title: CL0000_INPUT_PLUS_M32_REP_000

data_processing:
Raw sequencing data were aligned to the hg37 genome build using the Burrows-Wheeler Aligner (BWA) version 0.7.10.
Further indel realignment, base-quality score recalibration and duplicate-read removal were performed using the Genome Analysis Toolkit (GATK) version 3.2.2 following raw reads alignments guidelines
To call  enriched regions, we first applied Model-based Analysis of ChIP-Seq (MACS2 version 2.1.0) to all histone marks. For narrow histone marks (H3K4me) resulting raw peaks were filtered by by pval=0.01. Next, for each peak, RPKM (Reads Per Kilobase of transcript per Million mapped reads) was calculated for IP (immuno-precipitated) and INPUT bam files. Only those peaks with RPKM INPUT/RPKM  IP  ratio greater than 0.5 were reported to final result.
For broad histone marks (H3K36me3, H3K9me3, H3K27me3, H4K20me3) resulting raw peaks were filtered by by pval=0.1.
To ensure high stringency of broad peak calling, we applied the second peak caller called SICER version 1.1 following the instructions provided with download. Two sets of peaks were merged using bedtools merge tool, only intersecting broad peaks were reported.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files include peak coordinates and RPKM values for each sample.

source_name: INPUT PLUS M30

growth_protocol: Stable immortalized astrocytes were grown in DMEM + 10% FBS. Inducible astrocytes were grown in DMEM + Tetracycline-free FBS (10%) and IDH1 R132H expression was induced with the addition of 1 ug/ml of doxycycline. Tumorspheres were grown in NeuroCult NS-A Proliferation media (STEMCELL Technologies) with EGF and FGF.

extract_protocol:
ChIP was performed using the Magna ChIP™ G - Chromatin Immunoprecipitation Kit (Millipore) according to manufacturer's instructions.
Libraries were prepared according to Illumina's instructions.

value: +dox (IDH1 R132H)

value: INPUT


title: CL0000_INPUT_OFF_M70_REP_000

status: Public on Aug 23 2017

type: SRA

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

department: LRI

country: USA

institute: Cleveland Clinic

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: INPUT OFF M70

tag: cell type

value: immortalized human astrocytes

tag: genotype

value: off dox 40P (wild-type)

tag: passage

tag: chip antibody


title: empty vector, plus dox [P70_PLUS]

library_source: transcriptomic

data_processing:
Raw reads in the fastq format were aligned to Human Genome HG19 using the RNAseq STAR aligner version 2.4.0d.
Mapped reads for each sample were counted for each gene in annotation files in GTF format (gencode.v19.annotation.gtf available for download from GENECODE website using the  FeatureCounts read summarization program
Genome_build: HG19
Supplementary_files_format_and_content: raw feature counts

molecule: total RNA

source_name: immortalized human astrocytes

growth_protocol: Inducible astrocytes were grown in DMEM + Tetracycline-free FBS (10%) and IDH1 R132H expression was induced with the addition of 1 ug/ml of doxycycline. Tumorspheres were grown in NeuroCult NS-A Proliferation media (STEMCELL Technologies) with EGF and FGF.

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (Qiagen)
RNA-seq (Ribo-deplete protocol); Libraries were prepared according to Illumina's instructions.

tag: genotype/variation

value: empty vector

tag: dox

value: plus

value: 40 passages from baseline (passage 30)


title: RNA_total_16h_rep3

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Institute

description:
[processed data files:]
counts_labeled_exons.txt
counts_labeled_introns.txt
counts_total_exons.txt
counts_total_introns.txt
rpkms_labeled_exons.txt
rpkms_labeled_introns.txt
rpkms_total_exons.txt
rpkms_total_introns.txt

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
Only reads unmapped to ribosomal genome (retrieved from the GenBank) were aligned on the mouse reference genome (NCBI 37, MM9) with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-inds --library-type fr-unstranded
Reads falling on exons and introns were quantified for each gene using the function “makeRPKMs” of the INSPEcT R/bioconductor package version 1.6.0
Transcript abundance was quantified through ‘Reads Per Kilobase exon model per Million mapped reads’ (RPKM)
total and pre-mRNA concentrations, and synthesis, processing and degradation rates, were modeled using the INSPEcT R/Bioconductor package version 1.6.0
Genome_build: mm9
Supplementary_files_format_and_content: text files with counts, rpkms, and INSPEcT modeling results. INSPEcT modeling results contains, for each gene, the p-value of model capability in explaining the data (chi-squared test), p-values of the differential regulation by the synthesis, processing and degradation rates (brown method of the log-likelihood ratio tests), and the gene class (0='constant', 'a'=differential synthesis, 'b'=differential degradation, 'c'=differential proceesing)

