 3302


title: SCC4KO rep 2 RNAseq


title: CTCF-AB1-mESC-Eb5_E_Y-Eb5

source_name: mouse embryonic stem cell

value: mouse embryonic stem cell


title: CTCF-AB1-IPS-Rod_I_Y-8601

value: immature retinal-derived iPSCs 8601


title: SCC4KO rep 1 RNAseq


title: WaplKO_3.3 rep 3 RNAseq


title: WaplKO_3.3 rep 2 RNAseq


title: H3K27Ac-AB2-Adult-Rod_I_N-P0 replicate 1


title: CTCF-AB1-IPS-Fibr_F_Y-fMG03

value: derived iPSCs fMG03


title: H3K27Ac-AB2-Adult-Rod_M_N-P14 replicate 1


title: CTCF-AB1-IPS-Fibr_F_Y-fG140.03

source_name: fibroblast-derived iPSCs fG140.03

value: fibroblast-derived iPSCs fG140.03


title: CTCF-AB1-IPS-Fibr_F_Y-fG140.04

source_name: fibroblast-derived iPSCs fG140.04

value: fibroblast-derived iPSCs fG140.04


title: CTCF-AB1-Adult-Rod_M_N-WTM11 replicate 2

value: adult 11 month


title: WaplKO_3.3 rep 1 RNAseq


title: CTCF-AB1-Adult-Rod_M_N-WTM11 replicate 1


title: CTCF-AB1-Adult-Rod_T_N-MDMX replicate 1

value: p107 minus minus MDMXTg


title: Hap1 rep A2 RNAseq


title: DKO_3.3 SMC1 ChIPseq

data_processing:
Reads were mapped to hg19 using Bowtie2.1.0 with default settings.
Peak calling was performed using MACS2 (v2.1.1) (Feng et al., 2012) using IgG as control.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

extract_protocol:
Cells were fixed in 1% formaldehyde; 50mM Hepes-KOH; 100mM NaCl; 1 mM EDTA; 0,5 mM EGTA. Cell lysis was performed in LB1 buffer with final pH 7,5 (50 mM Hepes-KOH; 140mM NaCl; 1mM EDTA, 10% Glycerol, 0.5% NP-40; 0,25% Triton X-100; Proteinase inhibitor) for 20 minutes at 4°C. Subsequently, nuclei were lysed using LB2, pH 8,0 (10mM Tris-HCl; 200 mM NaCl; 1mM EDTA; 0,5mM EGTA; Proteinase inhibitor) for 10 minutes at 4°C. Pellets were resuspended in LB3 pH8,0 (10mM Tris-HCl; 100mM NaCl; 1 mM EDTA; 0,5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine; Proteinase inhibitor). Cross-linked chromatin was sheared (400-800 bp) using a Covaris S2 with Tube and Caps (Covaris, 520048), using the following settings: duty cycle: 10%, intensity: 4, cycles per burst: 200 time 40 seconds with 20 cycles. Chromatin precipitation was performed overnight using antibody-bound (CTCF 5 μl, SMC1 10 μl, Igg 10 μl per IP) proteinA coupled DynaBeads (Invitrogen). Elution and decrosslinking was performed overnight at 65°C in EB pH 8,0 (50mM Tris-HCl; 10mM EDTA; 1% SDS). Samples were treated with Proteinase K and RNAseA for 2 hours. DNA was isolated using phenol extraction and ethanol precipitation.
Library preparation was done using a KAPA Library preparation kit using the manufacturer’s protocol.

