title: Spl-4R3

city: Houston

first: Maria

last: Bettini

state: TX

address: 1102 Bates St

institute: Baylor College of Medicine

description:
Sorted cells
mRNA
Processed_data_file: Isl-4R_vs_Spl-4R.gene_exp.csv
Processed_data_file: Spl-4R_vs_Spl-mR.gene_exp.csv
Processed_data_file: Spl-4R_vs_Spl-mR.deseq.res.csv
Processed_data_file: Isl-4R_vs_Spl-4R.deseq.res.csv
Processed_data_file: Spl-4R_vs_Spl-mR_genes.rlog.csv
Processed_data_file: Isl-4R_vs_Spl-4R_genes.rlog.csv

data_processing:
All samples were run through both processing step A and step B for comparison using two bioinformatic approaches. Data processing B was used for figure generation in the manuscript.
NextSeq Control Software v2.0 used for base calling.
Step A: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using TopHat Alignment v1.0.0. Fragment per kilobase million of library size (FPKM) were calculated using Cufflinks Assembly & DE v1.1.0.
Step B: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using STAR v1.1.0. Fragment per kilobase million of library size (FPKM) were calculated using DESeq2 v1.1.0.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.gene_exp.csv: Cufflinks abundance measurements.
Supplementary_files_format_and_content: *.deseq.res.csv: DESeq2 results
Supplementary_files_format_and_content: *.genes.rlog.csv: DESeq2 rlog

source_name: Spleen

extract_protocol:
TritonX-100 cell lysis, reverse transcription, cDNA amplification.
Nextera XT

tag: strain/background

value: NOD

value: 4-8 TCR

value: Tregs

tag: age

value: 6.8 weeks


title: Spl-4R2

status: Public on Dec 29 2017

type: SRA

country: USA

description:
Sorted cells
mRNA
Processed_data_file: Isl-m1-Treg_vs_Spl-mR.gene_exp.csv
Processed_data_file: Spl-4R_vs_Spl-mR.gene_exp.csv
Processed_data_file: Spl-4R_vs_Spl-mR.deseq.res.csv
Processed_data_file: Isl-m1-Treg_vs_Spl-mR.deseq.res.csv
Processed_data_file: Spl-4R_vs_Spl-mR_genes.rlog.csv
Processed_data_file: Isl-m1-Treg_vs_Spl-mRgenes.rlog.csv

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype/variation

tag: cell type


title: Spl-4R1


title: Spl-mR1


title: Spl-mR3


title: Spl-mR2


title: Isl-4-8-Treg2

description:
Sorted cells
mRNA
Processed_data_file: Isl-4R_vs_Isl-m1-Treg.gene_exp.csv
Processed_data_file: Isl-4R_vs_Spl-4R.gene_exp.csv
Processed_data_file: Isl-4R_vs_Isl-m1-Treg.deseq.res.csv
Processed_data_file: Isl-4R_vs_Spl-4R.deseq.res.csv
Processed_data_file: Isl-4R_vs_Isl-m1-Treg_genes.rlog.csv
Processed_data_file: Isl-4R_vs_Spl-4R_genes.rlog.csv

source_name: Pancreatic islets


title: Isl-4R3


title: Isl-m1-Treg2

description:
Sorted cells
mRNA
Processed_data_file: Isl-4R_vs_Isl-m1-Treg.gene_exp.csv
Processed_data_file: Isl-m1-Treg_vs_Spl-mR.gene_exp.csv
Processed_data_file: Isl-4R_vs_Isl-m1-Treg.deseq.res.csv
Processed_data_file: Isl-m1-Treg_vs_Spl-mR.deseq.res.csv
Processed_data_file: Isl-4R_vs_Isl-m1-Treg_genes.rlog.csv
Processed_data_file: Isl-m1-Treg_vs_Spl-mRgenes.rlog.csv


title: Isl-mR3


title: H3K27me2me3_N5102_OY329_FGSC3670_AGTCAA_082114

city: Eugene

first: Eric

last: Selker

state: Oregon

address: 1370 Franklin Blvd.

department: Biology

institute: University of Oregon

library_source: genomic

data_processing:
For Poly-A mRNA seq: high quality, adapter-less reads were identified (Stacks); Kmer filtering reduced sequencing errors. Reads were mapped (TopHat) to the modified Neurospora genome assembly 12, and sorted (SAMTools), and directionality-preserved read numbers were calculated at each gene ID (HTSeq), adding one read count to prevent abnormal fold changes. Differential gene expression analysis (DESeq) examined replicate differences and pair-wise analyses between WT and translocations.
To make ChIPseq enrichment files for display in Integrative Genomics Viewer (IGV, Robinson et al., 2011, Nat. Biotechnol.), reads were mapped with bowtie2 to the nc12-fixed genome (Galazka et al., 2016) using default parameters, and reads were converted to .bam files, sorted, and indexed. The .bam files (and the corresponding .bai index files) were counted with the "Count" command of igvtools, using the mean window function and 200bp windows. Output file was a .tdf file, displayable on IGV.
For whole-genome-seq breakpoint analysis: Incongruous-paired and split-read alignments for input DNA samples were found using bwa-mem. The discordant and split-read alignments were analyzed with LUMPY v0.2.9 to determine the location of chromosomal breakpoints (Layer et al. 2014). A list of predicted breakpoints with a minimum call weight of five was generated and calls with an evidence set score <0.05.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024).
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011), using a window size of 25 -200bp (.tdf files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV). The bcf files were produced from bam files (mapped to the Neurospora crassa assembly 12 Fixed by samtools), and report enrichment values.
Supplementary_files_format_and_content: For Poly-A mRNA files: Text files contain counts for every gene as outlined in process above.
Supplementary_files_format_and_content: For whole-genome-seq: bedpe files contain list of predicted breakpoints predicted by LUMPY.

molecule: genomic DNA

organism: Neurospora crassa

source_name: germinated conidia

growth_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC.

extract_protocol:
RNA-seq: Mycelia were harvested and added to a tube containing ~350uL glass beads (260-300 micrometer, acid washed [Sigma Aldrich] and resuspended in sdH2O), 350uL NETS buffer (10mM Tris pH 7.5, 300mM NaCl, 1mM EDTA, 0.2% SDS) and 350uL phenol:chloroform:isoamyl alcohol (25:24:1) and lysed by a bead beater for 3 minutes at room temperature. Samples were cleared by centrifugation, and the aqueous (top) phase was mixed with 350uL of chloroform. After centrifugation, the aqueous phase was divided into two tubes containing 650uL cold 100% EtOH. Samples were precipitated at -20oC, pelleted by centrifugation, washed twice with 1mL 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNase (DNA-free™ DNA Removal Kit, Thermo Fisher Scientific) and cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter).
ChIP-seq: Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde for histone modification ChIP. Tissue added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% Triton + proteinase inhibitors) and was disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 2uL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A or Protein G slurry (agarose or magnetic beads) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC. Samples (IP and input) were decrosslinked at 65oC overnight. The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the QIAquick PCR purification kit and eluted in 30 μl of water.
Whole-genome-seq: Used input DNA from ChIP experiments.
RNA-seq: RNA-seq libraries were prepared (KAPA Stranded mRNA-seq kit, KAPA Biosystems).
ChIP-seq: Approximately 10 ng of DNA was used to generate ChIP-Seq libraries. Each library was prepared using the Illumina Tru-Seq kits A and B (Illumina, IP-202-1012 and IP-202-1024) according to the manufacturer’s instructions. “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606). Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 10 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.
Whole-genome-seq: Performed library prep same as ChIP-seq samples.

tag: tissue

value: germinated conidia

tag: chip antibody

value: H3K27me2me3 (ActiveMotif; cat# 39535)


title: M81-transformed LCLs sample 1

city: Heidelberg

first: Henri-Jacques

last: Delecluse

address: Im Neuenheimer Feld 280

department: Pathogenesis of Virus Associated Tumors

country: Germany

institute: DKFZ

description:
RNA-Seq M81 sample 1
Processed data file: Human genes_RPKM.tsv
Processed data file: M81 viral genes_RPKM.txt
Processed data file: M81_new viral genes_RPKM.txt

data_processing:
Sequenced reads were trimmed for adaptor sequences and mapped to the HG-19 human genome using star.
Unmapped sequences were then further mapped to the viral genomes of B95-8 (NC_007605.1) and M81 (KF373730.1) using tophat2.
The remaining unmapped sequences were then mapped to the new EBV genes identified by O'Grady et al.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated according to Mortazavi et al. Nature Methods 2008.
Genome_build: hg19 (GRCh37); NC_007605.1; KF373730.1
Supplementary_files_format_and_content: *_libraries_RPF.txt: Tab-delimited text files contain normalized ribosome coverage for each Sample.
Supplementary_files_format_and_content: *_RPKM.txt: Tab-delimited text files include RPKM values for each Sample.

organism: Homo sapiens

source_name: B cells

growth_protocol: EBV-transformed B cells and HEK293 cells were maintained in RPMI-1640 medium (Invitrogen). B cells were subpassaged every 3-4 days, depending on cell density. HEK293 cells were routinely split at a 1:7 ratio by resuspension and transfer onto a new culture dish.

extract_protocol:
Lysates were clarified by centrifugation and ribosome covered RNA was isolated by sucrose gradient ultracentrifugation and subsequent fractionation. Isolated fractions were RNase I treated for 15 minutes at room temperature. Following nuclease treatment, ribosome protected fragments were gel purified. For total RNA sequencing, cells were lysed with Trizol (Ambion) reagent and RNA was purified according to manufacturer's instructions.
Ribosome profiling libraries for high-throughput sequencing were generated according to the published protocol from Ingolia et al. 2012 published in Nature Protocols. The total RNA sequencing libaries were prepared by the DKFZ core facility using the strand-specific RNA preparation kit from Agilent.

treatment_protocol: Cycloheximide treatment was performed at 37°C for 10 minutes at a concentration of 100µg/ml. Harringtonine treatments were performed at 37°C for 2 or 5 minutes at a concentration of 2µg/ml. For total RNA sequencing, the samples were left untreated.

value: CD19+ B cells

tag: in vitro transformed by

value: EBV strain M81

tag: treatment


title: Isl-m1-Treg1


title: NB4-shNS-rep2 [RNA-Seq]

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

description:
processed data file:
KnockDown1_vs_Control1.all.gene.result.xls
JC-HW15_GTCCGC

data_processing:
sequence reads were aligned to the genome by using standard Illumina sequence analysis pipeline
Genome_build: GRCh19
Supplementary_files_format_and_content: the expression and p value

molecule: polyA RNA

extract_protocol:
RNA was extracted by using TRIzol reagent (Invitrogen, Carlsbad, CA). NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for polyA RNA purification.
Library was prepared by or NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA).

tag: cell line

tag: tumor

value: acute monocytic leukemia

tag: shRNA

value: shNS (non-specific control)


title: ATAC SPRET 90m B2

status: Public on Dec 28 2017

city: Boston

first: Michael

last: Greenberg

address: 200 Longwood Ave

institute: Harvard Medical School

data_processing:
Sequenced reads were demultiplexed, trimmed for adaptor sequences, and mapped to mm10 whole genome using Bowtie (1.1.1) with parameters -p 4 -S -n 2 -e 70 -m 1 -k 1 -l 49 --best mm10 --chunkmbs 200
Sam files were converted to bam files using samtools (1.1) view with parameters -h -b -F 3844 -q 10
Peaks were called via the IDR pipeline (https://sites.google.com/site/anshulkundaje/projects/idr). Optimal sets of peaks were called on pseudoreplicates of pooled data by both MACS (2.1.0) and SPP (phantompeakqualtools), and the two sets of peaks were intersected to obtain a consensus peakset for further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of histograms normalized to 10M reads for mapped, in silico extended reads

source_name: Primary fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were grown in DMEM with 10% FBS.

extract_protocol:
Growth media was removed and MEFs were lysed in hypotonic lysis buffer to isolate nuclei. Approximately 40,000 nuclei were used as input to the Nextera DNA Sample Preparation Kit (FC-121-1030).
ATAC libraries were prepared using the standard library preparation protocol outlined in the Nextera DNA Sample Preparation Kit (FC-121-1030).