organism: Mus musculus

source_name: embryonic fibroblasts, E13.5

growth_protocol: 3T9MycER fibroblasts were cultured in DMEM medium, supplemented with 10% fetal bovine serum, 2 mM L-glutamine and penicillin/streptomycin. Cells were used at sub-confluent cell densities for all experiments. Due to infection with the pBabe bleomycin MycER construct, cells are resistant for zeocin. Upon thawing, cells were maintained for 7-10 days in zeocin-containing medium (100µg/ml), but grown without zeocin for subsequent experiments.

extract_protocol:
Total RNA from 3T9MycER fibroblasts was purified using miRNeasy Mini columns (Qiagen) according to the manufacturers protocol, including the on-column DNase I digestion step.
cDNA of 1µg was transcribed using the reverse transcriptase ImPromII (Promega) and random primers. For RNA-sequencing, 5µg total RNA (RNA integrity number ≥ 7.5) were treated with Ribozero rRNA removal kit (Epicentre) and purified on RNeasy MinElute columns (Qiagen).

treatment_protocol: MycER activation was achieved by addition of 400nM of the synthetic 4-hydroxytamoxifen (OHT; Sigma-Aldrich)

value: 3T9 fibroblasts

value: c-mycflox/flox; in vitro infected with MycER


title: CL0000_INPUT_MINUS_M32_REP_000

source_name: INPUT MINUS M30

value: -dox (wild-type)


title: CL0000_H3K9me3_MINUS_M32_REP_002

description:
CL0000_H3K9me3_MINUS_M32_REP_002
processed data file: H3K9me3_MINUS_M32.rpkm.bedgraph

source_name: H3K9me3 MINUS M30


title: RNA_total_8h_rep3


title: empty vector, off dox [P31_OFF]

value: withdrawn

value: off 1 passage from baseline (P30)


title: CL0000_H3K9me3_OFF_M70_REP_002

description:
CL0000_H3K9me3_OFF_M70_REP_002
processed data file: H3K9me3_OFF_M70.rpkm.bedgraph

source_name: H3K9me3 OFF M70


title: CL0000_H3K4me3_MINUS_M32_REP_002

description:
CL0000_H3K4me3_MINUS_M32_REP_002
processed data file: H3K4me3_MINUS_M32.rpkm.bedgraph

source_name: H3K4me3 MINUS M30


title: CL0000_H3K27me3_PLUS_M32_REP_002

description:
CL0000_H3K27me3_PLUS_M32_REP_002
processed data file: H3K27me3_PLUS_M32.rpkm.bedgraph

source_name: H3K27me3 PLUS M30


title: ChIP_Myc_10min

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
Reads were aligned to the reference mouse genome (NCBI37, mm9) using bwa software (version 0.6.2-r126) with standard parameters.
ChIP-seq narrow peaks were called against the input using MACS2 software (version 2.0.9, p-value threshold = 1e-5, --mfold=7,30). For RNAPII samples, MACS2 was also used to call broad peaks.
Genome_build: mm9
Supplementary_files_format_and_content: text files with peaks identified by the macs2 software. For each peak, genomic coordinates (chromosome, start, end, length, summit), number of tags falling within, and confidence scores (-10*log10(pvalue), fold_enrichment and FDR(%)) are reported

