title: MV_C4

city: Saint Louis

first: Qinghong

last: Li

state: MO - Missouri

address: 1 Checkerboard Square 2S

department: Basic Research

institute: Nestle Purina Research

data_processing:
Basecalling was performed using Illumina's standard software for HiSeq2000.
Sequenced reads were trimmed for adaptor sequence using Cutadapt software with default setting -s 1, then mapped to CanFam3.1 referebce genome using bowtie1/tophat with maxmultihit: 20
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflink. Brieftly, 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: canFam3.1
Supplementary_files_format_and_content: tab-delimited text files include averaged RPKM values for each group and p value for each transcript.

organism: Canis lupus familiaris

source_name: mitral valve

extract_protocol:
Total RNA was extracted using the RNeasy Fibrous Tissue Mini Kit by Qiagen. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Beagle

value: mitral valve

value: 16 yrs old

tag: diagnosis

value: Degenerative mitral valve disease (DMVD)


title: MV_N1

status: Public on May 29 2015

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: age

value: 8 yrs old

value: Normal (Control)


title: MV_C3

value: 17 yrs old


title: MV_N3

value: Hound mix

value: 3 yrs old


title: MV_N2


title: MV_C2

value: Pomeranian

value: 9 yrs old


title: LV_N4

source_name: left ventricle

value: left ventricle


title: LV_N3


title: LV_N2


title: LV_N1


title: Origene_Adult_Stomach_1840

city: Singapore

first: Melissa

middle: Jane

last: Fullwood

address: 14 Medical Drive, #12-01

department: Centre for Translational Medicine

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Data quality check using fastQC version 0.11.2.
Alignment of unpaired unstranded reads using STAR version 2.4.0.
Quantification of transcripts and isoforms using RSEM version 1.2.21 using rsem-calculate-expression, both alignment and quantification was done using the STAR_RSEM.sh pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh)
The programe featurecounts version 1.4.6-p2 from the SourceForge Subread package was used to produce a summary file of counts from all the alignement .bam files.
The summary file of counts (RNAseq.counts) was used to plot the multidimensional scaling plot using edgeR version 3.1.3.
The *.osc.gz files were loaded into the genome browser ZENBU and was used visualize the transcripts. Screen shots were captured.
Genome_build: hg19 with Gencode V19 annotation
Supplementary_files_format_and_content: .osc files are simple tab delimited files. They were generated by combining the isoform.results files outputed by RSEM with the gencode v19 .gtf file. It contains abundance measurements and transcript isoforms. It also contains metadata that is inputed into ZENBU.
Supplementary_files_format_and_content: RNAseq.counts is a simple tab delimited file containing the counts for all the RNA-seq libraries for each gene (summary file of counts).

organism: Homo sapiens

source_name: Origene Adult Stomach

extract_protocol:
2 different fetal normal tissues and 6 different adult normal tissues were purchased from different sources (Agilent, Biochain and OriGene). The qualities of these total RNA were tested using the Agilent Bioanalyzer 2100 Eukaryote Total RNA Nano Series II. Only total RNAs with a RIN score of more than 7 were used for RNA-Seq library construction
Ribosomal RNA (rRNA) was removed from total RNA using the RiboMinus™ Eukaryote Kit for RNA-Seq from Ambion. The ribosomal RNA depleted RNA fraction is termed the RiboMinus™ RNA fraction and is enriched in polyadenylated (polyA) mRNA, non-polyadenylated RNA, pre-processed RNA, tRNA, and may also contain regulatory RNA molecules such as microRNA (miRNA) and short interfering RNA (siRNA), snRNA, and other RNA transcripts of yet unknown function. Ambion RiboMinus rRNA depletion was performed as described in the manufacturer’s protocol (Pub. Part no.: 100004590, Rev. date 2 December 2011) following the standard protocol.
TruSeq RNA Sample Preparation was performed on the RiboMinus™ RNA fraction as described in the manufacturer’s protocol (Pub. Part no.: 15026495 Rev. F March 2014) following the low sample protocol.
The libraries were sequenced on Illumina’s HiSeq 2000 instrument following standard protocol.

tag: vendor

value: Origene

value: Stomach

tag: gender

value: Female

tag: number of donors

value: 32 years old

tag: isolate


title: Agilent_Adult_Colon

source_name: Agilent Adult Colon

value: Agilent

value: Colon

value: Male

value: 82 years old


title: Biochain_Adult_Colon

source_name: Biochain Adult Colon

value: Biochain

value: 29 years old


title: PC9 + SA11 B

city: Seattle

first: E.

middle: Virginia

last: Armbrust

state: WA

address: Ben Hall IRB, 616 NE Northlake Pl, Room 306

department: Oceanography

institute: University of Washington

data_processing:
SOLiD reads were aligned to the P. multiseries gene catalog transcripts provided by JGI (Psemu1_GeneCatalog_transcripts_20111011.nt.fasta) using in-house pipelines and SAM tools.
Reads mapping to transcripts were assigned and tallied using seastar.
Seastar counts were then analyzed with edgeR for differential expression and significance testing using Benjamini Hochberg multiple testing corrections.
Count tables were then merged with KEGG annotations provided by JGI.
Genome_build: Sulfitobacter sp. SA11 (https://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2519103045)
Genome_build: Pseudo-nitzschia multiseries (http://genome.jgi.doe.gov/Psemu1/Psemu1.home.html)
Supplementary_files_format_and_content: SA11-expression.tab - tab delimited text files generated from edgeR that contain log fold change, log abundance, p-values, and fdr-corrected p-values for 3 biological replicates per condition; protein identification is also given
Supplementary_files_format_and_content: PC9-expression.tab - tab delimited text files generated from edgeR that contain log fold change, log abundance, p-values, and fdr-corrected p-values for 3 biological replicates per condition; protein identification is also given

molecule: polyA RNA

organism:
Pseudo-nitzschia multiseries
Sulfitobacter sp. SA11

source_name: diatom culture + diatom-associated bacterium

growth_protocol: P. multiseries was maintained at its optimum growth temperature (13C) without bubbling in semi-continuous batch cultures under a light/dark cycle (16/8 hr, 80 μmol photons m−2 s−1) in Aquil. Axenic culture was generated by applying a suite of antibiotics (per mL: 50 μg streptomycin, 67 μg gentamycin, 20 μg ciprofloxacin, 2.2 μg chloramphenicol, and 100 μg ampicillin). For cocultures, the diatom was inoculated from an early to mid-exponential phase growing culture was used to inoculate fresh media to achieve an initial diatom cell density of ~4000 cells/mL. Bacteria were plated freshly before each experiment on marine agar and were grown from single colonies in marine broth overnight (30oC, 150 rpm). Cells were centrifuged (5000 rpm for 5 min) and washed 2x with sterile Aquil and diluted to a stock cell density of ~ 1×10^8 cells/mL with sterile Aquil. This stock was used to inoculate the freshly prepared diatom culture to achieve a final bacterial cell density of ~1 ×10^5 cells/mL. Bacteria-only cultures were supplemented with 1 μM glucose.

extract_protocol: For the diatom, total RNA was isolated from filters using the ToTALLY RNA™ Total RNA Isolation Kit (Ambion; Life Technologies), and mRNA was purified from the total RNA using the MicroPoly(A)Purist™ Kit (Ambion; Life Technologies). For the bacteria, RNA was isolated from filters using the RNeasy Mini Kit along with RNAprotect Bacteria Reagent (Qiagen, Maryland, USA) according to the manufacturer’s instructions using 1 mg/mL lysozyme solution (Fisher) to lyse the cells. Total RNA was treated for DNA contamination using two successive treatments with Turbo-DNase (Ambion; Life Technologies) and cleaned/concentrated with RNeasy MinElute Cleanup Kit (Qiagen). Ribosomal RNAs (rRNAs) were selectively removed using a subtractive hybridization protocol with biotinylated rRNA probes specific to the organism(s) in each sample (e.g. 16S and 23S for SA11 and/or 16S, 18S and 28S for P. multiseries). Probe-bound RNAs were removed with strepdavidin-coated magnetic beads (New England Biolabs). rRNA-depleted samples were then linearly amplified using the MessageAmp II-Bacteria kit (Ambion; Life Technologies).

treatment_protocol: 2 L of the experimental cultures were filtered onto 3 μm polycarbonate filters (Millipore, Massachusetts, USA) followed by filtration of flow-through onto 0.2 μm polycarbonate filters. Filtered cells were immediately flash frozen in liquid nitrogen and stored at 80°C until later RNA extraction.

tag: culturing condition

value: + bacterium

tag: culture strain

value: PC9 + SA11


title: LV_C1

value: Jack Russell Terrier

value: 5 yrs old

value: Degenerative mitral valve disease (DMVD)


title: SA11 + PC9 A (paired-end)

source_name: diatom-associated bacterial culture + diatom culture

value: + diatom

value: SA11 + PC9


title: Origene_Adult_Stomach_0393

value: Origene

value: 44 years old


title: LV_C2

value: Pomeranian

value: left ventricle

value: 9 yrs old


title: Origene_Adult_Stomach_0288

value: Stomach

value: 59 years old


title: Agilent_Adult_Kidney

source_name: Agilent Adult Kidney

value: Agilent

value: Kidney

value: Female

value: 76 years old


title: Biochain_Adult_Kidney

source_name: Biochain Adult Kidney

value: Biochain

value: Male

value: 26 years old


title: PC9 Axenic B

organism: Pseudo-nitzschia multiseries

source_name: diatom culture

value: Axenic control


title: PC9 Axenic C


title: PC9 Axenic A


title: Input

first: Chadi

last: El Farran

address: 61 Biopolis Drive

institute: Institute of Molecular and Cell Biology

description: input

library_source: genomic

data_processing:
Mapping was performed using STAR Aligner v2.3.0e. Reads mapping to more than one locations and reads containing more than 3 mismatches were filtered out.
Peak Calling was performed using the findPeaks script of Homer with the following settings: -region and Enrichment Fold (20). Peaks were also detected using SICER with default parameters. The overlapping peaks between the outputs of the two software were detected using Bedtools and were used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files were generated using Homer. They contain information about the significant peaks detected using this software. Peaks with fold enrichment < 20 were filtered out. Interval files were generated using SICER. They contain the significant peaks (FDR < 0.01) and the fold change of each peak against the input. p-values of the enrichment over the control are provided in the files.

molecule: genomic DNA

source_name: Human Embryonic Stem Cells_input

extract_protocol:
HES-3 Cells were crosslinked with 1% formaldehyde and treated with 1% SDS-based cell lysis buffer. The lysates were sonicated using branson sonifier 250. Ring1B-bound DNA was enriched using antibodies.
Libraries were prepared using NEBNext Ultra DNA library Prep Kit for Illumina (New England Biolabs, Catalog # - E7370S) as per the manufacturer's instructions.