treatment_protocol: MEFs were serum starved for 26-30 hours in 0.5% serum MEF media and stimulated for the indicated times at a final concentration of 15% serum.

tag: strain

value: SPRET/EiJ

tag: genotype

value: wild-type

value: 90m stimulation with 15% serum media

tag: passage

value: Primary fibroblasts

tag: serum stimulation


title: ATAC 90m B2


title: ATAC SPRET 90m B1


title: SPRET Fos 90m B2

extract_protocol:
Growth media was removed and MEFs were crosslinked in 1% formaldehyde for 10 minutes at room temperature before quenching with glycine at a final concentration of 0.125M. Sonicated chromatin from isolated nuclei were used as input to ChIP.
2-40 ng of each ChIP sample was used to prepare ChIP-Seq libraries with the NuGEN Ovation Ultralow Library System v2 kit.

value: Santa Cruz sc-7202X lot A2513


title: ATAC 0hr B1

value: starved with 0.5% serum media


title: ATAC 90m B1


title: Isl-4R1


title: H3K27me2me3_N3752_WT_FGSC2489_CGTACG_102214


title: EX3_MRC5142_HCMV142T_9d

city: New York

first: Rasmus

last: Moeller

state: NY

address: 1 Gustave L. Levy Place

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

description:
Cells transduced with miR-142 exp lentivirus prior to infection
EX_MRC5-142-HCMV-9d_vs_MRC5-142-HCMV142T-9d.csv
EX_MRC5-142-HCMV-9d_vs_MRC5-142-HCMV142T-9d.host.deseq.res.csv

data_processing:
RNA Express v1.1.0 (Illumina, Inc.) was used for host gene expression analysis
RNA-seq reads are aligned with STAR
Differential gene expression is determined with DEseq2
Bowtie was used to map HCMV reads to the TB40/E reference genome EF999921.1
DEseq2 was used to determine differential gene expression for viral reads.
Genome_build: hg19 for host genes and EF999921.1 (GenBank) for HCMV genes
Supplementary_files_format_and_content: genecount and .csv containing differential gene expression

source_name: primary fibroblasts

extract_protocol:
RNA was extracted with TRIzol (Invitrogen) following product protocol.
Libraries were prepared with the TruSeq RNA Library Preparation Kit v2 (Illumina) from 100ng total RNA following the manufacturer’s instructions.

value: MRC-5 fibroblasts

tag: infection

value: HCMV TB40/E IE2-miR142T

tag: multiplicity of infection

tag: time point

value: 9 days


title: EX4_MRC5142_HCMV142T_9d_R


title: ATAC SPRET 0hr B2

tag: age


title: ATAC SPRET 0hr B1


title: EX2_MRC5142_HCMV_9d_R

value: HCMV TB40/E


title: EX1_MRC5142_HCMV_9d


title: CK8_THP1_HCMV142T_9d_R

description:
CK_THP1-HCMV-9d_vs_THP1-HCMV142T-9d.csv
CK_THP1-HCMV-9d_vs_THP1-HCMV142T-9d.host.deseq.res.csv

source_name: macrophage cell line

value: THP-1 macrophages


title: CK7_THP1_HCMV_9d_R


title: CK6_THP1_HCMV142T_9d


title: SPRET H3K27ac 90m B2

value: Abcam ab4729 lot GR150367-1


title: CK4_MRC5_HCMV142T_9d_R


title: SPRET H3K27ac 0hr B2


title: SPRET Fos 90m B1


title: SPRET H3K27ac 90m B1


title: hs_PB_orthochromatic_3

first: John

last: Hale

address: 310 East 67th Street

institute: New York Blood Center

data_processing:
Illumina Casava 1.8.2 software was used for basecalling.
FASTQ format sequencing reads were aligned to the hg19 using HISAT2 2.1.0 software with default parameters to hg19 reference annotation.
Raw read counts were extracted from the aligned reads using the featureCounts program.
Differential expression analysis was done at each stage comparing the two original sources of CD34+ cells using the DESeq2 bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: erythroblast

extract_protocol:
Total RNAs were extracted by RNeasy Plus Mini Kit (Cat# 74134, QIAGEN). Illumina TruSeq RNA Sample Prep Kit (Part # 15008136) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cultured CD34+ cells

value: Peripheral blood


title: H3K27me2me3_N5100_AR16_FGSC1614_CTTGTA_082114

value: germinated conidia

value: H3K27me2me3 (ActiveMotif; cat# 39535)


title: CK3_MRC5_HCMV_9d_R


title: CK2_MRC5_HCMV142T_9d


title: ATAC 0hr B2


title: hs_PB_orthochromatic_2


title: BW5_THP1_HCMV_24h

value: 24 hours


title: SPRET H3K27ac 0hr B1

value: SPRET/EiJ


title: hs_PB_orthochromatic_1


title: hs_PB_polychromatic_3


title: JunD 0hr B2

value: wild-type

value: Santa Cruz sc-74 lot I1014


title: JunD 90m B2

value: 90m stimulation with 15% serum media

value: Primary fibroblasts


title: BW3_MRC5_HCMV142T_24h


title: BW6_THP1_HCMV142T_24h


title: H3K27me2me3_input_N5858_OY337_FGSC3668_CTTGTA_121514


title: CK5_THP1_HCMV_9d


title: Fosl2 0hr B2

value: starved with 0.5% serum media

value: Santa Cruz sc-604X lot H2713


title: Fosl2 90m B1


title: hs_PB_late_basophilic_1


title: FosKO Fos 90m B2

value: Fos -/-

value: Santa Cruz sc-7202X lot A2513


title: Fosl2 0hr B1


title: FosKO Fos 90m B1


title: hs_PB_early_basophilic_2


title: Fos 90m B2

extract_protocol:
Growth media was removed and MEFs were crosslinked in 1% formaldehyde for 10 minutes at room temperature before quenching with glycine at a final concentration of 0.125M. Sonicated chromatin from isolated nuclei were used as input to ChIP.
10 ng of each ChIP sample was used to prepare ChIP-Seq libraries with Beijing Genomics Institute (BGI)'s standard library preparation protocols.

value: Santa Cruz sc-7202X lot A2513 and J1613


title: CK1_MRC5_HCMV_9d

value: MRC-5 fibroblasts

value: HCMV TB40/E

value: 9 days


title: Fos 0hr B2


title: Fosl2 90m B2


title: B6-4_1hr

data_processing:
Reads were aligned to the mouse genome (GRCm38/mm10 assembly, Dec. 2011) using the Burrows-Wheeler Aligner (bwa) tool. Two sets of target sequences were provided and incorporated into the bwa index in addition to the usual 21 chromosomal targets: (1) the 16,299-bp mouse mitochondrial genome (GenBank accession NC_005089.1); and (2) a set of ~ 8 million short (<= 96bp) exon-exon splice-junction sequences (see below). A third set of 92 short (< 2.1kb) spike-in oligos representing a wide range of reference concentrations (ERCC RNA Spike-In Mix, Life Technologies; Mix 1) was also incorporated into the index. Typically ~97% of all reads were mappable, allowing up to 2 mismatches, and of these ~85% were mapped uniquely. Multiple reads whose 5' ends were assigned to the same locus were not flattened to a single count.
The splice-junction target sequences were based on the NCBI RefSeq database for GRCm38. For each annotated transcript, we noted all subsets of two or more exons, not necessarily adjacent, that could be spliced together to produce a sequence at least as long as the read length (75 bp for chromatin-associated RNA and RNA from anisomycin treatment experiments; 49 bp for spike-in normalized RNA). Each of these sequences were then trimmed to the maximum number of bases such that a read mapping to the sequence would have to cross these ordered exons' splice junction(s). This procedure produced a library of all unique sets of exons whose intragenic splice junctions could possibly be covered by a read of the given length, based on the RefSeq annotation of exonic loci. Aligned reads thus had the opportunity to align either to genomic (chromosomal) sequences or to exon-junction-crossing sequences found only in mature mRNA.
Expression level quantification: An in-house software tool, MAPtoFeatures (Gray et al., 2014), was used to quantify expression levels for individual genes as follows. A database of genic features (CDSs and UTRs) was constructed from all 95,023 genomic transcripts annotated in RefSeq for GRCm38. Merged genes were constructed by unioning all exons in all transcripts assigned to each distinct gene; the resulting segments defined the gene's exonic coordinates used here (with the gaps between them defining introns). Genes with zero CDS exons were labeled "noncoding". These 33,102 genes were supplemented with 1,563 additional noncoding genes specified by the loci of all ribosomal RNA genes obtained from RepeatMasker (where the options Variations and Repeats, rmsk.repFamily="rRNA" yielded 480 LSU-rRNA_Hsa; 45 SSU-rRNA_Hsa; 1,038 5S). The purpose of this step was to allow the filtering out of reads stemming from transcription of repeats and rRNA genes, which tend to get populated to inconsistent degrees from sample to sample depending on the variable quality of rRNA depletion.
Reads that aligned uniquely were then queried for their intersection with the exonic ranges of any of the above 34,665 genes, including exon-exon splice junctions. The total number of read bases that overlapped an exonic range was divided by the range's length to give an average exonic read Density (i.e., coverage). All reads were assigned to genes or to intergenic regions. However, only those reads not assigned to noncoding genes counted towards the total normalization count N, which ultimately afforded a more stable comparison of expression levels between samples than simply using the total number of reads. All read densities were normalized to a reference total of 10 million reads and a reference read length of 35 bp through multiplication by the factor (10^7/N)x(35 bp/49 bp). (Division of these normalized densities by 0.35 yielded expression levels in alternative units of reads per kilobase of transcript per million mapped reads, RPKM.)
An additional normalization step was carried out exploiting the ERCC spike-in sequences. The normalized read Densities for these 92 targets were calculated as described above for each of our samples. Any residual sample-to-sample variation was accounted for by a model wherein log-transformed observed Densities log(Dobs) for each sample were assumed to have a simple linear dependence on the log-transform of the spike-in concentration C: log(Dobs) = ak + bk*log(C) (k = 1,...,36), with the expectation that bk ~ 1 for the slopes. The parameters (ak,bk) were obtained for each sample from a linear least-squares fit to the spike-in oligos' known concentrations and observed Densities in that sample; indeed, the slopes were found in the range 0.94-0.99, with an average standard error of the slope 0.047 over all the fits. (In particular, these fits were based on only those 49 oligos that were observed with nonzero expression in all samples.) Inverting each linear fit, any gene's Dobs for sample k could be replaced by an inferred concentration C that supposedly derives from a "true" Density value D. Renormalization among all samples was achieved by a transformation back to log-Densities that would yield the same value of D in any sample for a given C: log(D) = a0 + log(C), i.e., with exactly unit slope and with intercept a0 equal to the mean of all {ak}. Finally, each observed Density in sample k was replaced with a renormalized Density D via log(D) = a0 + ([log(Dobs) - ak]/bk). (Zero Densities were left unchanged.) Of course the base used for all the logarithms is arbitrary; the mean intercept for base-10 calculations was a0 = -1.618. For downstream analyses, genes with a normalized exon density value of 0 in any replicate at any timepoint were discarded to remove lowly expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of histograms normalized to 10M reads for mapped, in silico extended reads

extract_protocol:
Cells were washed once with PBS and lysed in 2mL of Trizol.  Prior to RNA extraction, an equal amount of ERCC spike-in control RNA was added to each sample, following the manufacturers specifications.  RNA was extracted using the Qiagen RNeasy Mini Kit with on-column DNAse digestion.
RNA-Seq libraries were prepared with Beijing Genomics Institute (BGI)'s standard library preparation protocols.