extract_protocol:
Cells were washed in PBS and fixed for 15 min in 1% of formaldehyde (Sigma) in PBS. Glycin was added (125 mM glycin) and cells were incubated for 5 min. Cells were washed with PBS and scraped in SDS buffer (100mM NaCl, 50mM Tris pH 8.1, 5mM EDTA, 0.2% NaN3, 0.5% (w/v) SDS). Cells were cleared by centrifugation and the pellet resuspended in cold ChIP buffer (100mM NaCl, 133mM Tris pH 8.0, 5 mM EDTA, 0.2% NaN3, 0.67% SDS, 1.67% Triton X-100) supplemented with protease inhibitors (cOmplete Protease Inhibitor Cocktail Tablets, Roche) and phosphatase inhibitors (50 mM NaF, 1 mM β-GP, 1 mM NaV). All following steps were performed on ice, if not specified differently. Chromatin was sonicated to an average length of 200-400bp, pre-cleared with proteinG-sepharose beads (blocked with 0.5% E. coli tRNA (Sigma) and 0.5% BSA).
10µg of the following antibodies were used per ChIPseq reaction: Myc N262 (Santa Cruz, sc-764), RNAPII N20 (Santa Cruz, sc-899). The antibody was incubated overnight with 500-1000µl of chromatin. Blocked proteinG-sepharose beads were added, incubated for 2-3h and washed as follows: 3x mixed micelle buffer (150 mM NaCl, 20 mM Tris pH 8.1, 5 mM EDTA, pH 8.0, 5.2% sucrose, 0.02% NaN3, 1% Triton X-100, 0.2% SDS), 2x buffer 500 (50 mM HEPES pH 7.5, 0.1% sodium deoxycholate, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.2% NaN3), 2x LiCl/detergent buffer (10 mM Tris pH 8.0, 0.5% sodium deoxycholate, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.2% NaN3) and once in TE. DNA:protein crosslinking was reverted overnight (2% SDS in TE, 65°C), DNA purified using QiaQuick columns (Qiagen) and quantified using PicoGreen (Invitrogen).
2-5 ng of ChIP DNA were used for ChIPseq library preparation as described in (Blecher-Gonen et al., Nat Protoc, 2013) and sequenced with the Illumina HiSeq sequencer according to the manufacturer.

value: Myc N262 (Santa Cruz, sc-764)


title: RNA_total_4h_rep3


title: CL0000_H3K4me3_PLUS_M32_REP_001

description:
CL0000_H3K4me3_PLUS_M32_REP_001
processed data file: H3K4me3_PLUS_M32.rpkm.bedgraph

source_name: H3K4me3 PLUS M30


title: CL0000_H3K36me3_OFF_M70_REP_002

description:
CL0000_H3K36me3_OFF_M70_REP_002
processed data file: H3K36me3_OFF_M70.rpkm.bedgraph

source_name: H3K36me3 OFF M70


title: RNA_total_2h_rep3


title: CL0000_H3K27me3_OFF_M70_REP_001

description:
CL0000_H3K27me3_OFF_M70_REP_001
processed data file: H3K27me3_OFF_M70.rpkm.bedgraph

source_name: H3K27me3 OFF M70


title: Sample_C6706-2

city: Göteborg

first: Sergiu

last: Netotea

address: Chalmersplatsen 4

country: Sweden

institute: Chalmers tekniska högskola AB

data_processing:
QC using FASTQC
Index the transcriptome using hg19 reference genome from iGenomes: tophat/2.0.12, bowtie2/2.2.3, samtools/0.1.19
Read alignment with tophat2 using hg19 as genome reference and as source for the transcriptome index: tophat/2.0.12, bowtie2/2.2.3, samtools/0.1.19
Transcript assembly with cufflinks: cufflinks/2.2.1
Merge transcripts with cuffmerge: cufflinks/2.2.1
Estimate counts with HTSEQ: htseq/0.6.1
Genome_build: HG19: ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
Supplementary_files_format_and_content: raw counts

source_name: colon carcinoma cells

growth_protocol: Human ileocecal colorectal adenocarcinoma (HCT8) cells were cultured in RPMI 1640 (GIBCO) medium, supplemented with 10% heat-inactivated fetal bovine serum and penicillin/streptomycin at 37°C in a humid 5% CO2 atmosphere.

extract_protocol:
RNA was extracted using the total RNA isolation kit according to the manufacturer’s protocol (RNeasy Mini Kit, Qiagen). Sequencing libraries were prepared from 1 μg total RNA using the TruSeq stranded mRNA library preparation kit (Illumina Inc) including poly-A selection.
Libraries were prepared according to Illimina's protocol (#15021047, rev E)
HiSeq2500 rapid mode,single read, 50 bp read length

treatment_protocol: Cells were seeded 16 h prior the infection, medium was changed and MVs or control (20mM Tris-HCl) were incubated with HCT8 cells for 5 hours.