tag: chip antibody

value: none (input)

tag: cell line

value: HES-3 (46 X,X) (ES Cell International)


title: Biochain_Adult_Liver

source_name: Biochain Adult Liver

value: Liver

value: 64 years old


title: Agilent_Adult_Lung

source_name: Agilent Adult Lung

value: Lung

value: 40 years old


title: ChIP_HA

description: DNA-bound to recombinantly expressed HA-RING1B in H3

source_name: Human Embryonic Stem Cells_HA

value: Pierce Anti-HA Agarose (Thermo Scientific, 26181)


title: Biochain_Adult_Lung

source_name: Biochain Adult Lung

value: 20 years old


title: Re-ChIP_WGA

description: DNA-bound to O-GlcNAcylated HA-RING1B

source_name: Human Embryonic Stem Cells_WGA

value: Agarose bound* Wheat Germ Agglutinin (Vector Laboratories, AL-1023)


title: Biochain_Adult_Heart

source_name: Biochain Adult Heart

value: Heart

value: 24 years old


title: Agilent_Adult_Liver

source_name: Agilent Adult Liver

value: Agilent

value: pooled male and female

value: 30, 44 and 55 years


title: Agilent_Adult_Heart

source_name: Agilent Adult Heart

value: Female

value: 73 years old


title: Biochain_Fetal_Stomach

source_name: Biochain Fetal Stomach

value: Biochain

value: Stomach

value: Male

value: 24 weeks old


title: Biochain_Fetal_Colon

source_name: Biochain Fetal Colon

value: Colon

value: 37 weeks old


title: Agilent_Fetal_Colon

source_name: Agilent Fetal Colon

value: 20 weeks gestation


title: Reproducibility test #3

status: Public on May 28 2015

city: Guangzhou

first: Gong

last: Zhang

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

country: China

institute: Jinan University

data_processing:
Adapter sequences were trimmed from the reads.
The reads were aligned to the tRNA reference sequences using modified Smith-Waterman algorithm that considered modified nucleotides matching any nucleotide. Maximum 3 errors (including mismatches, insertions and deletions) was allowed in the alignment and the minimal alignment length was set to 25bp.
Genome_build: Escherichia coli K-12 MG1655 tRNA reference sequences with the modifications (from Modomics database)

organism: Escherichia coli BL21(DE3)

source_name: Grown under normal condition

growth_protocol: E. coli BL21(DE3) cells were grown in M9 minimal medium under normal condition and oxidative stress (0.5mM H2O2). After application of H2O2, samples were taken at 15min, 30min and 90min. The tRNAs were sequenced. We also performed three independent biological replicates, growing cells under normal conditions, to assess the reproducibility of the tRNAome sequencing.

extract_protocol:
Total RNA was extracted using Trizol method.
tRNAs were deacylated at pH=10. Poly(A) tail was added to the deacylated 3’-CCA terminus by E. coli poly(A) polymerase (NEB) according to the manual. Prior to reverse transcription, polyadenylated tRNA were denatured with 100 µM TG primer (5’-T15GG-3’) and dNTP (25mM each) at 80°C for 5 min and then chilled on ice. The reverse transcription was performed with RevertAid Premium Reverse Transcriptase (Fermentas) according to the manual. After transcription of tRNA to cDNA, the second-strand synthesis was performed with RNase H, DNA Polymerase I and T4 DNA Polymearse (Fermentas) according to the manuals. The sequencing library was constructed using NEBNext Ultra DNA library prep master mix set for Illumina (NEB).

tag: strain


title: Reproducibility test #2


title: Agilent_Fetal_Stomach

source_name: Agilent Fetal Stomach

value: 18 (2 donors), 19 (3 donors), 20 (4 donors), 21 weeks gestation


title: Normal condition


title: Oxidative stress 30min


title: Agilent_Adult_Stomach

source_name: Agilent Adult Stomach


title: Reproducibility test #1


title: Oxidative stress 90min


title: Oxidative stress 15min


title: Jurkat_CTCF_ChIP

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: T-ALL

growth_protocol: Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 10 min.

extract_protocol:
The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin.

tag: cell type

value: Jurkat

value: CTCF

tag: antibody manu.

value: Millipore

tag: antibody catalog

tag: antibody lot


title: Jurkat_CTCF_input

value: WCE


title: lung_H441_cell_line_lung_adenocarcinoma

city: Ann Arbor

first: Oscar

middle: Alejandro

last: Balbin

state: Michigan

address: Comprenhensive Cancer Center

department: Pathology

institute: University of Michigan

description:
Sample name: MCTP_SAMPLE_162
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence alignment was performed using the Tuxedo pipeline: Bowtie2 (Bowtie2/2.0.2) and Tophat2 (TopHat/2.0.4)(Kim et al., 2013). We supplied TopHat with the set of transcript models annotated in the Homo sapiens Ensembl database version 69. The option fr-firststrand was used for the strand specific RNA-seq libraries while all other parameters were used with default values. When provided with ssRNA-seq data TopHat2 annotates aligned reads with the tag XS indicating the strand of origin in the DNA.
We used Ensembl v69 as the reference transcriptome to reconstruct the longest annotation for each gene based on the transcript and exon information provided by this assembly. We only included transcript isoforms that satisfied the following criteria: gene and transcript biotypes were annotated with the same type; transcript isoform annotation level was manual or automatic followed by manual revision (annotation levels 1 or 2) and transcript isoform was not reported as a problematic in the Encode-Gencode attributes table (e.g: transcript biotype is retained_intron, to be experimentally confirmed, or disruptive_domain).  Moreover, each transcript isoform used for our gene models was annotated with their “isoform expression rank” across the tissue cohorts, and their support level (tsl) provided by the Genecode project. Tsl equal to 1 indicates that all splice junctions of that transcript are supported by at least one non-suspect mRNA; any other number suggests that the transcript is supported by suspicious ESTs. These final gene models were used as the reference loci, or features, for downstream analysis.
The final gene models in the summarized transcriptome were used to compute strand specific expression. Paired-end reads mapping to the forward or opposite strand of a feature were counted in order to quantify the raw amount of forward and opposite transcription on a particular locus.  In order to determine what DNA strand a read pair was originated from, we first used the reads’ XS tag, provided by TopHat2, to identify the strand for each read in the pair. Then, we use the fact that in our ssRNA-seq protocol the second read is complementary to original mRNA and therefore the second read has to be on the same strand than the feature, while the first read on the opposite strand. These criteria unambiguously define a read pair DNA strand of origin. We discard all pairs in which one or both reads map to multiple locations in the genome, and all read pairs in which any of the reads was improperly mapped or did not have the XS flag provided by TopHat2 to indicate the strand of origin.
Genome_build: hg19
Supplementary_files_format_and_content: Feature (e.g. gene) raw read count over sense and antisense strands. Processed data files linked to SuperSeries record.

extract_protocol:
Total RNA from frozen tissues or cell lines were isolated using miRNeasy mini kit (Qiagen Valencia, CA) while RNA was isolated from FFPE sections using FFPE RNAeasy kit (Qiagen).  For RNA from frozen sections and cell lines only samples with RNA integrity number (RIN) >8.0, upon 2100 Bioanalyzer analysis (Agilent Santa Clara, CA) were subjected to RNA sequencing.
Transcriptome libraries were prepared following a modified protocol previously described for generating strand specific RNASeq libraries 8.  Briefly 2.5 μg of total RNA was subjected to polyA selection using oligodT beads (Invitrogen, Carlsbad, CA).  Purified polyA RNA was fragmented and reverse transcribed using Superscipt-II (Invitrogen, Carlsbad CA).  Second strand synthesis was performed with DNA Ploymerase I (New England Biolabs, Ipswich, MA) in the presence of dNTP mix containing dUTP instead of dTTP.  The product was then subjected to end repair, A base addition and adaptor ligation steps.  Libraries were next size selected in the range of 350 bps after resolving in a 3% Nusieve 3:1 (Lonza, Basel, Switzerland) agarose gel and DNA recovered using QIAEX II gel extraction reagent (Qiagen, Valencia, CA). Libraries were barcoded during the 14-cycle PCR amplification with Phusion DNA polymerase (New England Biolabs, Ipswich, MA) and purified using AMPure XP beads (Beckman Coulter, Brea, CA).

value: not collected

value: MCTP

value: lung

tag: disease

value: metastatic

value: LUCL


title: lung_H727_cell_line_lung_carcinoma

description:
Sample name: MCTP_SAMPLE_166
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: cancer


title: Biochain_Adult_Stomach

source_name: Biochain Adult Stomach

value: Biochain

value: Stomach

value: 24 years old


title: Jurkat_polyA_RNA-Seq

data_processing:
Aligned using TopHat v2.0.13 with configuration: library-type fr-firststrand -p 40 --microexon-search --coverage-search
Supplementary_files_format_and_content: Aligned reads were first separated into strand/direction using samtools view.  Density of strand-separated reads in 50bp bins was calculated using genomeCoverageBed.  The union of the resulting bedGraph files was taken using unionBedGraphs and converted to WIG format  using bedgraph_to_wig.pl (https://github.com/svigneau/)

extract_protocol:
Using 10 μg of total RNA, we prepared sequencing libraries according to the following protocol. Polyadenylated RNA was purified by two rounds of selection with Dynabeads mRNA Purification Kit for mRNA Purification from total RNA (Life Technologies, 610-06) following the manufacturer instructions. This resulting RNA was then further processed for RNA-Seq assays. Briefly, polyadenylated RNA was fragmented with divalent cations under elevated temperature. First strand cDNA synthesis was performed with random hexamers and Superscript III reverse transcriptase (Life Technologies, 18080-051). Second strand cDNA synthesis was performed by using RNase H and DNA Polymerase I. In the second-strand synthesis reaction, dTTP was replaced with dUTP. After cDNA synthesis, the double-stranded products were end repaired, a single “A” base was added, and Illumina PE adaptors were ligated onto the cDNA products. The ligation products with an average size of 300 bp were purified by using agarose gel electrophoresis. Following gel purification, the strand of cDNA containing dUTP was selectively destroyed during incubation of purified double-stranded DNA with HK-UNG (Epicenter, HU59100). The adaptor ligated single-stranded cDNA was then amplified with 15 cycles of PCR and PCR products were purified by using gel electrophoresis. These RNA-Seq libraries were subsequently sequenced on Illumina HiSeq 2000. Sequences were aligned by using Bowtie (version 0.12.2) to build version HG19 of the human. The RPKM (reads per kilobase of exon per million) was then computed for each gene.
Total RNA was purified using mirVana miRNA isolation kit (Life technologies) following the manufacturer instructions.


title: lung_H522_cell_line_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_164
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H460_cell_line_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_163
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H358_cell_line_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_161
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H526_cell_line_lung_small_cell_carcinoma

description:
Sample name: MCTP_SAMPLE_165
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_sw900_cell_line_lung_carcinoma

description:
Sample name: MCTP_SAMPLE_219
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_SKLU1_cell_line_lung_carcinoma

description:
Sample name: MCTP_SAMPLE_217
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H2009_cell_line_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_156
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H23_cell_line_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_160
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H1155_cell_line_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_148
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H2122_cell_line_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_157
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H1792_cell_line_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_152
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H1793_cell_line_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_153
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H838_cell_line_lung_carcinoma

description:
Sample name: MCTP_SAMPLE_168
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H1734_cell_line_lung_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_151
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H1437_cell_line_lung_carcinoma

description:
Sample name: MCTP_SAMPLE_149
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: lung_H1651_cell_line_lung_carcinoma

description:
Sample name: MCTP_SAMPLE_150
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: CR1 placenta_22

city: Leiden

first: Nannan

last: He

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Sequencing data was processed with Illumina Pipeline Software version CASAVA 1.8.2.
The FASTQ files were analyzed with a set of custom Perl scripts followed by aligning the sequences against the UCSC hg19 reference genome using Bowtie short read aligner 1.0.0.
The tags were annotated against Ensembl gene identifiers using BIOMART.
Genome_build: UCSC hg19 reference genome
Supplementary_files_format_and_content: raw counts

source_name: Fetal tissue

extract_protocol:
After washing with 0.9% NaCl (Fresenius Kabi, France), the organs and tissues were snap-frozen in buffer RLT (Qiagen, Germany) and stored at -80°C until further use. The organs and tissues were homogenized using a pestle or a syringe needle followed by the QIAshredder homogenizer (Qiagen, Germany). Total RNA was isolated with the RNeasy Kit (Qiagen, Germany) including on-column DNase digestion.
The DeepSAGE libraries were generated as previously described (Mastrokolias et al., 2012; GSE33701). Each library (8 pM) was loaded on a v3 flowcell and sequenced on an Illumina HiSeq2000 sequencer (Illumina, USA).