value: 1hr stimulation with 15% serum media


title: B6-4_4hr

value: 4hr stimulation with 15% serum media


title: BW2_MRC5_HCMV_24h


title: hs_PB_proerythroblast_2

value: Cultured CD34+ cells

value: Peripheral blood


title: hs_PB_polychromatic_1


title: hs_PB_late_basophilic_3


title: FFJ H3K27ac deltaCre 90m B1

value: Fos fl/fl; Fosb fl/fl; Junb fl/fl deltaCre

value: Abcam ab4729 lot GR150367-1


title: B6-4_CTL

value: wild-type

value: Control


title: B6-3_CTL

value: Primary fibroblasts


title: B6-3_4hr


title: FFJ H3K27ac deltaCre 90m B2

value: 90m stimulation with 15% serum media


title: hs_PB_polychromatic_2


title: B6-3_1hr


title: hs_PB_late_basophilic_2


title: hs_PB_proerythroblast_3


title: hs_PB_proerythroblast_1


title: B6-2_4hr


title: FFJ H3K27ac deltaCre 0hr B1

value: starved with 0.5% serum media


title: JunD 90m B1

value: Santa Cruz sc-74 lot I1014


title: hs_PB_early_basophilic_3


title: hs_PB_CFU_3

source_name: CFU-E cells


title: FFJ H3K27ac deltaCre 0hr B2


title: B6-2_1hr


title: JunD 0hr B1


title: FFJ H3K27ac Cre 90m B2

value: Fos fl/fl; Fosb fl/fl; Junb fl/fl Cre


title: hs_PB_early_basophilic_1


title: hs_PB_CFU_1


title: H3K27ac 90m B2


title: H3K27ac 90m B3


title: FFJ H3K27ac Cre 90m B1


title: H3K27ac 90m B1


title: CHX H3K27ac 90m B2

value: 90m stimulation with 15% serum media + cycloheximide


title: hs_PB_BFU_2

source_name: BFU-E cells


title: H3K27ac 10m B2

value: 10m stimulation with 15% serum media


title: FFJ H3K27ac Cre 0hr B1


title: FFJ H3K27ac Cre 0hr B2


title: 6hr input B2

value: 6hr stimulation with 15% serum media


title: hs_PB_CD34_2

source_name: CD34 positive cells


title: CHX H3K27ac 90m B1


title: hs_PB_CD34_3


title: hs_PB_BFU_3


title: hs_PB_CFU_2


title: 6hr input B3


title: CHX H3K27ac 0hr B2

value: starved with 0.5% serum media + cycloheximide


title: B6-2_CTL


title: hs_PB_BFU_1


title: H3K27ac 10m B1


title: hs_PB_CD34_1


title: 6hr input B1


title: hES-N2G2 day 12 FGF2

city: Ann Arbor

first: Fan

last: Meng

state: MI

address: 205 Zina Pitcher Place

department: Psychiatry

institute: U of Michigan

description:
Total RNA was harvested from one well of a six well plate of stable hES H9 cells after 12 days growth on matrigel coated plates. For the first 2 days, cells were grown in mTesrE8 media with 1 ug/ml doxycycline.  For the next 4 days cells were grown in 3N media with 1 ug/ml doxycycline.  For the final 6 days, cells were grown in 3N media with 20 ug/ml FGF2.
Sample name: 57096

data_processing:
basecalling by Illumina Real Time Analysis (RTA) software version 1.18.66.3
alignment to human genome GRCh38 primary assembly was performed using subread-align version 1.5.0
featureCounts v 1.5.0 was used to obtain gene level read counts using GenCode version 24 annotation.
limma-voom and DESeq2 were used for normalization and differential expression
DAVID Bioinformatics Resources 6.8 was used for gene ontology term enrichment analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files for 1) raw count values 2) limma-voom normalized log2 values 3) differential expression analysis results from limma-voom and DESeq2. These files are available on the series record.

source_name: 57096_hES-N1 (derived from H9) cell culture

growth_protocol: Cells were grown in E8 media for two days and then switched to 3N media for the remain time in culture

extract_protocol:
Total RNA was extracted with Trizol
The Illumina TruSeq RNA Library Prep Kit v2 (Illumina) was used following manufacturer’s instructions. The mRNA was then fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The 3' end of the cDNA was then adenylated and adapters were ligated. One of the ligated adapters had a 6-nt barcode that was unique for each sample that allowed us to sequence more than one sample in each lane of HiSeq Flow Cell (Illumina). The products were purified and enriched by PCR to create the final cDNA library. Final libraries were checked for quality and quantity by TapeStation (Agilent Technologies) and qPCR using Kapa’s Library Quantification kit for Illumina sequencing platforms (Kapa Biosystems). The libraries were clustered on the cBot (Illumina) and sequenced 4 samples per lane on a 50 cycle single end on a HiSeq 2500 (Illumina) in High Output mode using version 4 reagents according to manufacturers recommended protocols.

treatment_protocol: Cells were treated with or without 1 ug/ml doxycycline and with or without 20 ug/ml FGF2.

tag: sequence run

tag: data set

value: Data Set 3-FGF2 effects days 7-12

tag: source cell line

tag: days in culture

tag: days of dox treatment

tag: days of fgf treatment


title: CHX H3K27ac 0hr B1

tag: treatment

tag: chip antibody

tag: cell line


title: hES-N2G2 day 12 control

description:
Total RNA was harvested from one well of a six well plate of stable hES H9 cells after 6 days growth on matrigel coated plates. For the first 2 days, cells were grown in mTesrE8 media with 1 ug/ml doxycycline.  For the next 4 days cells were grown in 3N media with 1 ug/ml doxycycline. For the final 6 days, cells were grown in 3N media.
Sample name: 57095

source_name: 57095_hES-N1 (derived from H9) cell culture


title: 0hr input B3

tag: strain


title: 0hr input B4

tag: genotype


title: 0hr input B2

tag: passage


title: hES-N2G1 day 12 FGF2

description:
Total RNA was harvested from one well of a six well plate of stable hES H9 cells after 12 days growth on matrigel coated plates. For the first 2 days, cells were grown in mTesrE8 media with 1 ug/ml doxycycline.  For the next 4 days cells were grown in 3N media with 1 ug/ml doxycycline.  For the final 6 days, cells were grown in 3N media with 20 ug/ml FGF2.
Sample name: 57094

source_name: 57094_hES-N1 (derived from H9) cell culture


title: hES-N2G2 day 6 FGF2

description:
Total RNA was harvested from one well of a six well plate of stable hES H9 cells after 6 days growth on matrigel coated plates. For the first 2 days, cells were grown in mTesrE8 media with 1 ug/ml doxycycline and 20 ug/ml FGF2.  For the next 4 days cells were grown in 3N media with 1 ug/ml doxycycline and 20 ug/ml FGF2.
Sample name: 57092

source_name: 57092_hES-N1 (derived from H9) cell culture

value: Data Set 2-FGF2 effects days 1-6


title: H3K27ac 0hr B6

tag: serum stimulation


title: hES-N2G1 day 12 control

description:
Total RNA was harvested from one well of a six well plate of stable hES H9 cells after 6 days growth on matrigel coated plates. For the first 2 days, cells were grown in mTesrE8 media with 1 ug/ml doxycycline.  For the next 4 days cells were grown in 3N media with 1 ug/ml doxycycline. For the final 6 days, cells were grown in 3N media.
Sample name: 57093

source_name: 57093_hES-N1 (derived from H9) cell culture


title: H3K27ac 0hr B7


title: H3K27ac 0hr B5


title: hES-N2G2 day 6 control

description:
Total RNA was harvested from one well of a six well plate of stable hES H9 cells after 6 days growth on matrigel coated plates. For the first 2 days, cells were grown in mTesrE8 media with 1 ug/ml doxycycline.  For the next 4 days cells were grown in 3N media with 1 ug/ml doxycycline.
Sample name: 57091

source_name: 57091_hES-N1 (derived from H9) cell culture


title: hES-N2G1 day 6 control

description:
Total RNA was harvested from one well of a six well plate of stable hES H9 cells after 6 days growth on matrigel coated plates. For the first 2 days, cells were grown in mTesrE8 media with 1 ug/ml doxycycline.  For the next 4 days cells were grown in 3N media with 1 ug/ml doxycycline.
Sample name: 57089

source_name: 57089_hES-N1 (derived from H9) cell culture


title: H3K27ac 0hr B3


title: H3K27ac 0hr B2


title: H3K27ac 0hr B1


title: hES-N2G1 day 6 FGF2

description:
Total RNA was harvested from one well of a six well plate of stable hES H9 cells after 6 days growth on matrigel coated plates. For the first 2 days, cells were grown in mTesrE8 media with 1 ug/ml doxycycline and 20 ug/ml FGF2.  For the next 4 days cells were grown in 3N media with 1 ug/ml doxycycline and 20 ug/ml FGF2.
Sample name: 57090

source_name: 57090_hES-N1 (derived from H9) cell culture


title: H3K27ac 0hr B4


title: hES-N1 day 5 dox

description:
Total RNA was harvested from one well of a six well plate of stable hES H9 cells after 5 days growth on matrigel coated plates.  For the first 2 days, cells were grown in mTesrE8 media with 1 ug/ml doxycycline.  For the next three days cells were grown in 3N media with 1 ug/ml doxycycline.
Sample name: 55651

source_name: 55651_hES-N1 (derived from H9) cell culture

value: Data Set 1-Differentiation


title: hES-N1 day 11 dox

description:
Total RNA was harvested from one well of a six well plate of stable hES H9 cells after 11 days growth on matrigel coated plates.  For the first 2 days, cells were grown in mTesrE8 media with 1 ug/ml doxycycline.  For the next 9 days cells were grown in 3N media with 1 ug/ml doxycycline.
Sample name: 55653

source_name: 55653_hES-N1 (derived from H9) cell culture


title: Fos 90m B1

source_name: Primary fibroblasts

value: Santa Cruz sc-7202X lot A2513


title: 0hr input B1


title: hES-N1 day 5 control

description:
Total RNA was harvested from one well of a six well plate of stable hES H9 cells after 5 days growth on matrigel coated plates.  For the first 2 days, cells were grown in mTesrE8 media.  For the next 3 days cells were grown in 3N media.
Sample name: 55650

source_name: 55650_hES-N1 (derived from H9) cell culture


title: hES-N1 day 11 control

description:
Total RNA was harvested from one well of a six well plate of stable hES H9 cells after 11 days growth on matrigel coated plates.  For the first 2 days, cells were grown in mTesrE8 media.  For the next 9 days cells were grown in 3N media.
Sample name: 55652

source_name: 55652_hES-N1 (derived from H9) cell culture


title: hES-N1 day 0

description:
Total RNA was harvested from one well of a six well plate of stable hES H9 cells
Sample name: 55649

source_name: 55649_hES-N1 (derived from H9) cell culture


title: MYQ-F3-1

status: Public on Dec 27 2017

city: 无锡

first: 王

last: 永远

state: 江苏省

address: 滨湖区蠡湖街道1800号

country: China

institute: 江南大学

data_processing:
Illumina Hiseq4000 was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome of Agrobacterium sp. ATCC 31749 using tophat2.
We used cufflinks to calculate the espression of genes in all samples. Fragments Per Kilobase of exon model per Million mapped reads(FPKM) was used to stand for the espression level
Genome_build: AECL01000000
Supplementary_files_format_and_content: FPKM values of genes in all samples were included in the genes.fpkm.xlsx file

organism: Agrobacterium sp. ATCC 31749

source_name: curdlan-producing phase (micro-oxygen treated)

extract_protocol:
The cell of samples were gathered flash frozen in liquid nitrogen. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ATCC 31749deltafnrN

value: fnrN mutation strain

tag: time


title: MYQ-Y1

address: 滨湖区蠡湖街道1800号

source_name: cell growth phase (normoxia)

value: wild strain


title: Fos 0hr B1

value: wild-type


title: MYQ-Y2

address: 滨湖区蠡湖街道1800号

source_name: curdlan-producing phase (normoxia)


title: MYQ-F3

address: 滨湖区蠡湖街道1800号


title: MYQ-Y1-1

address: 滨湖区蠡湖街道1800号


title: MYQ-F2-1

address: 滨湖区蠡湖街道1800号


title: MYQ-F2

address: 滨湖区蠡湖街道1800号


title: MYQ-Y3

address: 滨湖区蠡湖街道1800号


title: MYQ-Y2-1

address: 滨湖区蠡湖街道1800号


title: MYQ-F1

address: 滨湖区蠡湖街道1800号


title: MYQ-F1-1

address: 滨湖区蠡湖街道1800号


title: MYQ-Y3-1

address: 滨湖区蠡湖街道1800号


title: WM193Stv_PD

city: Syracuse

last: Ow

address: 107 College Place

institute: Syracuse University

description: processed data file: WM193Stv.txt

data_processing:
Data analysis was conducted on the CLC Genomics Workbench v.8.5 with abundance measurements calculated the Empirical analysis of DGE algorithm (EdgeR test).
Genome_build: WS235
Supplementary_files_format_and_content: txt files include abundance measurents

organism: Caenorhabditis elegans

source_name: WM193 young adults

growth_protocol: Worms were maintained on Nematode Growth Medium (NGM) plates seeded with Escherichia coli OP50 at 20oC.