tag: cell line

tag: treatment

value: treated with V. cholerae membrane vesicles


title: CL0000_H3K9me3_MINUS_M32_REP_001

description:
CL0000_H3K9me3_MINUS_M32_REP_001
processed data file: H3K9me3_MINUS_M32.rpkm.bedgraph


title: CL0000_H3K4me3_OFF_M70_REP_002

description:
CL0000_H3K4me3_OFF_M70_REP_002
processed data file: H3K4me3_OFF_M70.rpkm.bedgraph

source_name: H3K4me3 OFF M70


title: IDH1 R132H, off dox [M31_OFF]

value: IDH1 R132H (off)


title: CL0000_H3K4me3_OFF_M70_REP_001

description:
CL0000_H3K4me3_OFF_M70_REP_001
processed data file: H3K4me3_OFF_M70.rpkm.bedgraph


title: RNA_total_1_5h_rep3


title: RNA_total_1h_rep3


title: CL0000_H3K4me3_PLUS_M32_REP_002

description:
CL0000_H3K4me3_PLUS_M32_REP_002
processed data file: H3K4me3_PLUS_M32.rpkm.bedgraph


title: CL0000_H3K27me3_OFF_M70_REP_002

description:
CL0000_H3K27me3_OFF_M70_REP_002
processed data file: H3K27me3_OFF_M70.rpkm.bedgraph


title: CL0000_H3K4me3_MINUS_M32_REP_001

description:
CL0000_H3K4me3_MINUS_M32_REP_001
processed data file: H3K4me3_MINUS_M32.rpkm.bedgraph


title: CL0000_H3K9me3_PLUS_M32_REP_001

description:
CL0000_H3K9me3_PLUS_M32_REP_001
processed data file: H3K9me3_PLUS_M32.rpkm.bedgraph

source_name: H3K9me3 PLUS M30


title: RNA_total_30min_rep3


title: RNA_total_20min_rep3


title: CL0000_H3K9me3_PLUS_M32_REP_002

description:
CL0000_H3K9me3_PLUS_M32_REP_002
processed data file: H3K9me3_PLUS_M32.rpkm.bedgraph


title: CL0000_H3K36me3_MINUS_M32_REP_001

description:
CL0000_H3K36me3_MINUS_M32_REP_001
processed data file: H3K36me3_MINUS_M32.rpkm.bedgraph

source_name: H3K36me3 MINUS M30


title: RNA_total_10min_rep3

description:
[processed data files:]
counts_labeled_exons.txt
counts_labeled_introns.txt
counts_total_exons.txt
counts_total_introns.txt
rpkms_labeled_exons.txt
rpkms_labeled_introns.txt
rpkms_total_exons.txt
rpkms_total_introns.txt


title: CL0000_H3K36me3_MINUS_M32_REP_002

description:
CL0000_H3K36me3_MINUS_M32_REP_002
processed data file: H3K36me3_MINUS_M32.rpkm.bedgraph


title: CL0000_H3K36me3_PLUS_M32_REP_002

description:
CL0000_H3K36me3_PLUS_M32_REP_002
processed data file: H3K36me3_PLUS_M32.rpkm.bedgraph

source_name: H3K36me3 PLUS M30


title: CL0000_H3K36me3_PLUS_M32_REP_001

description:
CL0000_H3K36me3_PLUS_M32_REP_001
processed data file: H3K36me3_PLUS_M32.rpkm.bedgraph


title: RNA_labeled_12h_rep3

description:
labeled RNA
[processed data files:]
counts_labeled_exons.txt
counts_labeled_introns.txt
counts_total_exons.txt
counts_total_introns.txt
rpkms_labeled_exons.txt
rpkms_labeled_introns.txt
rpkms_total_exons.txt
rpkms_total_introns.txt