value: placenta

tag: gestational age

tag: trimester

tag: Sex

value: Male


title: DF1 kidney_9

tag: tissue

value: kidney


title: CR1 lung_22


title: CV2 gonad_16

value: gonad


title: CF2 amnion_22

value: amnion

value: Female


title: DF1 spinal cord_9

value: cord


title: CR1 stomach_22

value: stomach


title: CV1 stomach_16


title: CC3 heart A_22

value: heart


title: DJ2 gonad_18


title: CV2 heart A_16


title: DJ1 skin_9

value: skin


title: CF2 intestine_22

value: intestine


title: CC3 heart V_22


title: CH1 gonad_9


title: DJ1 lung_9

value: lung


title: CR1 muscle_22

value: muscle


title: CF2 placenta_22


title: CR1 intestine_22


title: DJ1 liver_9

value: liver


title: CP1 eye_22

value: eye


title: CF2 pancreas_22

value: pancreas


title: DF1 placenta_9


title: CF2 adrenal_22

value: adrenal


title: CV2 eye_16


title: CR1 maternal endometrium_22

source_name: Maternal endometrium

value: endometrium


title: CR1 chorion_22

value: chorion

value: Male


title: CL3 gonad_9

value: gonad


title: CV1 heart A_16


title: CV1 eye_16


title: CV2 heart V_16


title: CF2 stomach_22


title: CV1 placenta_16

value: placenta


title: DF1 tongue_9

value: tongue


title: CV1 muscle_16

value: Female


title: CH1 muscle_9


title: CF2 eye_22


title: DF1 brain_9

value: brain


title: CR1 liver_22


title: DJ1 kidney_9

value: kidney


title: CF2 skin_22

value: skin


title: DJ1 brain_9


title: CV1 skin_16


title: CR1 brain_22


title: DF1 amnion_9

value: amnion


title: BP1 pancreas_9


title: DF1 stomach_9

value: stomach


title: DF1 heart V_9

value: heart


title: DA2 pancreas_9


title: CR1 spleen_22

value: spleen


title: CF2 muscle_22

value: muscle


title: CR1 amnion_22


title: BP1 lung_9

value: lung


title: DF1 umbilical cord_9

value: cord


title: CF2 heart A_22


title: DJ1 muscle_9


title: CR1 skin_22


title: damyR_Cel rep3

city: Qingdao

first: Guodong

last: Liu

state: Shandong

address: Binhai Road 72

department: State Key Laboratory of Microbial Technology

institute: Shandong University

data_processing:
Base-calling using Illumina Casava 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence.
Reads were mapped to Penicillium oxalicum 114-2 coding sequences using SOAPaligner/SOAP2 v2.21 with parameters -m 0 -x 10000 -s 28 -l 32 -v 3 -p 3
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Penicillium oxalicum 114-2 sequences (NCBI accession: PRJNA60877)
Supplementary_files_format_and_content: One matrix table in text format includes unique reads numbers, coverage and RPKM values for each genes. Samples were named according to the names of raw files.

organism: Penicillium oxalicum

source_name: Fungal mycelia

growth_protocol: All strains were grown in Vogel’s medium with indicated carbon sources at 30 degrees C, 200 rpm.

extract_protocol:
Total RNA was prepared from the mycelia by grinding under liquid nitrogen with a mortar and pestle, followed by extraction using the RNAisoTM reagent (TaKaRa, Japan) according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mycelia were filtered by filter paper.

tag: strain genotype

value: amyR deletion

tag: carbon source

value: 2% (wt/vol) cellulose

tag: time

value: first precultured in 2% glucose for 22 h and then transferred to no-carbon medium for 2 h, and then transferred to 2% cellulose for 4 h


title: CV1 amnion_16


title: CR1 tongue_22

value: Male


title: CF2 liver_22

value: liver


title: CR1 kidney_22


title: CH1 adrenal_9

value: adrenal


title: damyR_Cel rep1


title: dcreA-gpdA(p)::clrB_Cel rep3

value: creA deletion and clrB overexpression by gpdA promoter


title: dcreA-gpdA(p)::clrB_Cel rep2


title: BO1 pancreas_22

value: pancreas


title: dcreA-dclrB_Cel rep3

value: creA clrB double deletion


title: CP1 chorion_22

value: chorion


title: CV1 heart V_16

value: Female


title: CF2 kidney_22

value: kidney


title: dcreA-dclrB_Cel rep2


title: damyR_Cel rep2


title: dcreA_Cel rep2

value: creA deletion


title: DF1 eye_9

value: eye


title: dclrB_Cel rep3

value: clrB deletion


title: dcreA-gpdA(p)::clrB_Cel rep1


title: dcreA_Cel rep3


title: dclrB_Cel rep1


title: WT_Glu rep3

value: wild-type 114-2

value: 2% (wt/vol) glucose

value: first precultured in 2% glucose for 22 h and then transferred to no-carbon medium for 2 h, and then transferred to 2% glucose for 4 h


title: DA2 liver_9


title: dcreA-dclrB_Cel rep1

value: 2% (wt/vol) cellulose


title: WT_noC rep3

value: no carbon

value: first precultured in 2% glucose for 22 h, and then transferred to no-carbon medium for 4 h


title: CF2 lung_22

value: lung


title: CC2 intestine_18

value: intestine


title: dcreA_Cel rep1

value: first precultured in 2% glucose for 22 h and then transferred to no-carbon medium for 2 h, and then transferred to 2% cellulose for 4 h


title: CI1 brain_16

value: brain

value: Male


title: CP1 intestine_22


title: DF1 skin_9

value: skin


title: HEK293T_ILIRN_TVP64 replicate 6

city: Durham

first: Gregory

last: Crawford

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

data_processing:
Single-end basecalls were done by using Illumina CASAVA 1.3 software.
First 20 bp of Dnase-seq raw reads were mapped to hg19 with BWA, with 2 mismatches allowed, to generate bam files, then bam files were converted to bed file by bedtools. After removing PCR artifacts bigWig files were created by using fseq (PMID: 18784119).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig format (hg19)

source_name: HEK293T_ILIRN_TVP64 cell line

growth_protocol: HEK293T cells were obtained from the American Tissue Collection Center (ATCC) through the Duke University Cancer Center Facilities and were maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Cells were Lysed and nuclei were digested according to the publication PMID: 20150147.
Libraries were prepared according to the publication PMID: 20150147, except that 5' of Oligo1b was phosphated to enhance ligation.libraries were sequenced on a Illumina HiSeq 2000, with 4 barcodes per lane. Reads were aligned tohuman RefSeq using BWA .

treatment_protocol:
HEK293T cells were transfected with Lipofectamine 2000 (Invitrogen) according to manufacturer’s instructions. Transfection efficiencies were routinely higher than 95% as determined by fluorescence microscopy following delivery of a control eGFP expression plasmid. All samples for all assays were harvested at three days post-transfection.
The dCas9-VP64 expression plasmid was transfected at a mass ratio of 3:1 to either the individual gRNA expression plasmids or the identical amount of gRNA expression plasmid consisting of a mixture of equal
amounts of combinations of gRNAs. The expression plasmids for TALE-VP64 (Perez-Pinera et al.2013b) and dCas9-VP64 and gRNAs (Perez-Pinera et al. 2013a) have been previously described. TALE and gRNA target sequences are provided in Supplemental Table 1. TALEs targeted to the HBG1/2
promoter were designed using TALE-NT 2.0 (Doyle et al. 2012) and assembled using the GoldenGate kit (Cermak et al. 2011) acquired through Addgene as described previously (Perez-Pinera et al. 2013b).