tag: antibody


title: CTCF-AB1-Adult-Rod_M_N-P21 replicate 3

value: postnatal day 21


title: Hap1 rep A1 RNAseq

value: WT


title: SCC4KO SMC1 ChIPseq


title: CTCF-AB1-Adult-Rod_M_N-P21 replicate 2


title: Hap1 rep A3 RNAseq


title: Hap1 SMC1 ChIPseq


title: CTCF-AB1-Adult-Rod_M_N-P21 replicate 1


title: CTCF-AB1-Adult-Rod_M_N-P14 replicate 2

value: postnatal day 14


title: CTCF-AB1-Adult-Rod_M_N-P14 replicate 1


title: DKO_3.3 CTCF ChIPseq

value: CTCF


title: WaplKO_3.3 SMC1 ChIPseq


title: SCC4KO CTCF ChIPseq


title: CTCF-AB1-IPS-Fibr_F_Y-fMG02

value: derived iPSCs fMG02


title: CTCF-AB1-Adult-Rod_M_N-P10 replicate 2

value: postnatal day 10


title: CTCF-AB1-Adult-Rod_M_N-P10 replicate 1


title: WaplKO_3.3 CTCF ChIPseq


title: CTCF-AB1-Adult-Rod_M_N-P7 replicate 2

value: postnatal day 7


title: DKO_3.3 IgG ChIPseq

value: IgG


title: CTCF-AB1-Adult-Rod_M_N-P7 replicate 1


title: CTCF-AB1-Adult-Rod_I_N-P3 replicate 2

value: postnatal day 3


title: CTCF-AB1-Adult-Rod_I_N-P3 replicate 1


title: CTCF-AB1-Adult-Rod_I_N-P0 replicate 2

value: postnatal day 0


title: WaplKO_3.3 IgG ChIPseq


title: CTCF-AB1-Adult-Rod_I_N-P0 replicate 1


title: CTCF-AB1-Adult-Rod_E_N-E17.5 replicate 3

value: embryonic day 17.5


title: CTCF-AB1-Adult-Rod_E_N-E14.5 replicate 2

value: embryonic day 14.5


title: Hap1 IgG ChIPseq


title: SP140_siRNA_4hr

first: Kate

middle: L

last: Jeffrey

address: 50 Blossom St, Thier 340

department: Medicine

institute: Massachusetts General Hospital, Harvard Medical School

description: Tn5 transposase digested DNA

data_processing:
Library strategy: ATAC-seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using BWA
Wig files were generated by HotSpot v3.0
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: primary human macrophages

extract_protocol:
Cell lysis, digestion and tagmentation according to Buenrostro et al., 2013 using a Nextera DNA Sample Preparation kit.
ATAC-seq libraries were prepared for sequencing using Tn5 transposase mediated tagmentation (Buenrostro et al., 2013)

treatment_protocol: 1.5x10e6 differentiated macrophage cells were transfected with a final siRNA concentration of 5 nM using the HiPerfect Qiagen) fast forward protocol in medium containing 100ng/mL IFNg (peprotech). Cells were incubated at 37oC for an additional 48h and were subsequently stimulated with LPS (Sigma, 100 ng/mL).

value: macrophage

tag: transfection

value: SP140 siRNA

tag: growth medium

value: containing 100ng/mL IFNg

tag: treatment

value: LPS

tag: treatment time


title: SP140_siRNA_0hr

description: Tn5 transposase digested DNA

value: no LPS


title: Control_4hr

description: Tn5 transposase digested DNA

value: control


title: Control_0hr

description: Tn5 transposase digested DNA


title: BRD4-AB1-IPS-Rod_M_Y-7602

value: mature retinal-derived iPSCs 7602


title: CTCF-AB1-Adult-Rod_E_N-E17.5 replicate 1


title: RNA-WT-FW21

extract_protocol:
RNA was extracted from freshly isolated retinas using RNeasy Plus Mini kit (Qiagen #74134). Technologies #Q33120)
Libraries were prepared from ~ 500 ng total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 2500 sequencers according to the manufacturer’s directions (Illumina.)

value: fetal week 21


title: CTCF-AB1-Adult-Rod_E_N-E14.5 replicate 1


title: BRD4-AB1-IPS-Rod_I_Y-8601

value: immature retinal-derived iPSCs 8601


title: miR28 S6

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: S28_2bis miR28

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
ComBat was used to correct for effects associated to different library batches.
Genome_build: Ensembl genebuild 76 (human assembly GRCh38).
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

source_name: Ramos cell line

growth_protocol: Experiments were conducted with transudced Ramos Burkitt lymphoma human B cell line.

extract_protocol:
Total RNA was extracted from 12 samples (6 pairs of miR-28 and scrambled samples) with RNeasy columns (Qiagen)
cDNA was prepared using the standard Ilumina TrueSeq RNAseq library preparation kit.
Libraries were prepared in two batches.