extract_protocol:
Total RNA extraction was done using TRIzol Reagent.
Libraries were prepared using the NEBNext mRNA Library Prep Master Mix Set for Illumina.

tag: dauer inducing condition

value: Starvation

tag: tissue

value: Whole worms

tag: developmental stage

value: adult (24 hours post-L4 stage)


title: Chlorella sorokiniana UTEX 1602 grown at pH 7.6 in a modified freshwater medium Sor76

city: Saint Paul

first: Brett

middle: M

last: Barney

state: MN

address: 1500 Gortner Avenue

department: Bioproducts and Biosystems Engineering

institute: University of Minnesota

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence quality was accessed via FastQC. Illumina adapters and low quality bases were removed by Trimmomatic using the following setting: 3bp sliding-window trimming from 3' end requiring minimum Q16
Cleaned paired-reads were mapped to assembled draft genomes of M. conductrix and C. sorokiniana using HiSAT2 with curated annotation and default parameters.
Various Picard tools (CleanSam, Sort, CollectInsertSizeMetrics) were used to clean the resulted sam files.
Fragments mapped Per Kilobases of exons per Million (FPKM) mapped reads were calculated using Cuffquant and Cuffnorm with default parameters.
Genome_build: curated genome annotation for M. conductrix and C. sorokinians
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of each gene for each Sample

organism: Chlorella sorokiniana

source_name: whole cell lysate

growth_protocol: An endosymbiont of Paramecium bursaria, Chlorella sp. SAG 241.80 (Recently renamed Micractinium conductrix), was obtained from the Algal Culture Collection of the Plant Physiology Institute, University of Goettingen, Germany. The free living Chlorella sorokiniana UTEX 1602 was obtained from the Culture Collection of Algae at the University of Texas at Austin. M. conductrix was maintained on solid freshwater SAG medium containing 1.4 mM K2HPO4, 0.3 mM MgSO4·7H2O, 0.17 mM CaCl2·2H2O, 0.43 mM NaCl, 1.5 mM Na2SO4, 27 mM (NH4)5Fe(C6H4O7)2, 7.1 mM NaNO3, 12 mM Na2S2O3·5H2O, 100 µL vitamin solution, 2 mL BME vitamin solution (P/N B6891, Sigma Aldrich, St. Louis, MO), 1 mL trace element solution and 12 g of plant grade agarose (P/N A7921, Sigma Aldrich), pH 7.6. The vitamin solution contained 50 mg thiamine HCl, 1 mg biotin and 1 mg cyanocobalamin in 10 mL dH2O. The composition of the trace element solution (per L) was 1 g boric acid, 1 g sodium EDTA, 200 mg MnCl2·4H2O, 20 mg ZnCl2, 15 mg CuCl2·2H2O, 15 mg Na2MoO4.2H2O, 15 mg CoCl2·6H2O and 10 mg KBr. C. sorokiniana UTEX 1602 was maintained on agar plates of a derivative of Bold's Basal medium.

extract_protocol:
M. conductrix and C. sorokiniana UTEX 1602 cells were collected and frozen in liquid nitrogen for total RNA preparation. Briefly, cells were harvested by centrifugation at 14000 g for 1 minute and cell pellets were frozen in liquid nitrogen then stored at -80˚C. Frozen pellets were suspended in 1 mL Trizol and transferred to a bashing beads tube (ZR Fungal/Bacterial DNA Microprep kit, Zymo Research, Irvine, CA) and the solution was vortexed with the beads for 2 minutes, then incubated at room temperature for 5 minutes. Next, 200 µL of chloroform was added to the mixture, vortexed well and centrifuged (12000 g for 3 minutes). The upper layer was carefully collected in an RNase-free tube and mixed with an equivalent volume of 95% ethanol (Sigma) and vortexed well. The solution was further purified using the Direct-zol RNA kit (Zymo Research, Irvine, CA) as directed by the manufacturer, and the total RNA was collected and treated with RNase free DNase I (Zymo Research, Irvine, CA) for 10 minutes and then purified again following the Direct-zol RNA kit. Total RNA quantity and quality were measured using the Nanodrop 2000 spectrophotometer.
Poly(A)+ tag based mRNA isolation and RNA sequencing were performed at the University of Minnesota Genomics Center. Poly(A)+ RNA was isolated using oligo(dT) magnetic beads and isolated mRNA was fragmented into small pieces at elevated temperature. The fragmented mRNA was used as template for cDNA synthesis using random primers. Further, 5’and 3’adapters were ligated to the mRNA and the adapter-ligated RNA was reverse-transcribed and amplified using PCR. The final PCR products were size fractioned and used for cDNA sequencing library construction. The cDNA sequencing libraries were sequenced using the HiSeq 2500 Illumina sequencing technique.

tag: ph


title: WM193Stv_Con

description: processed data file: WM193Stv.txt

value: none (continuous development)


title: Chlorella sorokiniana UTEX 1602 grown at pH 7.6 in a modified freshwater medium Sor3


title: WM193Phe_Con

description: processed data file: WM193Phe.txt


title: Chlorella sorokiniana UTEX 1602 grown at pH 5.7 in a modified freshwater medium Sor57


title: Chlorella sorokiniana UTEX 1602 grown at pH 7.6 in a modified freshwater medium Sor1


title: MCF7_RBP2_rep3

city: Seoul

first: Hee-Joo

last: Choi

address: 222 Yangshimri-ro, Seongdonggu

country: South Korea

institute: Hanyang University

data_processing:
Illumina bcl2fastq2 v2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.5.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Cufflinks v2.2.1. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for all samples

source_name: breast cancer cell line_MCF7_RBP2_overexpression

extract_protocol:
Total RNA was extracted from control- or RBP2 overerxpressing-MCF7 cells using TRIzol® RNA Isolation Reagents (Life technologies, Carlsbad, CA). RNA integrity was confirmed by a bioanalyzer using an Agilent RNA 6000 Pico Kit (Agilent, Santa Clara, CA). The isolated total RNA was processed for preparing mRNA sequencing library using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA) according to manufacturer’s instruction. Simply, mRNAs were isolated from 400 ng total RNA by RNA purification bead using polyA capture, and followed by enzyme shearing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: breast cancer cell line


title: N2Stv_PD

description: processed data file: N2Stv.txt

source_name: N2 young adults

value: wildtype


title: WM193Phe_PD

description: processed data file: WM193Phe.txt

value: High pheromone


title: MCF7_CON_rep3

source_name: breast cancer cell line_MCF7_control


title: MCF7_RBP2_rep2


title: Chlorella sorokiniana UTEX 1602 grown at pH 5.7 in a modified freshwater medium Sor4


title: Micractinium conductrix SAG 241.80 grown at pH 7.6 in modified freshwater SAG medium SAG76

organism: Micractinium conductrix


title: N2Stv_Con

description: processed data file: N2Stv.txt


title: Chlorella sorokiniana UTEX 1602 grown at pH 5.7 in a modified freshwater medium Sor2


title: MCF7_RBP2_rep1


title: Micractinium conductrix SAG 241.80 grown at pH 7.6 in modified freshwater SAG medium SAG3


title: MCF7_CON_rep1


title: N2Phe_Con

description: processed data file: N2Phe.txt


title: N2Phe_PD

description: processed data file: N2Phe.txt


title: Micractinium conductrix SAG 241.80 grown at pH 7.6 in modified freshwater SAG medium SAG1


title: Micractinium conductrix SAG 241.80 grown at pH 5.7 in modified freshwater SAG medium SAG57


title: Micractinium conductrix SAG 241.80 grown at pH 5.7 in modified freshwater SAG medium SAG4


title: H79 [RhCMV]

status: Public on Dec 26 2017

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

institute: Regeneron

description:
processed data file:
rawCounts_GeneNames_AllSamples_RhCMV_mTB_2.csv

data_processing:
Alignment STAR version STAR_2.3.1d
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to MacaM assembly using star STAR_2.3.1d
Gene counts were calculated by using HTSeq count
Genome_build: MacaM assembly
Supplementary_files_format_and_content: tab delimited file including the raw read counts for all the detected genes

organism: Macaca mulatta

source_name: Whole Blood

extract_protocol:
Paxgene RNA
GlobinClear Globin transcript reduction followed by Illumina mRNA-Seq

value: whole blood

tag: monkey id

tag: study

value: Study 2

tag: harmonized disease score

tag: vaccine group

value: Unvaccinated


title: H78 [RhCMV]


title: G67 [RhCMV]


title: G68 [RhCMV]


title: I89 [RhCMV]


title: F57 [RhCMV]


title: E46 [RhCMV]


title: E45 [RhCMV]


title: C24 [RhCMV]


title: I90 [RhCMV]


title: D34 [RhCMV]


title: D35 [RhCMV]


title: MCF7_CON_rep2


title: B13 [RhCMV]


title: A1 [RhCMV]


title: A2 [RhCMV]


title: I94 [RhCMV]


title: B12 [RhCMV]


title: I95 [RhCMV]


title: H83 [RhCMV]


title: H85 [RhCMV]


title: I96 [RhCMV]


title: G72 [RhCMV]


title: G74 [RhCMV]


title: G73 [RhCMV]


title: H84 [RhCMV]


title: Micractinium conductrix SAG 241.80 grown at pH 5.7 in modified freshwater SAG medium SAG2


title: F61 [RhCMV]


title: F56 [RhCMV]


title: C23 [RhCMV]


title: E55 [RhCMV]


title: C30 [RhCMV]


title: D40 [RhCMV]


title: E50 [RhCMV]


title: D41 [RhCMV]


title: B18 [RhCMV]


title: B19 [RhCMV]


title: F63 [RhCMV]


title: A6 [RhCMV]


title: C28 [RhCMV]


title: A7 [RhCMV]


title: F62 [RhCMV]


title: I92 [RhCMV]


title: H82 [RhCMV]


title: G69 [RhCMV]


title: G70 [RhCMV]


title: C29 [RhCMV]


title: I91 [RhCMV]


title: I93 [RhCMV]


title: G71 [RhCMV]


title: F58 [RhCMV]


title: F60 [RhCMV]


title: H81 [RhCMV]


title: F59 [RhCMV]


title: E51 [RhCMV]


title: D39 [RhCMV]


title: H80 [RhCMV]


title: B17 [RhCMV]


title: E47 [RhCMV]


title: A8 [RhCMV]


title: E48 [RhCMV]


title: E49 [RhCMV]


title: C25 [RhCMV]


title: D37 [RhCMV]


title: D36 [RhCMV]


title: D38 [RhCMV]


title: C26 [RhCMV]


title: A4 [RhCMV]


title: C27 [RhCMV]


title: I99 [RhCMV]


title: H86 [RhCMV]


title: G77 [RhCMV]


title: G76 [RhCMV]


title: H87 [RhCMV]


title: B14 [RhCMV]


title: B16 [RhCMV]


title: G75 [RhCMV]


title: I98 [RhCMV]


title: F64 [RhCMV]


title: F65 [RhCMV]


title: E54 [RhCMV]


title: E52 [RhCMV]


title: F66 [RhCMV]


title: B15 [RhCMV]