tag: transfection

value: Tale_VP64 targetting IL1RN


title: dclrB_Cel rep2


title: WT_Cel rep2


title: CF2 spleen_22

value: spleen

value: Female


title: WT_Cel rep1


title: CJ1 pancreas_9

value: pancreas


title: WT_Glu rep2


title: WT_Glu rep1


title: WT_noC rep2


title: HEK293T_ILIRN_TVP64 replicate 4


title: CJ1 placenta_9

value: placenta


title: HEK293T_ILIRN_TVP64 replicate 1


title: CC2 stomach_18

value: stomach


title: WT_noC rep1

value: wild-type 114-2


title: CJ1 umbilical cord_9

value: cord


title: CI1 tongue_16

value: tongue


title: CJ1 heart V_9

value: V


title: CC2 tongue.2_18


title: HEK293T_ILIRN_Tale replicate 1

source_name: HEK293T_ILIRN_Tale cell line

value: Tale targetting IL1RN


title: HEK293T_ILIRN_TVP64 replicate 3


title: WT_Cel rep3

value: 2% (wt/vol) cellulose


title: CC2 brain_18


title: CI1 maternal endometrium_16

value: endometrium


title: HEK293T_ILIRN_TVP64 replicate 2


title: HEK293T_ILIRN_Tale replicate 5


title: HEK293T_ILIRN_Tale replicate 2


title: HEK293T_ILIRN_c9VP64 replicate 2

source_name: HEK293T_ILIRN_c9VP64 cell line

value: dcas9_VP64 targetting IL1RN


title: CC2 liver_18

value: liver


title: CJ1 intestine_9

value: intestine

value: Male


title: HEK293T_ILIRN_c9VP64 replicate 1


title: HEK293T_ILIRN_Tale replicate 4


title: CI1 chorion_16

value: chorion


title: HEK293T_ILIRN_TVP64 replicate 5

value: Tale_VP64 targetting IL1RN


title: HEK293T_ILIRN_c9 replicate 5

source_name: HEK293T_ILIRN_c9 cell line

value: dcas9 targetting IL1RN


title: HEK293T_ILIRN_c9 replicate 3


title: HEK293T_ILIRN_c9 replicate 4


title: HEK293T_ILIRN_c9VP64 replicate 6


title: HEK293T_ILIRN_c9VP64 replicate 5


title: CI1 amnion_16

value: amnion


title: HEK293T_ILIRN_c9VP64 replicate 4


title: HEK293T_ILIRN_Tale replicate 3


title: HEK293T_ILIRN_c9 replicate 1


title: HEK293T_ILIRN_c9VP64 replicate 3


title: CI1 muscle_16

value: muscle


title: HEK293T_ILIRN_c9 replicate 2


title: CI1 liver_16


title: HEK293T_HBG112_TVP64 replicate 2

source_name: HEK293T_HBG112_TVP64 cell line

value: Tale_VP64 targetting HBG1/2


title: CJ1 amnion_9


title: CJ1 tongue_9


title: CC2 amnion_18

value: Female


title: CI1 intestine_16


title: CC2 tongue_18


title: HEK293T_HBG112_TVP64 replicate 4


title: HEK293T_HBG112_TVP64 replicate 1


title: CC2 lung_18

value: lung


title: HEK293T_HBG112_Tale replicate 5

source_name: HEK293T_HBG112_Tale cell line

value: Tale targetting HBG1/2


title: CJ1 spinal cord_9

value: cord


title: CI1 placenta_16

value: placenta


title: CI1 pancreas_16

value: pancreas


title: HEK293T_HBG112_Tale replicate 3


title: HEK293T_HBG112_Tale replicate 1


title: CC2 kidney_18

value: kidney


title: HEK293T_HBG112_Tale replicate 4


title: HEK293T_HBG112_Tale replicate 2


title: HEK293T_HBG112_c9VP64 replicate 4

source_name: HEK293T_HBG112_c9VP64 cell line

value: dcas9_VP64 targetting HBG1/2


title: CI1 spleen_16

value: spleen


title: HEK293T_HBG112_TVP64 replicate 3


title: CC2 adrenal_18

value: adrenal


title: CI1 kidney_16

value: Male


title: CJ1 stomach_9

value: stomach


title: HEK293T_HBG112_c9VP64 replicate 5


title: CC2 placenta_18


title: HEK293T_HBG112_cas9 replicate 5

source_name: HEK293T_HBG112_cas9 cell line

value: dcas9 targetting HBG1/2


title: HEK293T_HBG112_c9VP64 replicate 3


title: HEK293T_HBG112_cas9 replicate 4


title: CI1 skin_16

value: skin


title: HEK293T_HBG112_cas9 replicate 3


title: CJ1 maternal endometrium_9

value: endometrium


title: CI1 lung_16


title: CC2 pancreas_18


title: HEK293T_HBG112_cas9 replicate 2


title: CJ1 eye_9

value: eye


title: HEK293T replicate 6

source_name: HEK293T cell line

tag: sample type

value: parent cell


title: UW240, cKIT+TAB-seq

city: Los Angeles

first: Sofia

last: Gkountela

state: California

address: 621 Charles E Young Dr S

department: MCDB

institute: UCLA

data_processing:
The bisulfite converted reads were aligned against the human genome (UCSC hg19) with BS-Seeker2 allowing up to three mismatches.
The methylation calling process was also performed on all aligned libraries by BS-Seeker2.
Genome_build: human hg19
Supplementary_files_format_and_content: Processed data (CGmap) is in text format.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

source_name: Fetal Ovary

growth_protocol: Human embryos were obtained following elected termination and pathological evaluation at the Laboratory of Developmental Biology at the University of Washington, Seattle. All consented material was anonymous and carried no personal identifiers. The BDRL estimates developmental age by prenatal intakes, foot length, Streeter’s stage and crown-rump length. Any conceptus with a documented birth defect or chromosomal abnormality was excluded from our study. Human ESCs line H1 and UCLA1 were maintained by culture under self –renewal conditions on mouse embryonic fibroblast (MEF) layer in DMEM:F12 (Gibco BRL), 20% KnockOut Serum (Gibco BRL), 1% nonessential amino acids (NEAA, Gibco BRL), 1 mM L-glutamine (Gibco BRL), 0.1 mM β-mercaptoethanol (Gibco BRL), and 10ng/ml of basic fibroblast growth factor (FGF) from R&D.

extract_protocol:
DNA was extracted from sorted cells using the Quick-gDNA MiniPrep Kit (Zymo) according to manufacturer’s instructions.
Bisulfite-Seq: Whole Genome Bisulfite-Seq libraries were genreated using the Ovation Ultralow Methyl-Seq Library Systems (Nugen) according to manufacturers instructions.
TAB-seq: TAB-Seq (Tet-assisted bisulfite sequencing) was perfomrmed using the 5hmC TAB-Seq kit from Wisegene followed by the Ovation Ultralow Methyl-Seq Library Systems (Nugen) according to manufacturers instructions.Bisulfite conversion was performed by performing two rounds using the EpiTect Bisulfite Kit (Qiagen) according to manufacturers instructions.

treatment_protocol: Human fetal gonads, were dissociated with 0.25% Trypsin-EDTA, supplemented with 2% chicken serum (Gibco BRL), for 5 min at 37oC. Dissociated cells were incubated in 1% BSA in PBS containing primary antibodies on ice for 20 min. Primary antibodies used were cKIT-APC conjugated (BD Biosciences).

tag: developmental stage

value: embryo

tag: age

value: 108 days

value: cKIT+ FACS sort

tag: molecule subtype

value: TET1 oxidized and Bisulfite converted DNA


title: HEK293T_HBG112_cas9 replicate 1


title: UW230, cKIT+ Bisulfite-Seq

source_name: Fetal Testis

value: 59 days

tag: cell type

value: Bisulfite converted DNA


title: HEK293T_HBG112_c9VP64 replicate 2

tag: cell line


title: HEK293T replicate 4


title: HEK293T replicate 3


title: UW162, cKIT+ Bisulfite-Seq Ovaries

description: Bisulfite converted DNA

extract_protocol:
DNA was extracted from sorted cells using the Quick-gDNA MiniPrep Kit (Zymo) according to manufacturer’s instructions.
Whole Genome Bisulfite-Seq libraries were genreated using the Ovation Ultralow Methyl-Seq Library Systems (Nugen) according to manufacturers instructions.

tag: sample

value: 113 days


title: CC2 spleen_18

value: Female


title: CC2 skin_18


title: HEK293T_HBG112_c9VP64 replicate 1

value: dcas9_VP64 targetting HBG1/2


title: UW160, cKIT+ Bisulfite-Seq Ovaries

description: Bisulfite converted DNA


title: UW165, cKIT+ Bisulfite-Seq Testes

description: Bisulfite converted DNA

value: 137 days


title: HEK293T replicate 1


title: UW188, cKIT+ Bisulfite-Seq Ovaries

description: Bisulfite converted DNA

value: 67 days


title: UCLA1 TRA-1-81+ RNA Seq RepA

data_processing:
Reads with low quality, and reads containing sequencing adapters were first filtered out.
Raw reads were mapped to hg19 with the gapped aligner Tophat2 allowing up to two mismatches.
Transcript expression levels were quantified using RPKM units using customized scripts written in Perl after normalization based on the geometric means as described in DESeq.
For the transposon analysis, repeat annotation file of h19 was downloaded from the UCSC genome browser (http://genome.ucsc.edu/). The RPKM values of repeats were calculated according to coding transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each sample.

source_name: UCLA1 hESCs

extract_protocol:
Cells were sorted directly in 75ul RLT buffer (Qiagen) and total RNA was extracted using the RNeasy Micro Kit (Qiagen) according to manufacturer’s instructions.
RNA Seq libraries were genreated using the Ovation RNA-Seq V2 (Nugen) followed by Encore Rapid Library System (Nugen) according to manufacturers instructions.

treatment_protocol: Human fetal gonads, H1 and UCLA1 hESCs were dissociated with 0.25% Trypsin-EDTA, supplemented with 2% chicken serum (Gibco BRL), for 5 min at 37oC. Dissociated cells were incubated in 1% BSA in PBS containing primary antibodies on ice for 20 min. Primary antibodies used were cKIT-APC conjugated (BD Biosciences) and TRA-1-81 (eBioscience).

value: passages 10-15

value: TRA-1-81+ FACS sort


title: H1 TRA-1-81+ RNA Seq RepB

source_name: H1 hESCs

value: passages 42-45


title: UW185, cKIT+ Bisulfite-Seq Ovaries

description: Bisulfite converted DNA

value: 57 days


title: UCLA1 TRA-1-81+ RNA Seq RepB


title: UW157, cKIT+ RNA Seq Testes

value: 72 days


title: UW161, cKIT+ RNA Seq Testes

value: 74 days


title: UW165, cKIT+ RNA Seq Testes

value: embryo


title: H1 TRA-1-81+ RNA Seq RepA


title: UW177cKIT+ RNA Seq Testes

value: 98 days


title: UW93, cKIT+ RNA Seq Testes

value: 54 days

value: cKIT+ FACS sort


title: UW162, cKIT+ RNA Seq Ovaries


title: HEK293T replicate 5

value: parent cell


title: UW202, cKIT+ RNA Seq Ovaries

value: 110 days


title: UW180, cKIT+ RNA Seq Ovaries

value: 108 days


title: UW169, cKIT+ RNA Seq Ovaries

value: 94 days


title: HEK293T replicate 2


title: UW200, cKIT+ RNA Seq Ovaries


title: UW156, cKIT+ RNA Seq Ovaries

value: 53 days


title: UW192, cKIT+ RNA Seq Ovaries


title: IgG_ChIPseq

first: Iva

last: Tchasovnikarova

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
ChIP-seq reads were aligned to the reference human genome hg19 using Bowtie2 with default settings.
Data were imported into SeqMonk analysis software with minimum mapping quality of 20.
Peaks were idenfied using the implementation of the MACS peak caller in SeqMonk using a p-value of 1e-5 and fragment size of 300 bp.
The H3K9me3 score for each gene was generated by dividing the total number of H3K9me3 ChIP-seq reads mapping to the gene by the length of the gene in kilobases.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files showing the H3K9me3 peaks identified and the H3K9me3 score for each gene.

source_name: KBM7 cells

growth_protocol: IMDM + 10% FCS + Penicillin/Streptomycin

extract_protocol:
Crosslinking: 1% formaldehyde; Shearing: Bioruptor (Diagenode) to target size of 300bp; IP: 5ug primary antibody overnight
Illumina TruSeq ChIP Sample Prep Kit

value: chronic myeloid leukemia (CML)

tag: karyotype

value: near-haploid


title: mES Tript_YY1_ChIP batch1

description: Young_ID: 20140425_2287

data_processing:
Reads were aligned using bowtie with configuration -p 4 --best -k 1 -m 1 --sam -l 40
Genome_build: mm9
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment and calculated by MACS 1.4

organism: Mus musculus

source_name: Embryonic stem cells

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

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin and target bound fragments were isolated with antibody
The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: 1 uM Triptolide under ES culture condiction

value: Embryonic stem cells

tag: genotype/variation

value: BirA BioYY1

tag: purification target (antibody)


title: mES DMSO_YY1_input batch1

description: Young_ID: 20140425_2292

treatment_protocol: 1uM DMSO under ES culture conditions for 6hr


title: H3K9me3_ChIPseq


title: mES DMSO_YY1_ChIP batch1

description: Young_ID: 20140425_2291


title: mES CDK7i_YY1_ChIP batch1

description: Young_ID: 20140425_2289

treatment_protocol: 10 uM THZ1 under ES culture condiction for 6hr


title: UW170, cKIT+ RNA Seq Testes

value: 122 days


title: mES DMSO_Input batch2

description: Young_ID: 20150219_3505


title: mES Untreated_YY1 batch3

description: Young_ID: 20150325_3638


title: mES DMSO_YY1 batch2

description: Young_ID: 20150219_3504


title: mES DRB_30_YY1 batch3

description: Young_ID: 20150325_3637

treatment_protocol: 100 uM DRB under ES culture conditions for 30min


title: mES Bio_yy1_input_batch3

description: Young_ID: 20150325_3639


title: dSP25 (maternal to dSP23)

city: Farmington

first: Stefan

middle: F

last: Pinter

state: CT

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut, UConn Health

data_processing:
Basecalls performed using Illumina software, version 1.8
ALIGNMENT: dSP23, dSP24 and dSP27 samples were aligned to mm9 reference and variant genomes using Tophat (v2.0.8) for a maximum of 3 mismatched or gapped bases per read, followed by removal of PCR duplicates and multiply mapping reads.
VARIANT OVERLAP: Read pairs considered allele-specific aligned a.) to only one parental genome, or b.) with both ends to one but only a single end to the other, or c.) with fewer nucleotide edits to one parental genome than the other. Read coordinates were mapped back to mm9 reference coordinates.
PROCESSED TRACKS: Reads were retained if they overlapped a referenced variant (bedtools intersect) and converted to strand-specific bedGraph tracks (bedtools genomecov) while scaling to fragments per million (fpm).  Bedgraph tracks were converted to BigWig tracks .(bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: Composite (comp) BigWig tracks include all uniquely mapping reads, allele-specific (mus, cas) tracks only those overlapping a variant. Forward (Watson) strand coverage in positive fpm, reverse (Crick) strand coverage in negative fpm.