treatment_protocol: Ramos cells transduced with miR-28 or scrambled pTRIPZ vectors were selected with puromycin (0.4ug/ml) and induced for 2 days with Dox (0.5ug/ml); RFP+ cells were isolated with a FACS Aria cell sorter

tag: transduction

value: miR-28 XENO 2

value: Doxyciclin

tag: library batch

tag: sample pair


title: miR28 S5

description: S28_1tris miR28

value: miR-28 XENO 1


title: BRD4-AB1-mESC-Eb5_E_Y-Eb5

value: mouse embryonic stem cell


title: miR28 S4

description: S28_1bis miR28


title: BRD4-AB1-IPS-Fibr_F_Y-fMG02

value: derived iPSCs fMG02


title: bulk_hek

description: bulk transcriptomics

value: HEK 293

tag: developmental stage

value: not applicable

tag: fixation

value: live, not fixed


title: Hap1 CTCF ChIPseq

value: WT

value: CTCF


title: miR28 S3

description: S28_3 miR28


title: SCC4KO IgG ChIPseq

value: IgG


title: miR28 S2

description: S28_2 miR28


title: BRD4-AB1-IPS-Fibr_F_Y-fMG03

source_name: fibroblast-derived iPSCs fMG03

tag: strain

value: derived iPSCs fMG03


title: BRD4-AB1-IPS-Fibr_F_Y-fG140.04

value: fibroblast-derived iPSCs fG140.04

tag: chip antibody


title: miR28 S1

description: S28_1 miR28


title: BRD4-AB1-IPS-Fibr_F_Y-fG140.03

tag: cell type

value: fibroblast-derived iPSCs fG140.03


title: Scramble S6

description: S2 bis Scramble

value: Scramble XENO 2


title: WaplKO_1.14-A Hi-C

description:
TruSeq libraries prepared from 3C template
WaplKO_1.14.validPairs


title: BRD4-AB1-IPS-Rod_M_Y-3302

value: mature retinal-derived iPSCs 3302


title: BRD4-AB1-Adult-Rod_M_N-WTM11 replicate 1

tag: age

value: adult 11 month


title: Scramble S5

description: S1 tris Scramble

value: Scramble XENO 1


title: DKO_3.3-C Hi-C

tag: cell line


title: Scramble S3

description: S3 Scramble

value: Scramble

value: Doxyciclin


title: WaplKO_3.3-C Hi-C


title: BRD4-AB1-Adult-Rod_M_N-P21 replicate 1

value: postnatal day 21


title: KSHV-VLV (microRNA)

description: no

data_processing:
TopHat under default parameter
Genome_build: hg38, KSHV JSC-1 clone BAC16
Supplementary_files_format_and_content: counts

organism:
Homo sapiens
Human gammaherpesvirus 8

growth_protocol: iSLK cells latently infected with KSHV-65stop

extract_protocol:
Trizol for total RNA, and then gel purify microRNA
TruSeq Small RNA Library Prep Kit

treatment_protocol: iSLK-KSHV-65stop cells were treat with TPA +NaB for three day, and then KSHV VLVs were purified from supernatant through sucrose density gradient

value: iSLK (epithelial cell)

tag: virus


title: DKO_3.3-B Hi-C

tag: genotype/variation


title: HOK16B.219_VLV2d#2 (mRNA)

description:
A10
KSHV.xlsx

source_name: HOK16B.219 cells

growth_protocol: HOK16B cells latently infected with KSHV.219

extract_protocol:
Trizol for total RNA, and then oligodT beads for polyA RNA
method based on ScriptSeq mRNA-Seq library preparation kit (Epicentre)

treatment_protocol: treat with or without KSHV VLV for one or two days

value: Oral epithelial cell

value: KSHV


title: BRD4-AB1-Adult-Rod_M_N-P14 replicate 1

value: postnatal day 14


title: Scramble S2

description: S2 Scramble


title: HOK16B.219_VLV2d#1 (mRNA)

description:
A9
KSHV.xlsx


title: BRD4-AB1-Adult-Rod_M_N-P10 replicate 1

value: postnatal day 10


title: SCC4KO-B Hi-C


title: WaplKO_1.14-B Hi-C


title: Scramble S1

description: S1 Scramble


title: BRD4-AB1-Adult-Rod_I_N-P3 replicate 1

value: postnatal day 3


title: WaplKO_3.3-B Hi-C


title: HOK16B.219_VLV1d#2 (mRNA)

description:
A8
KSHV.xlsx


title: BRD4-AB1-Adult-Rod_M_N-P7 replicate 1

value: postnatal day 7


title: BRD4-AB1-Adult-Rod_T_N-MDMX replicate 2

value: p107 minus minus MDMXTg