title: D42 [RhCMV]


title: A5 [RhCMV]


title: D44 [RhCMV]


title: A3 [RhCMV]


title: I97 [RhCMV]


title: D43 [RhCMV]


title: C31 [RhCMV]


title: B22 [RhCMV]


title: A9 [RhCMV]


title: B20 [RhCMV]


title: C32 [RhCMV]


title: B21 [RhCMV]


title: A10 [RhCMV]


title: B12-06_6-L6-29284-00 [RhCMV]

description:
processed data file:
rawCounts_GeneNames_AllSamples_RhCMV_mTB_1.csv

value: Study 1


title: B09-59_59-L5-28188-28 [RhCMV]


title: B08-58_58-L4-28174-28 [RhCMV]


title: B09-32_32-L5-28188-14 [RhCMV]


title: B09-05_5-L5-28188-00 [RhCMV]


title: B12-60_60-L6-29284-28 [RhCMV]


title: E53 [RhCMV]


title: B12-33_33-L6-29284-14 [RhCMV]


title: B08-31_31-L4-28174-14 [RhCMV]


title: B06-57_57-L3-28164-28 [RhCMV]


title: B06-03_3-L3-28164-00 [RhCMV]


title: B06-30_30-L3-28164-14 [RhCMV]


title: B08-04_4-L4-28174-00 [RhCMV]


title: B05-70_70-N3-28536-28 [RhCMV]


title: B05-16_16-N3-28536-00 [RhCMV]


title: B13-47_47-N7-28241-14 [RhCMV]


title: B13-20_20-N7-28241-00 [RhCMV]


title: A11 [RhCMV]


title: B11-46_46-N6-28114-14 [RhCMV]


title: B13-74_74-N7-28241-28 [RhCMV]


title: H88 [RhCMV]


title: B11-73_73-N6-28114-28 [RhCMV]


title: B11-19_19-N6-28114-00 [RhCMV]


title: B10-72_72-N5-27545-28 [RhCMV]


title: B10-45_45-N5-27545-14 [RhCMV]


title: B05-43_43-N3-28536-14 [RhCMV]


title: B08-44_44-N4-27543-14 [RhCMV]


title: B04-69_69-N2-27530-28 [RhCMV]


title: B08-17_17-N4-27543-00 [RhCMV]


title: B04-42_42-N2-27530-14 [RhCMV]


title: B13-27_27-G7-28402-00 [RhCMV]


title: B12-53_53-G6-28275-14 [RhCMV]


title: B04-15_15-N2-27530-00 [RhCMV]


title: B13-54_54-G7-28402-14 [RhCMV]


title: B12-26_26-G6-28275-00 [RhCMV]


title: B13-81_81-G7-28402-28 [RhCMV]


title: B08-71_71-N4-27543-28 [RhCMV]


title: B12-80_80-G6-28275-28 [RhCMV]


title: B10-79_79-G5-28274-28 [RhCMV]


title: B10-52_52-G5-28274-14 [RhCMV]


title: B10-25_25-G5-28274-00 [RhCMV]


title: B07-78_78-G4-28273-28 [RhCMV]


title: B07-24_24-G4-28273-00 [RhCMV]


title: B07-51_51-G4-28273-14 [RhCMV]


title: B06-77_77-G3-28263-28 [RhCMV]


title: B06-23_23-G3-28263-00 [RhCMV]


title: B10-18_18-N5-27545-00 [RhCMV]


title: B06-50_50-G3-28263-14 [RhCMV]


title: B01-75_75-G1-28019-28 [RhCMV]


title: B04-49_49-G2-28084-14 [RhCMV]


title: B01-21_21-G1-28019-00 [RhCMV]


title: B01-48_48-G1-28019-14 [RhCMV]


title: B14-67_67-U7-28277-28 [RhCMV]

value: BCG


title: B05-09_9-U3-28192-00 [RhCMV]


title: B05-36_36-U3-28192-14 [RhCMV]


title: B14-13_13-U7-28277-00 [RhCMV]


title: B07-10_10-U4-28237-00 [RhCMV]


title: B01-34_34-U1-26603-14 [RhCMV]


title: B07-64_64-U4-28237-28 [RhCMV]


title: B09-65_65-U5-28242-28 [RhCMV]


title: B09-11_11-U5-28242-00 [RhCMV]


title: B11-66_66-U6-27874-28 [RhCMV]


title: B01-07_7-U1-26603-00 [RhCMV]


title: B09-38_38-U5-28242-14 [RhCMV]


title: B01-61_61-U1-26603-28 [RhCMV]


title: B04-22_22-G2-28084-00 [RhCMV]


title: B11-12_12-U6-27874-00 [RhCMV]


title: E17_5

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay St

country: Canada

institute: Hospital for Sick Children

data_processing:
FASTQ sequencing reads were processed, aligned to the mouse genome (mm10) and converted to digital gene expression matrices using the Drop-seq tools (version 1.12, http://mccarrolllab.com/dropseq/) with settings as described in the Drop-seq Alignment Cookbook (version 1.2 Jan2016, http://mccarrolllab.com/dropseq/)
The number of cell barcodes per embryonic age was identified by calculating the cumulative fraction of reads attributable to each individual cell barcode and arranging these in decreasing order.
2000 Barcodes were selected at E11.5, E13.5 and E17.5 and 5000 Barcodes at E15.5
Two batches data collected from E15.5 embryos (Batch1 and Batch2) were combined together.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing raw digital gene expression for each embryonic age. Two processed data files are included per age. One containing all data for all cells and one containing only cells predicted as cortical in origin.

source_name: Brain

extract_protocol:
Embryonic cortices were dissected, dissociated into single-cell suspensions, FACS sorted for vialbility (except E11.5) and single-cell transcriptomes were collected as described previously by Macosko et al., Cell, 2015.
Standard Illumina libraries were constructed as described by Macosko et al., Cell, 2015.

value: embryonic cortex

tag: embryonic age

value: Wildtype CD1

value: Brain


title: B05-63_63-U3-28192-28 [RhCMV]


title: B14-40_40-U7-28277-14 [RhCMV]


title: Ingolf53: diff_WT_male rep1

city: Worcester

first: Ingolf

last: Bach

state: MA

address: 364 Plantation St

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
data were processed as described previously (Wang et al., 2016)
The bcl2fastq 2.16.0.10 software package was used to convert base call (BCL) files generated on the NextSeq system to fastq files
Sequenced reads were aligned to the mouse genome (mm10) using TopHat (version 2.0.12) with default setting except set parameter read-mismatches to 2
HTSeq (version 0.6.1p1) was used to count the features after the alignment
Bioconductor packages edgeR (version 3.10.0 ) and ChIPpeakAnno (version 3.2.0)  for transcriptome quantification, differential gene expression analysis and annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the raw count values from HTSeq for each sample

source_name: ESCs

growth_protocol: ESCs were grown in standart ESC medium with LIF. ESCs were differentiated in vitro via embryoid body (EB) formation (3 days) in the absence of LIF in a bacterial dish, followed by additional cell culture (6 days) in 7.5% O2.

extract_protocol:
Library was constructed as described (Vallaster et al., 2016)
RNA libraries were prepared for sequencing using standard Illumina protocols.  A total of 187 samples were distributed on two 96-well plates (plus 5 mock wells) and thawed at RT for 10 minutes prior to RNA purification using Ampure RNA beads (Beckmann-Coulter). RNA samples were re-suspended in solution containing 3’ RT primer and dNTPs. Reverse transcription was performed with SSII (Life Technologies), whose terminal transferase activity allows incorporation of a PCR binding site at the 3’ end of the cDNA using a template-switching oligonucleotide (custom synthesized from Exiqon) as a template. Subsequently, cDNA was amplified using 12 cycles of PCR, followed by tagmentation with Nextera kit (Illumina). Final libraries were amplified by 12 cycles of PCR and sequenced on a NextSeq 500.

value: WT

tag: gender

value: male

value: differentiated ESCs


title: B04-76_76-G2-28084-28 [RhCMV]


title: B07-37_37-U4-28237-14 [RhCMV]


title: E15_5_Batch1

description: Processed data are in series supplementary files


title: E11_5


title: Ingolf52: diff_KO_female rep2

value: RlimKO

value: female


title: Ingolf51: diff_KO_female rep1


title: E13_5


title: B11-39_39-U6-27874-14 [RhCMV]


title: E15_5_Batch2


title: Ingolf50: diff_WT_female rep2


title: CDX2KO_Braf_2

city: Piscataway

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

data_processing:
Read alignment and mapping done with TopHat2, version 2.1.0
Gene and transcript level computation done with CuffQuant, Version 2.2.1
Normalized abundance measurements generated by CuffNorm, Version 2.2.1, using geometric normalization
CuffDiff, Version 2.2.1, geometric normalization, per-condition dispersion
Genome_build: mm9
Supplementary_files_format_and_content: genes.fpkm_table containing normalized gene expression levels outputted by CuffNorm

source_name: jejunal crypts

growth_protocol: RNAs were extracted from crypt jejunal epithelia of the indicated genotypes (BRAF-V600Ef/+;Villin-CreER(T2), Smad4f/f BRAF-V600Ef/+;Villin-CreER(T2)  and Cdx2f/f BRAF-V600Ef/+Villin-CreER(T2)) one day following 4 consecutive days of tamoxifen injection. After flushing the freshly harvested jejunum with cold PBS, the epithelia was dissociated from underlying mesenchyme by incubating with 3 mM EDTA/PBS at 4°C as described previously (Perekatt, 2014), and filtered through 70 micron filter to isolate the crypts. The crypts were washed with PBS, and pelleted to remove excess PBS prior to addition of TRIzol for RNA extraction according to manufacturer’s protocols.

extract_protocol:
Illumina TruSeq RNA Library Prep kit v2
50bp single end reads collected on Illumina HiSeq

value: jejunal crypts

value: Cdx2 f/f BRAF-V600E f/+

tag: treatment

value: tamoxifen


title: Ingolf8: diff_WT_male rep2

tag: strain


title: Ingolf39: undiff_KO_female rep1

tag: genotype

value: undifferentiated ESCs


title: Ingolf38: undiff_WT_female rep2


title: Ingolf41: undiff_WT_male rep1


title: CDX2KO_Braf_1


title: Ingolf37: undiff_WT_female rep1


title: SMAD4KO_Braf_2

value: Smad4 f/f BRAF-V600E f/+


title: Ingolf42: undiff_WT_male rep2


title: SMAD4KO_Braf_1


title: SMAD4KO_Braf_3


title: BRAF_3

value: BRAF-V600E f/+


title: BRAF_1


title: BRAF_2


title: FL_HSC_rep2

city: Philadelphia

first: Long

last: Gao

state: PA

address: 4002 Colket Translational Research Building (CTRB) 3501 Civic Center Boulevard

institute: The Children’s Hospital of Philadelphia

data_processing:
Paired-end reads were mapped to the reference mouse genome
Uniquely mapped reads with fewer than 2 mismatches were used
Cufflinks was used to assemble transcripts and estimate expression level
Gene level read count was estimated using FeatureCounts
Differential gene expression ananlysis was conducted using edgeR and DESeq
Genome_build: mm9
Supplementary_files_format_and_content: Gene level FPKM values across all samples(excel file)

source_name: FL-HSC

growth_protocol: C57BL/6J WT (CD45.2) females were paired with B6.Cg-Tg(Ly6a-GFP)G5Dzk/J or C57BL/6 WT males to obtain conceptuses. The Ly6a-GFP transgene was detected by PCR using GFP primers: FW:5’-CAGATGAAGCAGCACGACTTCT, RV:5’-AACTCCAGCAGGACCATGTGAT. PCR reaction: denaturation 5’ 94⁰C, 35 cycles of denaturation 30’’ 94⁰C, annealing 30’’ 56⁰C, elongation 1’30’’ 72⁰C and final extension 10’ 72⁰C. Product size ~400bp. PD-1 null mice (Pdcd1tm1.1Shr) were a gift from Arlene Sharpe (Keir et al., 2007). NSG mice were provided by the University of Pennsylvania Xenograft Core.