source_name: Tail-tip genomic DNA

growth_protocol: Cells were cultured in regular fibroblast medium (1% Pen/Strep, 1% L-glutamine, high-glucose DMEM) with 15% FBS close to confluency before harvest

extract_protocol:
Total RNA from TTFs was harvested using the mirVana RNA extraction kit (Ambion), total DNA was harvested from parental tail-tip clippings using Laird's buffer followed by phenol:chloroform:isoamyl alcohol extraction.
RNA-seq libraries were made by polyA selection of mRNA and directional RNA-seq library generation on the Apollo 324 system (IntegenX) at the biopolymers facility (Harvard Medical School). Parental genomic DNA libraries were similarly prepared in automated fashion.

tag: strain

value: Mm. mus (M)

tag: cross


title: UW168, cKIT+ RNA Seq Ovaries

value: 93 days


title: UW203, cKIT+ RNA Seq Ovaries

value: 67 days


title: dSP26 (paternal to dSP24)


title: dSP24c (clone 11F)

source_name: Tail-tip fibroblasts (TTF)

value: F1 hybrid (CxM)

value: Forward Cross (CAST/EiJ mother)


title: dSP27a (parental line representative)


title: dSP27c (parental line representative)

source_name: Embryonic fibroblasts (MEF)

value: Mm. musculus (M)


title: dSP23b (clone 4D)

value: F1 hybrid (MxC)

value: Reverse Cross (CAST/EiJ father)


title: dSP24a (clone 3E)


title: dSP27b (parental line representative)

value: Mm. castaneus (C)


title: Jurkat_H3K27ac

source_name: T-ALL

growth_protocol: Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin.

value: Jurkat

tag: chip antibody

tag: antibody vendor

value: Abcam

tag: antibody cat. #


title: Jurkat_Gata3

value: Santa Cruz

tag: antibody lot #


title: dSP23a (clone 1E)


title: Jurkat_input


title: mES ACTD_YY1 batch2

description: Young_ID: 20150219_3503

treatment_protocol: 1 uM ACTD treated 6hr


title: Jurkat_Runx1


title: Smc1_ChIAPET_rep1

description: ChIA-PET against Smc1 in Jurkat T-ALL cells

data_processing:
Library strategy: ChIA-PET
Images analysis and base calling was done using the solexa pipeline.
Reads were examined for the presence of at least 10 base pairs of linker. Reads that did not contain linker were not processed further. Reads containing linker were trimmed using cutadapt (cutadapt -m 17 -a forward=ACGCGATATCTTATCTGACT -a reverse=AGTCAGATAAGATATCGCGT --overlap 10).
Trimmed mate pairs were mapped independently to hg19 using bowtie version 1.1.1 (bowtie -e 70 -k 1 -m 1 -v 2 -p 4 --best --strata –S)
Aligned reads were paired with mates using read identifiers and, to remove PCR bias artifacts, were filtered for redundancy: PETs with identical genomic coordinates and strand information at both ends were collapsed into a single PET. The PETs were further categorized into intrachromosomal PETs, where the two ends of a PET were on the same chromosome, and interchromosomal PETs, where the two ends were on different chromosomes. The end read positions of all non-chimeric PETs were used to call PET peaks that represent local enrichment of the PET.
To identify long-range chromatin interactions, we first removed intra- chromosomal PETs of length < 5 kb because these PETs may originate from self-ligation of DNA ends from a single chromatin fragment in the ChIA-PET procedure. We next identified PETs that overlapped with PET peaks at both ends by at least 1bp. Operationally, these PETs were defined as putative interactions. Applying a statistical model based upon the hypergeometric distribution identified high-confidence interactions, representing high-confidence physical linking between the PET peaks. Specifically, the numbers of PET sequences that overlapped with PET peaks at both ends as well as the number of PETs within PET peaks at each end were counted. The PET count between two PET peaks represented the frequency of the chromatin interaction between the two genomic locations. A hypergeometric distribution was used to determine the probability of seeing at least the observed number of PETs linking the two PET peaks. A background distribution of interaction frequencies was then obtained through the random shuffling of the links between two ends of PETs, and a cutoff threshold for calling significant interactions was set to the corresponding p-value of the most significant proportion of shuffled interactions (at an FDR of 0.01). This method yielded similar number of interactions as the correction of p-values by the Benjamini-Hochberg procedure to control for multiple hypothesis testing. Operationally, the pairs of interacting sites with three independent PETs were defined as high-confidence interactions in the SMC1 ChIA-PET merged dataset and with two independent PETs in the individual SMC1 ChIA-PET replicates.
Genome_build: hg19
Supplementary_files_format_and_content: BED12 files: For each replicate the PET sequences were categorized into intrachromosomal PETs, where the two ends of a PET were on the same chromosome, and interchromosomal PETs, where the two ends were on different chromosomes. The unique intrachromosomal PETs are parsed into BED12 format file and high-confidence interactions were identified (N=2, FDR = 0.01 for each replicate; N=3, FDR=0.01 for merged)

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 300-700 bp were immunoprecipitated using SMC1 antibody. Immunoprecipitated DNA was end-repaired, A-tailed, and proximity ligation was performed in the presence of a bridge-linker sequence. Unligated DNA was digested with exonuclease treatment followed by RNAse A, and Proteinase K treatment. DNA was then phenol:chloroform:isoamyl alcohol preciptated and subjected to library preperation.
Purified immunoprecipitated DNA were prepared for sequencing according to the Illumina Nextera Tagmentation protocol. Tagmented DNA was subjected to 12 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 300 and 500bp (representing shear fragments between 200 and 400 nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody catalog number

value: Bethyl A300-055A


title: dSP24b (clone 9G)


title: H3K9me3_sgSETDB1

data_processing:
ChIP-seq reads were aligned to the reference human genome hg19 using Bowtie2 with default settings.
Data were imported into SeqMonk analysis software with minimum mapping quality of 20.
Genome was considered as a series of 1 kb 'windows' and the number of H3K9me3 ChIP-seq reads in each window quantitated for each sample, correcting for total read counts.
Windows containing low (H3K9me3 score <40) levels of H3K9me3 were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file showing the H3K9me3 score for each cell type for each window.

source_name: HeLa cells

growth_protocol: RPMI + 10% FCS + Penicillin/Streptomycin

treatment_protocol: Transfected with pool of Cas9/sgRNA expression plasmids, and sorted for knockout cells that become GFP+ owing to de-repression of a silent GFP reporter construct

value: HeLa

value: epithelial

tag: disrupted gene

tag: antibody

value: anti-H3K9me3  Abcam  ab8898


title: dSP23c (clone 12E)


title: Smc1_ChIAPET_rep2


title: H3K9me3_sgMPP8


title: H3K9me3_sgTASOR

value: TASOR (FAM208A)


title: H3K9me3_sgPeriphilin

value: Periphilin


title: NKX2.5:GFP+ CTR

data_processing:
Base quality trimming on the raw sequencing files was performed with SICKLE 1.33.
The sequences were aligned to a custom hg19 human genome using GSNAP (release 2014-12-06) with the following flags: --batch (set to 4), --novelsplicing (set to 1), --npaths (set to 1), and --quiet-if-excessive.
The SAM file was compressed into a BAM file, name-sorted, and indexed using SAMTOOLS 0.1.18.
The gene read count data were generated using HTSeq-count 0.6.1p1 using the Ensembl reference (http://genome.ucsc.edu), using the non-stranded and intersection-nonempty option flags (--stranded no and --m intersection-nonempty respectively).
Genome_build: hg19 reference genome

source_name: hESC-derived

growth_protocol: Differentiation of hESCs to cardiac lineage was performed by Spin EB method. Cytokine cocktail is added on day 0 to the cells and refreshed on day 3. Beating EBs are observed on day 10.

extract_protocol:
RNA extraction was performed with Macherey-Nagel Nucleospin Kit. DNAse treatment was performed on the column and quality of samples was asessed on Agilent bioanalyzer.
The strand-specific RNA-Seq libraries of the NKX2.5:GFP-positive and -negative cells were generated as described (Parkhomchuk et al., 2009; PMID: 19620212).

treatment_protocol: hESCs differentiations were treated with 1 uM Retinoic Acid (Sigma) from day 4 to day 7 (Devalla et al., 2015; PMID: 2570017). Control differentiations were treated with DMSO from day 4 to day 7.

value: NKX2.5:GFP hESCs

tag: treatment

value: DMSO

tag: facs


title: H3K9me3_WT

tag: cell type

value: none (wildtype)


title: Normal condition BW25113

data_processing:
Adapter sequences were trimmed from the reads.
The reads were aligned to the tRNA reference sequences using modified Smith-Waterman algorithm that considered modified nucleotides matching any nucleotide. Maximum 3 errors (including mismatches, insertions and deletions) was allowed in the alignment and the minimal alignment length was set to 50bp.
Genome_build: Escherichia coli K-12 MG1655 tRNA reference sequences with the modifications (from Modomics database)

organism: Escherichia coli BW25113

source_name: Normal condition

growth_protocol: E. coli BW25113 cells were grown in M9 minimal medium under normal condition and oxidative stress (0.5mM H2O2). After application of H2O2, samples were taken at 15min and 90min. The tRNAs were sequenced.

extract_protocol:
Total RNA was extracted using Trizol method.
tRNAs were deacylated at pH=10. Poly(A) tail was added to the deacylated 3’-CCA terminus by E. coli poly(A) polymerase (NEB) according to the manual. Prior to reverse transcription, polyadenylated tRNA were denatured with 100 µM TG primer (5’-T15GG-3’) and dNTP (25mM each) at 80°C for 5 min and then chilled on ice. The reverse transcription was performed with RevertAid Premium Reverse Transcriptase (Fermentas) according to the manual. After transcription of tRNA to cDNA, the second-strand synthesis was performed with RNase H, DNA Polymerase I and T4 DNA Polymearse (Fermentas) according to the manuals. The sequencing library was constructed using NEBNext Ultra DNA library prep master mix set for Illumina (NEB).
Pair-end (sequenced in single-end)

value: Grown under normal condition


title: NKX2.5:GFP- CTR

tag: cell line


title: Oxidative stress 15min BW25113

source_name: Oxidative stress 15min


title: Oxidative stress 90min BW25113

source_name: Oxidative stress 90min


title: Control_TALE_Rep3

status: Public on May 27 2015

first: Christopher

last: Vockley

address: 101 science drive rm 2193

data_processing:
Base-calling was performed on instrument using CASAVA software
Reads were aligned to the hg19 version of the human genome using bowtie2-align version 2.1.0, and the  -p 32 --end-to-end --very-sensitive t" alignment options
Reads were converted from .sam to .bam files using samtools view version 0.1.19-44428cd with the  "-bS" option
Bam files were sorted using Samtools sort version 0.1.19-44428cd with the options "32 -m 2G"
Bam files were indexed using Samtools Index version 0.1.19-44428cd
Duplicate reads were removed using samtools rmdup  version 0.1.19-44428cd  usint the "-s option"
Bam files were re-indexed after duplicates were removed using Samtools Index version 0.1.19-44428cd
Reads were counted using samtools idxstats version 0.1.19-44428cd
Counts from replicates with low sequencing were combined as follows:
# combine replicates with low sequencing
final_data
<- data.frame(IL1RN_Rep1=full_data$IL1RN_Rep1+full_data$IL1RN_Rep3,
IL1RN_Rep2=full_data$IL1RN_Rep2,
HBG_Rep1=full_data$HBG_Rep1+full_data$HBG_Rep2+full_data$HBG_Rep3,
Ctl_Rep1=full_data$Ctl_Rep1+full_data$Ctl_Rep2,
Ctl_Rep2=full_data$Ctl_Rep3);
Differential expression was computed using R version 3.1.2 using the DEseq2 package version 1.6.2  with following settings: design <- data.frame(condition=c("I","I","H","C","C"))
dds2 <- DESeqDataSetFromMatrix(final_data, design, design= ~ condition)
dds2 <- DESeq(dds2)
res_HBG_TALE_VP64   <- results(dds2, name="condition_H_vs_C")
res_IL1RN_TALE_VP64 <- results(dds2, name="condition_I_vs_C")
Genome_build: RefSeq transcripts from hg19
Supplementary_files_format_and_content: Counts of the number of reads aligned to each RefSeq transcript.

source_name: cultured HEK293T_Control_TALE

extract_protocol:
Between 0.5-1 million cells were trypsinized, washed with PBS, pelleted and snap frozen. Total RNA was extracted using Qiagen RNeasy mini-columns with 1% β-mercaptoethanol in RLT buffer and a 15 min on column DNase digestion. mRNA was isolated using the Dynabeads mRNA Direct Kit (Invitrogen).
First strand cDNA was generated using SuperScript Vilo cDNA synthesis master mix (Invitrogen), and second strand cDNA was synthesized using E. coli DNA Polymerase I (New England Biolabs) with random hexamer primers. Double stranded cDNA was purified using 1.8X Agentcourt SPRI beads (Beckman Coulter). Double stranded cDNA was fragmented and sequencing adaptors added using Nextera transposase (Illumina) and indexed for sequencing by PCR as described previously. Samples were pooled in equimolar ratios and sequenced on an Illumina HiSeq 2000.

treatment_protocol: HEK293T cells were transfected with Lipofectamine 2000 (Invitrogen) according to manufacturer’s instructions. Transfection efficiencies were routinely higher than 80% as determined by fluorescence microscopy following delivery of a control eGFP expression plasmid. dCas9-VP64 expression plasmid was transfected at a mass ratio of 3:1 to the total amount of gRNA expression plasmid consisting of a mixture of equal amounts of the four gRNAs.

tag: transfected with

value: GFP control


title: Control_TALE_Rep1


title: HBG_TALE_Rep1

source_name: cultured HEK293T_HBG_TALE

value: TALE-activator targeting HBG1


title: IL1RN_TALE_Rep2

source_name: cultured HEK293T_IL1RN_TALE

value: TALE-activator targeting IL1RN


title: HBG_TALE_Rep2


title: IL1RN_TALE_Rep1


title: HBG_TALE_Rep3


title: Control_TALE_Rep2


title: IL1RN_TALE_Rep3


title: mRNA_S1GOF4_nc_3d_841

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

description: for exp ID: 130626_SN923_0203_s07.fq

data_processing:
alignment, ChIP-seq: Reads of 50 bases were aligned to the mouse genome build mm9 with Bowtie 0.12.8, allowing two mismatches. Uniquely mapped and non-redundant reads were retained and used for peak calling.
peaks, ChIP-seq: Peak detection was performed with MACS1.4.2 with the default parameters and a p value <1.0E-05.
alignment, RNA-seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 50 bases were mapped to the  genome using TopHat 2.0.8
RPKM, RNA-seq: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek GS.
Genome_build: mm9 for mouse data, hg18 for human data
Supplementary_files_format_and_content: bw for ChIP-seq peak files, excel for a RPKM file

source_name: human primary CD4+ T cells

growth_protocol:
mouse Th0: CD4+ T cells from spleens and lymph nodes of 6-8 week-old mice were purified by negative selection and magnetic separation (Miltenyi Biotec) followed by sorting of naïve CD4+CD62L+CD44-CD25- population using FACSAria III (BD). All cells were activated by plate-bound anti-CD3 (10 μg ml-1; eBioscience) and anti-CD28 (10 μg ml-1; eBioscience)  in RPMI medium with 10% (vol/vol) FCS, 2 mM glutamine, 100 IU ml-1 of penicillin, 0.1 mg ml-1 of streptomycin and 20mM HEPES buffer, pH 7.2-7.5 (all from Invitrogen) and 2 mM β–mercaptoethanol (Sigma-Aldrich) for indicated duration of time (6h, 24h, 3d).
human Th0: Peripheral blood mononuclear cells were prepared from venous blood by Ficoll-gradient centrifugation. Naïve CD4+CD45RAhighCD45ROlow population was purified by the flow cytometry using FACSAria IIi (BD) and were activated by plate-bound anti-CD3 (5 μg ml-1; eBioscience) and anti-CD28 (5 μg ml-1; eBioscience) in media (the same as protocol1) for 3 days.

extract_protocol:
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
RNA-Seq: Total RNA was prepared from approximately 1 million cells by using mirVana miRNA Isolation Kit (AM1560, ABI).
RNA-Seq: 200 ng of total RNA was subsequently used to prepare RNA-seq library by using TruSeq SR RNA sample prep kit (FC-122-1001, Illumina) by following manufacturer’s protocol.
RNA-Seq. The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.

treatment_protocol:
For mouse cells, mIL6 (20 ng ml-1; R&D Systems) was added. For human cells, hIL6 (50 ng ml-1; R&D Systems) was added.
For mouse cells, mIL27 (20 ng ml-1; R&D Systems) was added. For human cells, hIL27 (50 ng ml-1; R&D Systems) was added.

tag: culture condition

value: 3 day in vitro culture for Th0

tag: genotype

value: STAT1 GOF patient 4

tag: lab data id


title: mRNA_S1GOF5_nc_3d_844

description: for exp ID: 130626_SN923_0203_s10.fq

value: STAT1 GOF patient 5


title: mRNA_S1GOF5_IL27_3d_846

description: for exp ID: 130626_SN923_0203_s12.fq

value: 3 day in vitro culture for Th0, treatment (IL27)


title: mRNA_S1GOF4_IL6_3d_842

description: for exp ID: 130626_SN923_0203_s08.fq

value: 3 day in vitro culture for Th0, treatment (IL6)


title: mRNA_S1GOF5_IL6_3d_845

description: for exp ID: 130626_SN923_0203_s11.fq


title: mRNA_S1GOF4_IL27_3d_843

description: for exp ID: 130626_SN923_0203_s09.fq


title: mRNA_S1GOF3_IL27_3d_840

description: for exp ID: 130626_SN923_0203_s06.fq

value: STAT1 GOF patient 3


title: NKX2.5:GFP+ RA

value: Retinoic Acid


title: mRNA_S1GOF2_IL6_3d_796

description: for exp ID: 130604_SN923_0201_s11.fq

value: STAT1 GOF patient 2


title: mRNA_S1GOF3_nc_3d_838

description: for exp ID: 130626_SN923_0203_s04.fq


title: mRNA_S1GOF2_IL27_3d_797

description: for exp ID: 130604_SN923_0201_s12.fq


title: mRNA_S1GOF1_nc_3d_621

description: for exp ID: 130423_SN923_0192_s08.fq

value: STAT1 GOF patient 1


title: mRNA_S1GOF1_IL6_3d_622

description: for exp ID: 130423_SN923_0192_s09.fq


title: NKX2.5:GFP- RA


title: mRNA_HC2_IL27_3d_788

description: for exp ID: 130604_SN923_0201_s03.fq

value: healthy control 2


title: mRNA_HC1_IL27_3d_695

description: for exp ID: 130506_SN923_0196_s23.fq

value: healthy control 1


title: mRNA_S1GOF2_nc_3d_795

description: for exp ID: 130604_SN923_0201_s10.fq


title: mRNA_HC1_nc_3d_693

description: for exp ID: 130506_SN923_0196_s21.fq


title: mRNA_S1GOF1_IL27_3d_623

description: for exp ID: 130423_SN923_0192_s10.fq


title: mRNA_S3KO_IL27_24h_rpt1_1334

description: for exp ID: 140225_SN923_227_s23.fq

source_name: mouse primary CD4+ T cells

tag: strain

value: 24 hr in vitro culture for Th0, treatment (IL27)

value: STAT3 KO 1


title: mRNA_S1KO_IL27_24h_rpt1_1330

description: for exp ID: 140225_SN923_227_s19.fq

value: STAT1 KO 1


title: mRNA_S3KO_nc_24h_rpt1_1332

description: for exp ID: 140225_SN923_227_s21.fq

value: 24 hr in vitro culture for Th0


title: mRNA_S1KO_nc_24h_rpt1_1328

description: for exp ID: 140225_SN923_227_s17.fq


title: mRNA_HC4_IL27_3d_837

description: for exp ID: 130626_SN923_0203_s03.fq

value: healthy control 4


title: mRNA_HC4_IL6_3d_836

description: for exp ID: 130626_SN923_0203_s02.fq


title: BJ_H3K4me1

first: Jingxian

state: Singpaore

address: 61 Biopolis Drive Proteos

department: IMCB

institute: Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations : -v 2 -m 1 -p 2 --best --strata --quiet --solexa1.3-quals
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, wig files were generated from the BAM alignment files using BedTools genomeCoverageBed (v2.14.2); bedGraph files were automatically generated as an output of MACS 2.0.10

source_name: BJ (hTert/sT)

growth_protocol: Fibroblast cells were routinely generated typically by re-plating 1-2 10e6 cells into a 140x20mm plate on uncoated plastic in DMEM medium (Gibco, Life technologies) supplemented with BSF and penicillin/streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Fibroblast cells were treated with H2O2 (final concentration 0.2mM) for 30 minutes and 2 hours.

tag: tissue

value: skin

value: fibroblast cell line

tag: chip antbody

value: H3K4me1 (ab8895, Abcam)

value: BJ

tag: tiime

value: untreated


title: mRNA_HC3_IL27_3d_791

description: for exp ID: 130604_SN923_0201_s06.fq

value: 3 day in vitro culture for Th0, treatment (IL27)

value: healthy control 3


title: MRC5_RNAPII-2 hours

value: lung

value: RNAPII, (N20, Santa Cruz)

value: 2 hours


title: mRNA_HC4_nc_3d_835

description: for exp ID: 130626_SN923_0203_s01.fq

value: 3 day in vitro culture for Th0


title: mRNA_HC1_IL6_3d_694

description: for exp ID: 130506_SN923_0196_s22.fq

value: 3 day in vitro culture for Th0, treatment (IL6)

value: healthy control 1


title: mRNA_WT_IL6_24h_rpt1_1325

description: for exp ID: 140225_SN923_227_s14.fq

value: 24 hr in vitro culture for Th0, treatment (IL6)

value: wild type 1


title: BJ_H3K27ac

source_name: BJ (hTerst/sT)

value: H3K27ac (ab4729, Abcam)


title: mRNA_WT_nc_24h_rpt1_1324

description: for exp ID: 140225_SN923_227_s13.fq

value: 24 hr in vitro culture for Th0


title: mRNA_HC3_nc_3d_789

description: for exp ID: 130604_SN923_0201_s04.fq


title: mRNA_S1GOF3_IL6_3d_839

description: for exp ID: 130626_SN923_0203_s05.fq

value: STAT1 GOF patient 3


title: mRNA_HC2_IL6_3d_787

description: for exp ID: 130604_SN923_0201_s02.fq

value: healthy control 2


title: mRNA_HC3_IL6_3d_790

description: for exp ID: 130604_SN923_0201_s05.fq


title: BJ_Input DNA-untreated

value: skin

value: fibroblast cell line


title: mRNA_HC2_nc_3d_786

description: for exp ID: 130604_SN923_0201_s01.fq


title: mRNA_S3KO_IL6_24h_rpt1_1333

description: for exp ID: 140225_SN923_227_s22.fq

value: STAT3 KO 1


title: MRC5_Input DNA-2 hours

value: 3 hours


title: MRC5_Input DNA-30 minutes

value: 31 minutes


title: mRNA_S1KO_IL6_24h_rpt1_1329

description: for exp ID: 140225_SN923_227_s18.fq

value: STAT1 KO 1


title: RNA-seq TH-ProB no treatment, rep2

city: Linkoping

first: Rajesh

last: Somasundaram

address: Dept of Clinical and Experimental Medicine (IKE)

department: Microbiology and Molecular Medicine

country: Sweden

institute: Linkoping University

data_processing:
For RNA-Seq samples, data analysis was performed with Arraystar (DNA STAR). The reads were aligned to mouse reference genome (mm9, NCBI 37) and RPKM normalized. Statistical analysis in Arraystar was performed with Student´s t-test with correction for multiple testing (Benjamini Hochberg). A p-value > 0.05 was considered as statistically significant.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Processed data files include BED files. All genomic coordinates are relative to the mm9 mouse assembly.