extract_protocol:
Cells were sorted into Trizol-LS. Total RNA was prepared using RNeasy micro kit (Qiagen, Valencia, CA, USA). DNase treatment was performed either on-column (Qiagen) or using DNA-free DNA Removal Kit (Life Technologies). Total RNA was quantified with RNA HS Kit (Q32852) for Qubit fluorometer (Life Technologies) and analyzed for integrity using RNA 6000 Pico Kit (5067-1513) for 2100 Bioanalyzer (Agilent).
mRNA was isolated from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, NEB). PolyA-selected mRNA was fragmented to average size of 300 nt, reverse transcribed to generate double-stranded cDNA, and converted to a paired end library using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) according to manufacturer's instructions including the optional double size selection procedure using Agencourt AMPure XP beads. Prepared libraries were quantified with dsDNA HS Kit (Q32851) for Qubit and the size distribution was assessed using High Sensitivity DNA Kit (5067-462) for Bioanalyzer. Libraries were sequenced on Illumina HiSeq2500 in paired-end mode with the read length of 75 nt.

treatment_protocol: Sorted populations from one AUV were mixed with 105 OP9 cells as previously described (Rybtsov et al., 2011; Taoudi et al., 2008). The reaggregates were expelled onto 0.65mm Durapore filters (Millipore) and cultured at the air-liquid interface for 4 days in Myelocult (M5300, STEMCELL Technologies) supplemented with 100 ng/ml SCF, 100 ng/ml IL-3 and 100 ng/ml Flt3L (Peprotech). Reaggregates were dissociated using collagenase I (Sigma) prior to analysis. OP9-cells were obtained from the ATCC (CRL-2729) and maintained in alpha-Minimal Essential Medium (Gibco), 20% FBS (Gibco), 1% Penicillin-streptomycin (Hyclone, Thermo Scientific). Cultures on Akt-EC cells were performed as described previously

tag: strain background

value: embryonic day 14.5

value: Hematopoietic stem cells (HSCs)


title: exHSC_rep3

source_name: ex-HSC

value: in vitro


title: exHSC_rep2


title: preHSC_rep3

source_name: pre-HSC

value: embryonic day 11.5


title: preHSC_rep2


title: FL_HSC_rep1


title: H3.3-K9R_H3.2-HWT_3_RNA

status: Public on Dec 25 2017

city: Chapel Hill

first: Taylor

last: Penke

state: NC

address: 3344 Genome Sciences Building, 250 Bell Tower Drive

department: Genetics and Molecular Biology

institute: University of North Carolina Chapel Hill

description:
processed data file:
deseq2.H3.3-K9R_H3.2-HWT.over.HWT.txt
H3.3-K9R_H3.2-HWT.bw

data_processing:
FAIRE-seq Sequenced reads were mapped to the 6.04 dm6 reference genome using Bowtie2 v2.3.2
FAIRE-seq The resulting bam file was indexed and sorted using samtools v1.5
FAIRE-seq macs v. 2015-06-03 was used to generate peaks using macs2 callpeak with the parameter --shift 110. Resulting peak files were merged using bedtools merge function
FAIRE-seq Bedtools v2.2.25.0 bam2bed was used to generate a bed file and coverage was used to determine coverage over peaks
FAIRE-seq DESeq2 used to determine statistical significance
FAIRE-seq Bedtools genomecov -bg was used to generate bedgraph scaled to reads per million and bigwigs were generated using UCSC bedgraph2bigwig
RNA-seq Sequenced reads were mapped to the 6.04 dm6 reference genome using Tophat v.2.1.1
RNA-seq The resulting bam file was indexed and sorted using samtools v1.5
RNA-seq Cufflinks v. 2.1.1 used to generate transcriptome with supplemental gtf file obtained from release 6.04 on flybase
RNA-seq Bedtools v2.2.25.0 bam2bed was used to generate a bed file and coverage was used to determine coverage over transcripts from above generated transcriptome
RNA-seq DESeq2 used to determine statistical significance
RNA-seq Bedtools genomecov -bg was used to generate bedgraph scaled to reads per million and bigwigs were generated using UCSC bedgraph2bigwig
Genome_build: dm6
Supplementary_files_format_and_content: DESeq2 output in csv or txt format
Supplementary_files_format_and_content: Genome browsing tracks in bigwig format

organism: Drosophila melanogaster

extract_protocol: NUGEN Ovation RNA-Seq 1-16 for Model Organisms

tag: genotype/variation

value: H3.3B K9R mutation in an H3.3A null and HWT background (H3.3-K9R_H3.2-HWT)

value: 1st instar larvae

value: whole larvae


title: H3.3-K9R_H3.2-K9R_1_RNA

description:
processed data file:
deseq2.H3.3-K9R_H3.2-K9R.over.HWT.txt
H3.3-K9R_H3.2-K9R.bw

value: H3.3B K9R mutation in an H3.3A null and H3.2-K9R background (H3.3-K9R_H3.2-K9R)


title: H3.3-K9R_H3.2-K9R_2_RNA


title: H3.3-K9R_H3.2-K9R_3_RNA


title: Ingolf49: diff_WT_female rep1

value: WT

value: differentiated ESCs


title: Ingolf40: undiff_KO_female rep2

value: RlimKO

value: female


title: H3.3-K9R_H3.2-HWT_2_RNA


title: H3.3-K9R_H3.2-HWT_1_RNA


title: H3.2-K9R_3_RNA

description:
processed data file:
deseq2.H3.2-K9R.over.HWT.txt
H3.2-K9R.bw

value: endogenous histone deletion mutant rescued by a 12x array of canonical histone genes with a K9R mutation (H3.2-K9R)


title: H3.3-K9R_2_FAIRE

description:
processed data file:
deseq2.H3.3-K9R.over.WT.csv
deseq2.H3.3-K9R.over.H3.3A-null.csv
H3.3-K9R.bw

extract_protocol: Rubicon Thruplex DNA-seq kit

value: double mutant  (H3.3-K9R)

value: wandering 3rd instar larvae

value: imaginal wing discs


title: H3.2-K9R_2_RNA


title: H3.2-K9R_1_RNA


title: H3.3B-K9R_3_FAIRE

description:
processed data file:
deseq2.H3.3B-K9R.over.WT.csv
H3.3B-K9R.bw

value: H3.3B with an endogenous K9R mutation (H3.3B-K9R)


title: preHSC_rep1


title: HWT_2_RNA

description:
processed data file:
HWT.bw

value: endogenous histon_1e deletion mutant rescued by a 12x array of wild-type canonical histone genes (HWT)


title: H3.3B-K9R_1_FAIRE


title: C33 [RhCMV]

value: whole blood

value: Study 2


title: exHSC_rep1

value: in vitro

value: Hematopoietic stem cells (HSCs)


title: H3.3-K9R_1_FAIRE


title: H3.3A-null_2_FAIRE

description:
processed data file:
deseq2.H3.3A-null.over.WT.csv
H3.3A-null.bw

value: H3.3A null mutant


title: WT_3_FAIRE

description:
processed data file:
WT.bw

value: yw (WT)


title: H3.3B-K9R_2_FAIRE


title: H3.3A-null_1_FAIRE


title: WT_1_FAIRE

description:
processed data file:
WT.bw


title: ANBG (AGA, non-balding area, bulge)

city: GuangZhou

first: Qian

last: Qu

address: 1838 North Guangzhou AV

institute: Nanfang Hospital of Southern Medical University

description: bulge portion of hair follicle

data_processing:
Illumina bcl2fastq  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped hg38 whole genome using tophat2 with parameters -read-mismatches 2 -read-edit-dist 2 -max-intron-length 5000000 -library-type fr-unstranded -num-threads 8 -mate-inner-dist 40.
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Trapnell et al., Nature Biotechnology, 2010.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Hair follicle

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following manufacturer’s recommendations. RNA quality and quantity of all samples were evaluated by using Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.5.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hair follicles obtained by FUE technique(0.8mm, 0.9mm, 1mm wide) were immediately placed in a sterile petri dish containing normal saline at 4℃.With an operating microscope and microsurgical instruments, fat and redundant tissues were removed from the hair follicle gently.Then two parts were cut away from the tissue: end-bulb areaand bulge region(4-6 mm below thesebaceous gland). The separated tissues were collected in TRIZOL Reagent(Invitrogen, Carlsbad, CA, USA) for next test.

value: hair follicle

tag: tissue section

value: bulge

tag: age

value: range 27-45, median 31.9

tag: diagnosis

value: Hamilton-Norwood baldness scale score 3-5


title: CNBL (control, non-balding area, bulb)

description: bulb portion of hair follicle

tag: tissue

value: bulb

value: range 21-34, median 29.1

value: normal


title: ABBL (AGA, balding area, bulb)

description: bulb portion of hair follicle


title: ABBG (AGA, balding area, bulge)

description: bulge portion of hair follicle


title: ANBL (AGA, non-balding area, bulb)

description: bulb portion of hair follicle


title: AngII BRD4_ChIP-seq rep1

city: Duarte

first: Nancy

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

data_processing:
Basecalls performed using CASAVA version 1.7
Paired-end ChIP-seq reads were aligned to the rn4 genome assembly using bowtie2 ( version 2.1.0) with the following parameters --phred33 --local -N 1
peaks were called using MACS2 version 2.1.1.20160309 with the following parameters --broad -g mm -p 0.05 -f BAM -B
Genome_build: rn4
Supplementary_files_format_and_content: tdf (tiled data file) coverage file generated by igvtools which is the binary read count density file for faster display in IGV.

organism: Rattus norvegicus

source_name: AngII BRD4_ChIP-seq

growth_protocol: Rat Vascular smooth muscle cells were cultured in M199 (PAA) medium supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C in 5% CO2.

extract_protocol:
Chromatin lysates were clarified from sonicated cells and histone-DNA complexes were isolated with respective antibodies.
Sequencing library preparation and reactions were conducted at City of Hope’s Integrative Genomics Core. Briefly, 10 ng of immunoprecipitated DNA was end-repaired (Epicenture), and a single adenosine was added using Klenow exo- (New England Biolabs (NEB)) and ligated to Illumina adaptor oligonucleotides (Illumina).

treatment_protocol: Angiotensin (Ang II) treatment, RVSMCs were serum depleted in M199 medium containing 0.2% BSA for 48h and stimulated without (control) or with 100 nM Ang II (Bachem) for indicated time periods.

value: Sprague-Dawley

value: Vascular Smooth Muscle Cells (VSMCs)

tag: passages

tag: treated with

value: Angiotensin II for 3 hours

tag: chip antibody

value: BRD4 (Cat. No. A301-985A100; Bethyl, Montgomery, TX


title: H3.3-K9R_3_FAIRE

value: double mutant  (H3.3-K9R)

tag: developmental stage

value: wandering 3rd instar larvae

value: imaginal wing discs


title: HWT_3_RNA

description:
processed data file:
HWT.bw

value: endogenous histon_1e deletion mutant rescued by a 12x array of wild-type canonical histone genes (HWT)

value: 1st instar larvae

value: whole larvae


title: AngII BRD4_ChIP-seq rep2

tag: cell type


title: HWT_1_RNA

description:
processed data file:
HWT.bw


title: Control BRD4_ChIP-seq rep2

source_name: Control BRD4_ChIP-seq


title: H3.3A-null_3_FAIRE

value: H3.3A null mutant


title: H3K27ac_Treat_1_ChIP

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the rn4 genome assembly using novoalign 2.07.05 with the following configurations -F ILM1.8 -i PE 200 50 -r None
peaks were called using MACS2 version 22.0.10 with the following setting --broad -g mm -p 0.05 -f BAM -B
Genome_build: rn4
Supplementary_files_format_and_content: tdf (tiled data file) coverage file generated by igvtools which is the binary read count density file for faster display in IGV.