source_name: Ebf1+/- Pax5+/- ProB, no treatment

growth_protocol: ProB-cell isolation / culture protocol: For sorting of Pro B cells, CD16/CD32 (FC) -blocked (93, eBioscience) cells were stained with antibodies against lineage markers CD11b/Mac1 (M1/70), Gr1 (RB6-8C5), TER119 (Ter119), CD3 (17A2, BD Pharmingen), CD11c (N418) and NK1.1 (PK136) and further stained with CD19 (ID3), CD45R/B220 (RA3-6B2), CD43 (S7), IgM (RMM-1) and IgD (11-26. eBioscience, San Diego, CA). Cell sorting was performed on a BD FACSAriaTM (BD Biosciences, San Jose, California) using propidium iodide (PI, Invitrogen, Paisly, UK) as viability marker. For  expansion, Pro-B cells were cultured on OP9 stromal cells supplemented with 10ng/mL KIT ligand, 10ng/mL Fms-like tyrosine kinase 3 ligand (FLT3L), and 10ng/mL Interleukin-7 in Optimem supplemented with 10% FCS, Beta-mercaptoethanol, HEPES and Penstrep.

extract_protocol:
RNA-Seq: RNA was extracted with the Qiagen RNeasy Micro Kit.
RNA-Seq not treated: Total RNA was isolated from four Wt CD19+CD43highIgM- and four Pax5+/-Ebf1+/- pro-B samples using RNeasy MicroKit (Qiagen) according to manufacturer’s recommendations, and sent to UCLA Clinical Microarray Core for library preparation where they used Nugen Ovation Ultra Low DR kit and the libraries were run on the Illumina HiSeq 2500.

treatment_protocol: See above.

tag: strain/background

tag: genotype/variation

value: ProB


title: mRNA_WT_IL27_24h_rpt1_1326

description: for exp ID: 140225_SN923_227_s15.fq

value: 24 hr in vitro culture for Th0, treatment (IL27)


title: mRNA_WT_IL6_6h_rpt1_1313

description: for exp ID: 140225_SN923_227_s2.fq

value: 6 hr in vitro culture for Th0, treatment (IL6)


title: MRC5_RNAPII-untreated

value: lung

value: RNAPII, (N20, Santa Cruz)

value: Untreated


title: MRC5_RNAPII-30 minutes

value: 30 minutes


title: MRC5_Input DNA-untreated


title: mRNA_S3KO_IL27_6h_rpt1_1322

description: for exp ID: 140225_SN923_227_s11.fq

value: 6 hr in vitro culture for Th0, treatment (IL27)


title: RNA-seq WT-ProB no treatment, rep4

source_name: WT ProB, no treatment

value: WT


title: RNA-seq Ebf1+/- ProB no treatment, rep1

source_name: Ebf1+/- ProB, no treatment


title: RNA-seq Ebf1+/- ProB no treatment, rep2


title: mRNA_S3KO_IL27_3d_rpt2_201

description: for exp ID: 120905_s9.fq

value: 3 day in vitro culture for Th0, treatment (IL27)

value: STAT3 KO 2


title: mRNA_S3KO_IL6_6h_rpt1_1321

description: for exp ID: 140225_SN923_227_s10.fq


title: RNA-seq Pax5+/- ProB no treatment, rep2

source_name: Pax5+/- ProB, no treatment


title: mRNA_WT_nc_6h_rpt1_1312

description: for exp ID: 140225_SN923_227_s1.fq

value: 6 hr in vitro culture for Th0

value: wild type 1


title: mRNA_S1KO_nc_6h_rpt1_1316

description: for exp ID: 140225_SN923_227_s5.fq


title: mRNA_S3KO_IL6_3d_rpt2_200

description: for exp ID: 120905_s8.fq

value: 3 day in vitro culture for Th0, treatment (IL6)


title: RNA-seq Pax5+/- ProB no treatment, rep1


title: RNA-seq WT-ProB no treatment, rep1


title: DNA for Ebf1 ChIP-seq Ebf1+/- ProB no treatment

description:
DSG+formaldehyde cross-linked.
This Sample represents 2 replicates.

data_processing:
For ChIP-Seq samples, reads were aligned to the mm9 genome using default parameter for Bowtie. Aligned read files from ChIP-seq experiments were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, perform motif- and other analyses in the study.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Processed data files include BED files. All genomic coordinates are relative to the mm9 mouse assembly.

source_name: Ebf1+/- ProB, no treatment, input

extract_protocol:
ChIP-Seq: Chromatin immunoprecipitation using anti-Ebf1 antibody (Vendor: Millipore, cat# ABE1294, lot# Q2399134).
ChIP-Seq: Samples were sent to UCLA Clinical Microarray Core for library preparation. Covaris M220 was used to shear ChIP-DNA. The library was generated using Nugen Ovation Ultra Low DR kit following standard procedures. Libraries were run on the Illumina HiSeq 2500.

tag: chip (antibody)


title: mRNA_S1KO_IL27_6h_rpt1_1318

description: for exp ID: 140225_SN923_227_s7.fq


title: RNA-seq TH-ProB no treatment, rep4


title: mRNA_S1KO_IL6_6h_rpt1_1317

description: for exp ID: 140225_SN923_227_s6.fq


title: RNA-seq TH-ProB no treatment, rep3


title: DNA for Ebf1 ChIP-seq Pax5+/- ProB no treatment

source_name: Pax5+/- ProB, no treatment, input


title: mRNA_WT_IL27_6h_rpt1_1314

description: for exp ID: 140225_SN923_227_s3.fq


title: mRNA_S3KO_IL6_3d_rpt1_140

description: for exp ID: 120621_s14.fq

value: STAT3 KO 1


title: RNA-seq TH-ProB no treatment, rep1


title: mRNA_S3KO_nc_3d_rpt1_139

description: for exp ID: 120621_s13.fq

value: 3 day in vitro culture for Th0


title: Ebf1 Chip-seq Pax5+/- ProB no treatment

source_name: Pax5+/- ProB, no treatment, Ebf1 ChIP


title: mRNA_S1KO_IL27_3d_rpt2_198

description: for exp ID: 120905_s6.fq

value: STAT1 KO 2


title: Ebf1 ChIP-seq TH-ProB no treatment

source_name: Ebf1+/- Pax5+/- ProB, no treatment, Ebf1 ChIP

value: ProB


title: mRNA_S3KO_nc_6h_rpt1_1320

description: for exp ID: 140225_SN923_227_s9.fq


title: Ebf1 ChIP-seq WT-ProB no treatment

source_name: WT ProB, no treatment, Ebf1 ChIP


title: RNA-seq WT-ProB no treatment, rep3


title: mRNA_S1KO_IL6_3d_rpt2_197

description: for exp ID: 120905_s5.fq


title: RNA-seq WT-ProB no treatment, rep2


title: mRNA_S3KO_nc_3d_rpt2_199

description: for exp ID: 120905_s7.fq


title: mRNA_S3KO_IL27_3d_rpt1_141

description: for exp ID: 120621_s15.fq


title: mRNA_S1KO_nc_3d_rpt2_196

description: for exp ID: 120905_s4.fq


title: DNA for Ebf1 ChIP-seq TH-ProB no treatment

source_name: Ebf1+/- Pax5+/- ProB, no treatment, input


title: mRNA_S1KO_IL27_3d_rpt1_110

description: for exp ID: 120614_s12.fq

value: STAT1 KO 1


title: DNA for Ebf1 ChIP-seq WT-ProB no treatment

source_name: WT ProB, no treatment, input


title: BJ Cytosol-2hours

description: rRNA-depleted total RNA

data_processing:
The sequenced reads were mapped to hg19 build of the human genome using TopHat version 1.1.4 with the aligner Bowtie 0.12.7 with their default parameters except –m 1 and –segment-mismatches 2.
The mapped reads were further manipulated by removing the reads that mapped to multiple locations (-q 0) using SAMtools.
Genome_build: hg19
Supplementary_files_format_and_content: Each BAM alignment file was divided into two groups based on their relative DNA strand using SAMtools. Each BAM files was converted into Wig file format using BedTools genomeCoverageBed (v2.16.2). Bigwig files generated by converting Wig files using wigToBigWig from UCSC.

source_name: BJ

extract_protocol:
Total RNA was harvested using Trizol reagent. Applied Biosystems SOLiD System (3.5 and 4) directional RNA-Seq was used with 5 ug of total RNA for the construction of sequencing libraries.Total RNA was depleted twice from rRNA using the RiboMinus Eukaryote Kit for RNA-Seq (ABI, #A1083708)
RNA libraries were prepared for sequencing using standard ABI SOLiD protocols

value: skin

value: fibroblast cells

value: BJ

value: 5 hours


title: BJ Cytosol-30 minutes

description: rRNA-depleted total RNA

value: 33 minutes


title: mRNA_S1KO_IL6_24h_rpt2_1653

description: for exp ID: 140516_SN7001365_0121_s18.fq

value: 24 hr in vitro culture for Th0, treatment (IL6)


title: mRNA_S1KO_IL6_3d_rpt1_109

description: for exp ID: 120614_s11.fq


title: mRNA_S3KO_nc_24h_rpt2_1656

description: for exp ID: 140516_SN7001365_0121_s21.fq

value: 24 hr in vitro culture for Th0


title: Ebf1 Chip-seq Ebf1+/- ProB no treatment

source_name: Ebf1+/- ProB, no treatment, Ebf1 ChIP


title: BJ Cytosol-untreated

description: rRNA-depleted total RNA

value: Untreated


title: mRNA_S1KO_nc_3d_rpt1_108

description: for exp ID: 120614_s10.fq


title: mRNA_S1KO_IL27_24h_rpt2_1654

description: for exp ID: 140516_SN7001365_0121_s19.fq

value: 24 hr in vitro culture for Th0, treatment (IL27)


title: mRNA_WT_IL6_3d_rpt2_106

description: for exp ID: 120614_s8.fq

value: wild type 2


title: mRNA_S3KO_IL27_6h_rpt2_1646

description: for exp ID: 140516_SN7001365_0121_s11.fq

value: 6 hr in vitro culture for Th0, treatment (IL27)