value: H3K27ac (Cat. Nos. ab4729, Abcam, cambridge, UK)


title: H3K27ac_Control_2_ChIP


title: CNBG (control, non-balding area,bulge)

description: bulge portion of hair follicle

value: hair follicle

value: bulge


title: H3K4me1_Treat_2_ChIP

value: H3K4me1 (Cat. Nos. ab8895, Abcam, cambridge, UK)


title: H3K27ac_Treat_2_ChIP


title: H3K27ac_Control_1_ChIP


title: Treat_input


title: H3K4me1_Treat_1_ChIP


title: Control_input


title: Control BRD4_ChIP-seq rep1


title: H3K4me1_Control_2_ChIP


title: WT_2_FAIRE

description:
processed data file:
WT.bw

value: yw (WT)


title: 5E_GCC

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description: Genome conformation capture

data_processing:
Library strategy: GCC
To identify interacting DNA fragments from the paired-end sequence reads, network assembly was performed using the Topography suite v1.19 (Rodley et al. 2012). GCC networks were constructed from 100 bp paired-end Illumina Genome Analyser sequence reads. Except where indicated, bioinformatics and statistical analyses were performed on interactions identified by sequence reads that were uniquely mapped onto the reference genome and were above the cut-off value derived from the ligation control interactions . All bioinformatics analysis was performed using in house Perl and Python scripts . Statistical analyses were performed in R.
Bioinformatics and statistical analyses were performed on interactions identified by sequence reads that were uniquely mapped onto the reference genome and were above the FDR cut-off value derived from the ligation control interactions. All bioinformatics analysis was performed using in house Perl scripts, as previously described (Cagliero, C., Grand, R. S., Jones, M. B., Jin, D. J. & O’Sullivan, J. M. Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription. Nucleic Acids Res. 41, 6058–6071 (2013)).
During the preparation of the GCC samples, random ligation events can occur during: 1) the ligation of the cross-linked fragments, and 2) the sequencing preparation step (i.e. the addition of linkers during sequencing library preparation). Two methods were employed for the identification of significant interactions: 1) a statistical method that calculates a false detection rate (FDR) cut off; and 2) external controls were added during the GCC library preparation to obtain estimates of the rates of inter-molecular ligation events. Two inter-molecular ligations events were detected which was the same frequency as the calculated significance cut-off value. Therefore, the cut-off for filtering out random ligations was set to 3 interactions; only fragment pairs that occurred 3 or more times were considered for analysis.
Genome_build: Escherichia coli MG1655 reference genome (NC_00091313-Feb-2011
Supplementary_file: unique interaction file: *.dat.txt
Supplementary_file: all interactions file: *.datcomb.txt
Supplementary_file: multiple interactions file: *.datmult.txt

organism: Escherichia coli

source_name: Growing t=1 hour

growth_protocol: Synchronization was achieved by passaging cells through one round of stationary phase according to Cutler and Evans 1966. Briefly: Individual colonies (LB plate, 37°C, 24 h) were inoculated into M9 media and grown O/N (37°C, 200 rpm). M9 media was inoculated to a final OD600 = 0.25 (early-logarithmic phase). Cultures were grown (37°C, 200 rpm) and maintained in stationary phase (OD600 1.8) for approximately 2 hours. An appropriate amount of each culture was used to inoculate pre-warmed (37°C) M9 media to a final OD600 = 0.25 (approximate 7-fold dilution).

extract_protocol:
E. coli chromatin was prepared according to Cagliero et al. 2013 with the following modifications. For each successive time point (T0, T60, T120), 100 mL of culture was cross-linked with formaldehyde (1% final v/v, 20 min, RT) and then quenched with glycine (125 mM final concentration, 10 min); 30 mL of culture was used for RNA extraction (see below); 2 x 1 mL samples were harvested for FACS and fluorescence microscopy. Following cross-linking and quenching, cells were collected in a 50 mL falcon tube by two successive rounds of centrifugation (4000 rpm, 15 min, 4°C). Pelleted cells were washed twice with 5 mL of 1% PBS, 1% Triton X-100, and then sedimented (4000 rpm, 15 min, 4°C). To break cells open, the cell pellets for each time point were suspended in 800 µL B1 lysis buffer (10 mM Tris pH 8.0, 50mM NaCl, 10mM EDTA, 20% (w/v) sucrose, 1mg/ml lysozyme) and transferred to 2 ml tubes. Each tube was incubated for 30 min at 37°C. 800 µL of B2 lysis buffer (200 mM Tris pH 8.0, 600 mM NaCL, 4 % TritonX-100, with 1 protease inhibitor tablet [Roche] per 10 ml of buffer added just prior to use) was gently added to each 2 mL tube, mixed by inversion 3-4 times, and incubated (30 min, 37°C). Cell lysates were centrifuged (21,500 g, 20 min, 4°C) and the supernatant removed. Chromatin pellets were washed once with 1 ml FA-lysis buffer (5 mM HEPES-potassium hydroxide pH 7.5, 14 mM NaCl, 100 µm EDTA pH 8.0, 9% of 11% Triton-x-100 (v/v), 1% of 10% deoxychlolic acid (v/v), with 1 protease inhibitor tablet [Roche] per 10 mL of buffer added just prior to use) by inversion (3-4 times) before centrifugation (21,500 g, 20 min, 4°C). The supernatant was decanted and the chromatin pellet suspended in 500 µL chromatin digestion buffer (10 mM Tris-HCL pH 8.0, 5 mM MgCL2, 0.1% TritonX-100). At this point samples were stored at -80°C until further use.   5 µL of 10% SDS was added to each tube and incubated for 10 min at 37°C. 45 µL of 11% TritonX-100 was added to make a final concentration of 1%. Each chromatin sample was aliquoted into 5 sets of 2 ml tubes (~5*108 cells per 55 µL aliquot) in order to carry out restriction enzyme digestion. A ligation control was added to the un-digested chromatin (either pRS426 or Lambda phage – see below). Samples were digested (37°C) with 5 µL HhaI (100U, New England Biolabs) for 2 hr with inversion every 20 min. 10% SDS (10 µL) was added to each tube and incubated for 20 min (65°C) to inactivate the restriction enzyme.  Following restriction enzyme digestion, samples were diluted ~20 fold and ligated (2 hr at 16°C) with 20 µL T4 DNA ligase (20 U, Invitrogen). Ligation reactions were inactivated by adding: 20 µL 0.5 M EDTA (pH 8.0), 12 µL 5 M NaCl, 1.2 µL 1 M Tris-HCL (pH 7.5). Cross-links were removed by incubation O/N at 65°C in the presence of proteinase K (0.45 U, Fermentas). RNA was removed by the addition of 2 µL of RNAseA (10 mg/ml) to each tube and incubation for 15 min at 37°C. 2 µL of 13.7 ng/mL pUC19 plasmid was added to each 2 mL tube (a concentration that was equivalent to one plasmid per E. coli genome) to act as a sequencing control. Three extractions were carried out with equal volumes of phenol:chloroform (1:1) in large Oakridge tubes. DNA was column purified (Zymo, DNA clean and concentratorTM-5 kit) according to the manufacturer’s instructions. Each of the 12 columns was eluted using 11 µL of 65°C mQ H2O into 4 tubes, giving a final volume of 33 µL in each tube. Approximately 10 µg of purified DNA for each sample was sent for paired-end sequencing (100 bp) at the BGI Hong Kong sequencing facility.
Production of external ligation controls for GCC library preparation  Two sets of primers were designed to obtain two PCR products (of approximately the same length between 150-200 bp) to act as ligation controls from the pRS426 and Lambda phage genome templates (Table S2). Both sets of primers were designed to include HhaI site at one end of the final product. Putative sequences of the ligation controls were aligned against the E. coli MG1655 genome using BLAST software to check for regions of homology. External ligation controls were produced by PCR amplification of short regions of the Lambda phase genome and the pRS426 plasmid using the two sets of primers. PCR amplification (95oC, 2min; [95oC, 30 s; 58oC, 20s;; 72oC, 20s] x35; 72oC, 2min) was performed on a GeneAmp® PCR System 9700. PCR products were analyzed following electrophoresis through a 2.0 % (w/v) agarose and subsequently viewed under ultraviolet illumination. PCR products were then gel purified using QIAquick Gel Extraction Kit (Quiagen), following the manufacturer’s instructions. Purified PCR products were digested with 4 U of HhaI and incubated for 2 hr at 37°C. Purified, digested PCR products were introduced into the GCC samples at a 1:1 ratio with the number of genomes prior to the restriction digestion step during GCC preparation. The Lambda ligation control was added to all time points of biological replicate one, and pRS426 ligation control was added to all time points of biological replicate two.   Except where indicated, bioinformatics and statistical analyses were performed on interactions identified by sequence reads that were uniquely mapped onto the reference genome and were above the FDR cut-off value derived from the ligation control interactions (see below). All bioinformatics analysis was performed using in house Perl scripts, as previously described22.

treatment_protocol: Released cultures were grown (37°C, 200 rpm) and harvested (time = 0, 1 hr, or 2 hr) for GCC and RNA isolation.

tag: time post release

value: E. coli cells 1 hour following release from Stationary phase (t=1)

tag: biological replicate

value: Replicate 2


title: 6F_GCC

description: Genome conformation capture

source_name: Dividing t=2 hours

value: E. coli cells 2 hour following release from Stationary phase (t=2)


title: 2B_GCC

description: Genome conformation capture

value: Replicate 1


title: 1A_GCC

description: Genome conformation capture

source_name: Stationary phase t=0

value: E. coli cells immediately following release from Stationary phase t=0


title: 4D_GCC

description: Genome conformation capture


title: 12L.120

data_processing:
RNA sequences were quality assessed and trimmed using FastQC version 0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The identification of differentially expressed genes was performed using cufflinks version 2.0.2 to analyse the trimmed sequences as a time course. Briefly, trimmed reads were aligned to the E. coli MG1655 reference genome (NC_000913 13-Feb-2011) using Tophat version 2.0.7. Aligned reads were assembled for differential expression using cufflinks version and merged using cuffmerge with an ‘assemblies’ file containing the transcript.gtf output files from culfflinks. Differential expression analysis was performed using the merged.gtf output file from cuffmerge.
Genome_build: Escherichia coli MG1655 reference genome (NC_00091313-Feb-2011

growth_protocol: Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966. Briefly: Individual colonies (LB plate, 37°C, 24 h) were inoculated into M9 media and grown O/N (37°C, 200 rpm). M9 media was inoculated to a final OD600 = 0.25 (early-logarithmic phase). Cultures were grown (37°C, 200 rpm) and maintained in stationary phase (OD600 1.8) for approximately 2 hours. An appropriate amount of each culture was used to inoculate pre-warmed (37°C) M9 media to a final OD600 = 0.25 (approximate 7-fold dilution). Released cultures were grown (37°C, 200 rpm) and harvested (time = 0, 1 hr, or 2 hr) for GCC and RNA isolation. Samples (1 mL) were also taken for FACS analysis and fluorescence microscopy (t=0, 1 hr, and 2 hr).

extract_protocol:
RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water).   RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water).
RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies).
200 bp insert, rRNA depletion

treatment_protocol: E. coli were sampled at times = 0, 1 hour, and 2 hours following release from stationary phase.