value: STAT3 KO 2


title: mRNA_WT_IL6_24h_rpt2_1649

description: for exp ID: 140516_SN7001365_0121_s14.fq


title: mRNA_WT_IL27_24h_rpt2_1650

description: for exp ID: 140516_SN7001365_0121_s15.fq


title: mRNA_S3KO_nc_6h_rpt2_1644

description: for exp ID: 140516_SN7001365_0121_s9.fq

value: 6 hr in vitro culture for Th0


title: MRC5 Cytosol-30 minutes

description: rRNA-depleted total RNA

value: lung

value: 31 minutes


title: mRNA_S1KO_nc_24h_rpt2_1652

description: for exp ID: 140516_SN7001365_0121_s17.fq

value: STAT1 KO 2


title: BJ Nucleus-2 hours

description: rRNA-depleted total RNA

value: 4 hours


title: mRNA_S1KO_IL27_6h_rpt2_1642

description: for exp ID: 140516_SN7001365_0121_s7.fq


title: MRC5 Cytosol-untreated

description: rRNA-depleted total RNA


title: mRNA_WT_nc_24h_rpt2_1648

description: for exp ID: 140516_SN7001365_0121_s13.fq


title: mRNA_S1KO_IL6_6h_rpt2_1641

description: for exp ID: 140516_SN7001365_0121_s6.fq

value: 6 hr in vitro culture for Th0, treatment (IL6)


title: mRNA_WT_IL27_3d_rpt2_107

description: for exp ID: 120614_s9.fq

value: 3 day in vitro culture for Th0, treatment (IL27)


title: mRNA_S3KO_IL27_24h_rpt2_1658

description: for exp ID: 140516_SN7001365_0121_s23.fq


title: mRNA_S3KO_IL6_24h_rpt2_1657

description: for exp ID: 140516_SN7001365_0121_s22.fq


title: BJ Nucleus-30 minutes

description: rRNA-depleted total RNA

value: skin

value: fibroblast cells

value: BJ

value: 32 minutes


title: STAT1_S3KO_IL27_1708

description: for exp ID: 140609_SN923_0253_s25

value: STAT3 KO

tag: chip antibody

value: STAT1 (Santa Cruz Biotechnology, sc-592)(Lot #E1209)


title: MRC5 Nucleus-untreated

description: rRNA-depleted total RNA

value: Untreated


title: mRNA_WT_nc_6h_rpt2_1636

description: for exp ID: 140516_SN7001365_0121_s1.fq

value: wild type 2


title: input_S3KO_nc_1706

description: for exp ID: 140609_SN923_0253_s23

value: 3 day in vitro culture for Th0

value: none, input


title: input_S3KO_IL6_1707

description: for exp ID: 140609_SN923_0253_s24

value: 3 day in vitro culture for Th0, treatment (IL6)


title: mRNA_WT_nc_3d_rpt2_105

description: for exp ID: 120614_s7.fq


title: BJ Nucleus-untreated

description: rRNA-depleted total RNA


title: mRNA_S3KO_IL6_6h_rpt2_1645

description: for exp ID: 140516_SN7001365_0121_s10.fq

value: STAT3 KO 2


title: mRNA_WT_IL27_3d_rpt1_101

description: for exp ID: 120614_s3.fq

value: wild type 1


title: STAT1_S3KO_IL6_1704

description: for exp ID: 140609_SN923_0253_s21


title: MRC5 Cytosol-2hours

description: rRNA-depleted total RNA

value: lung

value: 3 hours


title: mRNA_S1KO_nc_6h_rpt2_1640

description: for exp ID: 140516_SN7001365_0121_s5.fq

value: 6 hr in vitro culture for Th0

value: STAT1 KO 2


title: mRNA_WT_IL6_3d_rpt1_100

description: for exp ID: 120614_s2.fq


title: mRNA_WT_nc_3d_rpt1_99

description: for exp ID: 120614_s1.fq


title: STAT3_S1KO_IL27_1700

description: for exp ID: 140609_SN923_0253_s17

value: 3 day in vitro culture for Th0, treatment (IL27)

value: STAT1 KO


title: STAT1_S3KO_nc_1701

description: for exp ID: 140609_SN923_0253_s18


title: MRC5 Nucleus-2 hours

description: rRNA-depleted total RNA

value: fibroblast cells

value: 2 hours


title: input_S3KO_IL27_1710

description: for exp ID: 140609_SN923_0253_s27

value: STAT3 KO


title: mRNA_WT_IL27_6h_rpt2_1638

description: for exp ID: 140516_SN7001365_0121_s3.fq

value: 6 hr in vitro culture for Th0, treatment (IL27)


title: RNA-seq TH-ProB cultured 1 day on OP9DL1, rep1

source_name: Ebf1+/- Pax5+/- ProB, 1 day culture on OP9DL1 stromal cells

extract_protocol:
RNA-Seq: RNA was extracted with the Qiagen RNeasy Micro Kit.
RNA-seq 1 day on OP9DL1 and OP9: Libraries were constructed using Nugen's Ovation Ultralow Library systems. Detailed protocol is available on their website. In short, input DNA were fragmented using sonication, end repaired, followed by ligation of adapters, amplification and finally bead purification. The samples were run on NextSeq 500.

value: ProB

value: 1 day culture on OP9DL1 stromal cells


title: MRC5 Nucleus-30 minutes

description: rRNA-depleted total RNA

value: 30 minutes


title: input_S1KO_IL6_1699

description: for exp ID: 140609_SN923_0253_s16

source_name: mouse primary CD4+ T cells

value: none, input


title: RNA-seq Imp KD replicate 3

city: Copenhagen

first: Mireya

last: Plass

address: Robert-Rössle Str. 10

country: Germany

institute: MDC-Berlin

description:
Cytoplamic mRNA
sample_vs_control_all_fcs_symbol.txt

data_processing:
Base-calling was performed with CASAVA-1.8.2
Reads were demultiplexed using their fixed barcodes
Reads were trimmed at the 3'end to remove adapter sequences and low-quality sequences using custom python scripts. Reads shorter than 18nt were discarded.
Duplicated reads were collapsed using random barcodes to discriminate between identical sequences.
Reads were mapped to the Drosophila genome (dm3) + exon junction index (ensembl72) using BWA-PSSM with parameters -n 0.04 -l 1024-m 400 -P 0.99. PAR-iCLIP experiments were mapped modeling C>T conversions that arise due to the use of 4SU assuming a 12.5% conversion rate.
Confidently mapped reads with a posterior probability > 0.99 were further clustered according to their genomic positions.
Genome_build: dm3
Supplementary_files_format_and_content: Bedgraph files containing the read clusters
Supplementary_files_format_and_content: Plain text file containing the counts per gene, fold changes and p-values as calculated by DESeq

organism: Drosophila melanogaster

source_name: Schneider 2  (S2) cells

growth_protocol: S2 cells were growth at 26C in Schneider's Drosophila Medium containing 10% heat inactivated fetal bovine serum, 100U/ml Penicillin and 100ug/ml Streptomycin

extract_protocol:
5x106 cells  were treated with 40µg/ml dsRNA corresponding to imp gene with boosts of dsRNA each day. On the third day the cells were harvested and total RNA was purified using TriReagent. 30ug of total RNA was enriched for mRNA using Poly(A)Purist MAG kit (Ambion) according to manufacturer’s specifications. Library was performed as described in (Kielpinski et al. 2013, Deep Sequencing Data Analysis). The 3' ligation adapter contains a 7'mer random barcode. 20 cycles of PCR was used to create the final library.
See individual experiment

tag: rt primer with random barcode / index


title: RNA-seq Imp KD replicate 2


title: mRNA_WT_IL6_6h_rpt2_1637

description: for exp ID: 140516_SN7001365_0121_s2.fq

value: 6 hr in vitro culture for Th0, treatment (IL6)

value: wild type 2


title: STAT3_WT_IL6_1688

description: for exp ID: 140609_SN923_0253_s05

value: 3 day in vitro culture for Th0, treatment (IL6)

value: wild type


title: RNA-seq Imp KD replicate 1


title: RNA-seq Luc Control replicate 2

extract_protocol:
5x106 cells  were treated with 40µg/ml dsRNA corresponding to luciferase gene with boosts of dsRNA each day. On the third day the cells were harvested and total RNA was purified using TriReagent. 30ug of total RNA was enriched for mRNA using Poly(A)Purist MAG kit (Ambion) according to manufacturer’s specifications. Library was performed as described in (Kielpinski et al. 2013, Deep Sequencing Data Analysis). The 3' ligation adapter contains a 7'mer random barcode. 20 cycles of PCR was used to create the final library.
See individual experiment


title: RNA-seq TH-ProB cultured 1 day on OP9DL1, rep4

tag: treatment


title: input_WT_IL6_1691

description: for exp ID: 140609_SN923_0253_s08

value: none, input_


title: STAT3_S1KO_nc_1693

description: for exp ID: 140609_SN923_0253_s10

value: 3 day in vitro culture for Th0


title: RIP-seq replicate 2

description: Cytoplamic RNA

extract_protocol:
4 x 107 S2 cells were lyzed, and Imp was IP'ed using anti-Imp antibody. RNA was isolated using TriReagent. Library was performed as described in (Kielpinski et al. 2013, Deep Sequencing Data Analysis). 28 cycles of PCR was used to create the final library.
See individual experiment


title: STAT3_WT_IL27_1690

description: for exp ID: 140609_SN923_0253_s07


title: RIP-seq replicate 1

description: Cytoplamic RNA


title: RNA-seq WT-ProB cultured 1 day on OP9DL1, rep4

source_name: WT ProB, 1 day culture on OP9DL1 stromal cells

value: WT


title: RNA-seq TH-ProB cultured 1 day on OP9, rep2

source_name: Ebf1+/- Pax5+/- ProB, 1 day culture on OP9 stromal cells

value: 1 day culture on OP9 stromal cells


title: RNA-seq TH-ProB cultured 1 day on OP9, rep3


title: input_S1KO_nc_1695

description: for exp ID: 140609_SN923_0253_s12

value: STAT1 KO


title: RNA-seq TH-ProB cultured 1 day on OP9DL1, rep3


title: input_S1KO_IL27_1703

description: for exp ID: 140609_SN923_0253_s20

value: 3 day in vitro culture for Th0, treatment (IL27)


title: RNA-seq Luc Control replicate 3


title: RNA-seq Luc Control replicate 1


title: RNA-seq TH-ProB cultured 1 day on OP9DL1, rep2


title: input_WT_nc_1687

description: for exp ID: 140609_SN923_0253_s04


title: RNA-seq TH-ProB cultured 1 day on OP9, rep1


title: RNA-seq replicate 1 (Control for iCLIP rep1)

description: Cytoplamic mRNA

extract_protocol:
Total RNA was isolated from 5x107 S2 cells using the standard TRI Reagent protocol (Sigma Aldrich). Poly(A) RNA was enriched from 100ug total RNA using Poly(A)Purist MAG kit (Ambion) according to manufacturer’s specifications. Poly(A) RNA was fragmented using MgCl2. The rest of the library preparation was performed as described in (Konig et al, 2011) with PCR amplification using 17 cycles.
See individual experiment

tag: random barcode

value: NNNNN Random Barcode at the read beginning


title: RNA-seq WT-ProB cultured 1 day on OP9, rep3

source_name: WT ProB, 1 day culture on OP9 stromal cells

tag: cell type