value: E. coli cells 2 hour2 following release from Stationary phase  (t=2)


title: 7G.0

source_name: Stationary phase  t=0

value: E. coli cells immediately following release from Stationary phase  t=0

value: t=0 replicate 2


title: 11K.60

source_name: Growing  t=1 hour

value: E. coli cells 1 hour following release from Stationary phase  (t=1)


title: 10J.0

value: t=0 Replicate 1


title: 4C-seq of  Eed -/- Nkx2-2_DMV_bait2 rep1

status: Public on Dec 24 2017

city: Beijing

first: Yuanyuan

last: Li

address: Tsinghua University, Qinghua Yuan, Haidian District

institute: Tsinghua Universary

data_processing:
Library strategy: 4C-seq
ChIP-seq reads were aligned to mm9 with Bowtie2 (version 2.2.2) with parameters -t -q -N 1 -L 25. All unmapped reads, multiplely mapped reads and PCR duplicates were removed. To generate the ChIP-Seq signals for each histone modification shown in the UCSC genome browser, we normalized the read counts by computing the number of reads per kilobase of bin per million reads sequenced (RPKM). To minimize the batch and cell type variation, the RPKM values were further normalized through Z-score transformation, by subtracting the mean of RPKM across the genome and divided by the standard deviation of RPKM across the genome.
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). The expression levels for each transcript were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
MethylC-seq reads were aligned to mm9 using BSMAP with parameters –r 0 –w 100 –v 0.1 –A AGATCGGAAGAGC. Multiple-mapped reads and PCR duplicates were removed. After mapping, those reads with total CG coverage less than 5 within 200 bp were removed. Methylation level was calculated using methylated CpG versus total CpG in each bin.
4C-seq reads with 5’ end mapped to 4C forward primer were selected from total fastq file. The selected reads were mapped to mm9 assembly by Bowtie2 (version 2.2.2). The mapped reads were secondly mapped to HindIII sites by softeware fourSig. The fragment counts were finally normalized per one million reads.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited BEDGRAPH files including number of reads in 100bp bin in the genome for each ChIP-seq sample
Supplementary_files_format_and_content: Tab-delimited BEDGRAPH files for methylC-seq including the average mCG level in 200bp bins.
Supplementary_files_format_and_content: Tab-delimited txt files for RNA seq including FPKM values for each gene
Supplementary_files_format_and_content: Tab-delimited bedGraph files including number of reads for each HindIII fragment loci in the genome for each 4C-seq sample

source_name: 4C-seq of  Eed -/- Nkx2-2_DMV_bait2

growth_protocol: mESCs were passaged every 48-72h in DMEM(Gibco) supplemented with 15% FBS (HyClone), 1% non-essential amino acids(Gibco), 0.5% 2-mercaptoethanol(Gibco), 1% penicillin/streptomycin(Millipore), 0.01% leukemia inhibiting factor(LIF)(Millipore) and 1% glutamine(Gibco) on gelatinized plates.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37°C. Crosslinked cells were incubated in lysis buffer (5mM Tris at pH 7.5, 150mM NaCl, 5mM EDTA, 0.5% NP-40, 1% TritonX-100 and fresh proteinase inhibitor) for 1h. After centrifuged at 3000 rpm for 5 min, supernatants were removed.  The cell pellets were resuspended in 1X NEB buffer.
Resuspended cell pellets were digested by HindIII(NEB) at 37°C overnight and ligated by T4 DNA ligase (NEB) at 24°C for 6h. After reverse crosslinked, ligation products were cut by Dpn II (NEB) at 37°C overnight and ligated by T4 DNA ligase (NEB) at 4°C for 16h. The DNA was purified with phenol-chloroform extraction and precipitated with EtOH. 200 ng of DNA for each 4C libraries were amplified by specific inverse primers using the Expand Long Range PCR system (Roche). The final PCR products purified by AMPure beads were sequenced on Illumina HiSeq instrument per manufacturer’s instructions.

value: Eed -/-

value: mESCs


title: 4C-seq of WT Nkx2-2_DMV_bait2 rep2

source_name: 4C-seq of WT Nkx2-2_DMV_bait2

value: WT


title: 4C-seq of  Eed -/- Nkx2-2_DMV_bait1 rep1

source_name: 4C-seq of  Eed -/- Nkx2-2_DMV_bait1


title: 4C-seq of  Eed -/- Nkx2-2_DMV_bait1 rep2


title: H3K4me1_Control_1_ChIP

last: Chen

value: Sprague-Dawley

value: Vascular Smooth Muscle Cells (VSMCs)


title: 4C-seq of  Eed -/- Nkx2-2_DMV_bait2 rep2


title: 4C-seq of WT Nkx2-2_DMV_bait2 rep1


title: 4C-seq of WT Nkx2-2_DMV_bait1 rep1

source_name: 4C-seq of WT Nkx2-2_DMV_bait1


title: 4C-seq of WT Nkx2-2_DMV_bait1 rep2


title: 4C-seq of  Eed -/- Pax6_DMV_bait2 rep2

source_name: 4C-seq of  Eed -/- Pax6_DMV_bait2


title: 4C-seq of  Eed -/- Pax6_DMV_bait1 rep2

source_name: 4C-seq of  Eed -/- Pax6_DMV_bait1


title: 4C-seq of  Eed -/- Pax6_DMV_bait2 rep1


title: EED ChIP-seq of WT mESC

data_processing:
ChIP-seq reads were aligned to mm9 with Bowtie2 (version 2.2.2) with parameters -t -q -N 1 -L 25. All unmapped reads, multiplely mapped reads and PCR duplicates were removed. To generate the ChIP-Seq signals for each histone modification shown in the UCSC genome browser, we normalized the read counts by computing the number of reads per kilobase of bin per million reads sequenced (RPKM). To minimize the batch and cell type variation, the RPKM values were further normalized through Z-score transformation, by subtracting the mean of RPKM across the genome and divided by the standard deviation of RPKM across the genome.
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). The expression levels for each transcript were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
MethylC-seq reads were aligned to mm9 using BSMAP with parameters –r 0 –w 100 –v 0.1 –A AGATCGGAAGAGC. Multiple-mapped reads and PCR duplicates were removed. After mapping, those reads with total CG coverage less than 5 within 200 bp were removed. Methylation level was calculated using methylated CpG versus total CpG in each bin.
4C-seq reads with 5’ end mapped to 4C forward primer were selected from total fastq file. The selected reads were mapped to mm9 assembly by Bowtie2 (version 2.2.2). The mapped reads were secondly mapped to HindIII sites by softeware fourSig. The fragment counts were finally normalized per one million reads.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited BEDGRAPH files including number of reads in 100bp bin in the genome for each ChIP-seq sample
Supplementary_files_format_and_content: Tab-delimited BEDGRAPH files for methylC-seq including the average mCG level in 200bp bins.
Supplementary_files_format_and_content: Tab-delimited txt files for RNA seq including FPKM values for each gene
Supplementary_files_format_and_content: Tab-delimited bedGraph files including number of reads for each HindIII fragment loci in the genome for each 4C-seq sample

source_name: EED ChIP-seq of WT mESC

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37°C;Chromatin was fragmented by sonication to obtain fragments 100–700bp in length. For each ChIP assay,5 ug of antibodies were added and incubated at 4◦C overnight. Chromatin was reverse-crosslinked, purified and quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit
DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 200-500bp DNA fragments.

value: EED(Active Motif,61203 )


title: 4C-seq of WT _Pax6_DMV_bait1  rep1

source_name: 4C-seq of WT _Pax6_DMV_bait1


title: 4C-seq of WT_Pax6_DMV_bait1 rep2

source_name: 4C-seq of WT_Pax6_DMV_bait1


title: 4C-seq of WT_Pax6_DMV_bait2  rep1

source_name: 4C-seq of WT_Pax6_DMV_bait2


title: 4C-seq of WT hoxb3

source_name: 4C-seq of WT hoxb3


title: 4C-seq of  Eed -/- Pax6_DMV_bait1 rep1


title: RNA-seq of Eed -/- mESC

source_name: RNA-seq of Eed -/- mESC

extract_protocol:
Cells were lysed using TRIzol reagent (Ambion, Cat. 15596026). RNA was extracted by isopropanol precipitation and diluted in DEPC-treated water.
10ug RNA was DNase I (Fermentas, Cat. EN0521) treated at 37°C for 1 hour. RNA was purified using AMPure beads. Then ribosomal RNA was removed using Ribo-Zero Magnetic Gold Kit (Epicentre). Purified RNA was fragmented with RNA Frag. Buffer (NEB, Cat. E6186A) at 95°C for 5 min. Reaction was stopped and RNA was purified. First stand cDNA was synthesized with commercial kit using both oligo dT and random primers (Invitrogen, Cat. 18080-051). Second strand cDNA was synthesized with second strand synthesis buffer (Invitrogen, Cat. 10812014), MgCl2, DTT, dUNTP, RNase H (Fermentas, Cat. EN0202), E. coli DNA ligase (NEB, Cat. M0205S) and DNA polymerase I (NEB, Cat. M0209S). DNA was purified after 2 hour incubation on thermomixer at 16°C. Then, synthesized cDNA was end-repaired, adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG (AMPErase, Cat. N808-0096) at 37°C for 1 hour and purified before PCR amplification. 200-500bp fragments were selected for subsequent sequencing.


title: 4C-seq of   Eed -/- hoxb3

source_name: 4C-seq of   Eed -/- hoxb3


title: 4C-seq of WT_Pax6_DMV_bait2_rep2

source_name: 4C-seq of WT_Pax6_DMV_bait2_rep2


title: Met-seq of Ezh2WT mESC

source_name: Met-seq of Ezh2WT mESC

extract_protocol:
Cells were treated using Cell Lysis Solution (Qiagen, Cat. 1045723) and proteins were removed using Protein Precipitation Solution (Qiagen, Cat. 1045701). Genome DNA was precipitated by isopropyl alcohol and cleaned by wash with 75% ethanol.
A total amount of 6ug genomic DNA was mixed with 25ng lambda DNA and sonicated to 200-500bp.DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Bisulfite treatment is performed using commercial kit (Zymo research, Cat. D5005). DNA was amplified and 200-500bp fragments were gel selected.


title: Met-seq of Eed -/- mESC

source_name: Met-seq of Eed -/- mESC


title: Met-seq of TetWT mESC

source_name: Met-seq of TetWT mESC


title: Met-seq of Tet/Eed QKO mESC

source_name: Met-seq of Tet/Eed QKO mESC


title: LNCaP Et PSF-CLIP2

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
Library strategy: CLIP-Seq
To remove rRNA sequence, we used bowtie 2 version 2.2.6. Mapping to human genome (hg19) was performed using tophat 2.1.0.with bowtie.
Generate alignments in the SAM format from BAM given single-end reads. The reads were mapped to the human RefSeq mRNA database for RIP-seq data.
The expression levels of mapped transcripts were normalized into Reads Per Kilobase of exon per Million mapped reads (RPKM) to facilitate comparison among different samples.
For CLIP, signal scores were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-4 or -5).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include RPKMs.
Supplementary_files_format_and_content: Bed files can be visualized by Integrative Genomics Viewer ver 2.3 (IGV ver 2.3). They include MACS signal scores.

source_name: prostate cancer cells LNCaP, vehicle, PSF-CLIP

growth_protocol: LNCaP and 22Rv1 cells were cultured in RPMI 1640 containing 10% FBS. LTAD cells were treated with phenol-red free RPMI1640 containing 10% charcoal/dextran treated FBS. Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol:
For RIP, cell lysates were immunoprecipitated using EZ-magna RIP RNA binding protein immunoprecipitation kit (Millipore 17-701). For CLIP, cells were crosslinked using UV crosslinker (150 mJ/cm2). Beads were prepared by mixing protein G beads with PSF specific antibodies. Harvested cells were lysed in lysis buffer (50mM Tris-HCl, PH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, proteinase inhibitors) and added RNase dilution and DNase to digest RNA and DNA. Cell lysates were immunoprecipitated by prepared protein G beads for 4 h. Beads were washed and suspended in SDS-PAGE sample buffer for SDS-PAGE electrophoresis. The protein-RNA complexes from the beads were transfered to a nitrocellulose membrane. Protein-RNA complexes were cut and isolated using PK buffer (100 mM Tris-HCl PH 7.4, 50 mM NaCl, 10 mM EDTA) and protein kinase K(10μl). Extracted RNA were collected for RNA-seq library construction.
SureSelect RNAXT RNA Target Enrichment for Illumina Multiplexed Sequencing (Agilent) was used for library construction according to the manufacturer's protocol.

treatment_protocol: LNCaP, 22Rv1 and LTAD cells were treated with vehicle or DHT 10 nM for 24 h.

tag: cell line

value: LNCaP

value: prostate cancer cell line

value: 24h ethanol

tag: antibody

value: PSF


title: RNA-seq of WT mESC

source_name: RNA-seq of WT mESC

tag: strain


title: H3K27ac ChIP-seq of WT mESC

source_name: H3K27ac ChIP-seq of WT mESC

tag: genotype