extract_protocol:
Total RNA from 3T9MycER fibroblasts was purified using miRNeasy Mini columns (Qiagen) according to the manufacturers protocol, including the on-column DNase I digestion step.
4sU-labeling and sequencing of 4sU-labeled RNA of 3T9 MycER fibroblasts was performed as described previously with minor modifications. MycER fibroblasts were treated with OHT for the time indicated in the treatment. Cells were labeled with 300µM of 4-thiouridine (4sU; Sigma T4509) for 10 min. Medium was removed, cells were put on ice, washed 3x with cold PBS. Cells were scraped in cold PBS and pelleted. RNA was extracted with the Qiagen miRNeasy kit according to the manufacturer including the recommended DNase I digest. 50µg of total RNA was used for the biotinylation reaction: RNA was diluted in 100µl of RNAse free water. 100µl of biotinylation buffer (2.5x stock; 25 mM Tris, pH 7.4, 2.5 mM EDTA) and 50µl of EZ-link Biotin-HPDP (1mg/ml in DMF; Pierce/Thermo Scientific 21341) were added and incubated for 2 hours at room temperature. RNA was precipitated and unbound Biotin-HPDP was removed by a combination of chloroform/isamylalcohol (24:1) precipitation with purification using MaXtract high density tubes from Qiagen. Biotinylated RNA was purified using Dynabeads MyOne Streptavidin T1 (Invitrogen). Before addition of RNA, 50µl of beads were washed 2x in washing buffer A (100 mM NaOH, 50 mM NaCl) and once in washing buffer B (100 mM NaCl). Beads were resuspended in 100µl of buffer C (2M NaCl, 10 mM Tris, pH 7.5, 1 mM EDTA, 0.1% Tween-20) to a final concentration of 5 μg/μl. RNA was added in an equal volume and rotated at room temperature for 15 min. Beads were washed 3x with washing buffer D (1M NaCl, 5 mM Tris, pH 7.5, 0.5 mM EDTA, 0.05% Tween-20). RNA was eluted from the beads in 100µl of 10mM EDTA in 95% formamide (65°C, 10 min). RNA was extracted with the RNeasy MinElute Spin columns from Qiagen according to the manufacturer and eluted in 14µl of RNase free water. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies). The 4sU-sequencing library was prepared with the Tru-Seq Illumina kit following the manufacturer’s instructions starting from RNA fragmentation.
cDNA of 1µg was transcribed using the reverse transcriptase ImPromII (Promega) and random primers. For RNA-sequencing, 5µg total RNA (RNA integrity number ≥ 7.5) were treated with Ribozero rRNA removal kit (Epicentre) and purified on RNeasy MinElute columns (Qiagen).
The 4sU-sequencing libraries were prepared with the TruSeq RNA Sample Prep Kits v2 (Illumina) following the manufacturer’s instructions starting from the RNA fragmentation step.

tag: 4su labeling time

value: 10 minutes


title: RNA_total_0min_rep3


title: CL0000_H3K36me3_OFF_M70_REP_001

description:
CL0000_H3K36me3_OFF_M70_REP_001
processed data file: H3K36me3_OFF_M70.rpkm.bedgraph


title: CL0312_H3K4me3_MUT_02_REP1_130

description:
CL0312_H3K4me3_MUT_02_REP1_130
processed data file: H3K4me3_MUT_02.rpkm.bedgraph

source_name: H3K4me3 MUT P2

value: IDH1 R132H


title: CL0000_H3K27me3_MINUS_M32_REP_002

description:
CL0000_H3K27me3_MINUS_M32_REP_002
processed data file: H3K27me3_MINUS_M32.rpkm.bedgraph

source_name: H3K27me3 MINUS M30


title: RNA_labeled_16h_rep3


title: RNA_labeled_8h_rep3


title: CL0000_H3K27me3_MINUS_M32_REP_001

description:
CL0000_H3K27me3_MINUS_M32_REP_001
processed data file: H3K27me3_MINUS_M32.rpkm.bedgraph


title: CL0225_H3K9me3_PAR_40_REP1_134

description:
CL0225_H3K9me3_PAR_40_REP1_134
processed data file: H3K9me3_PAR_40.rpkm.bedgraph

source_name: H3K9me3 PAR P40

value: parental


title: CL0625_H3K27me3_PAR_40_REP2_134

description:
CL0625_H3K27me3_PAR_40_REP2_134
processed data file: H3K27me3_PAR_40.rpkm.bedgraph

source_name: H3K27me3 PAR P40


title: CL0310_H3K4me3_PAR_02_REP1_128

description:
CL0310_H3K4me3_PAR_02_REP1_128
processed data file: H3K4me3_PAR_02.rpkm.bedgraph

source_name: H3K4me3 PAR P2


title: RNA_labeled_4h_rep3

source_name: embryonic fibroblasts, E13.5


title: CL0000_H3K27me3_PLUS_M32_REP_001

description:
CL0000_H3K27me3_PLUS_M32_REP_001
processed data file: H3K27me3_PLUS_M32.rpkm.bedgraph

value: +dox (IDH1 R132H)


title: CL0615_H3K27me3_MUT_10_REP1_133

description:
CL0615_H3K27me3_MUT_10_REP1_133
processed data file: H3K27me3_MUT_10.rpkm.bedgraph

source_name: H3K27me3 MUT P10

value: immortalized human astrocytes


title: CL0613_H3K27me3_PAR_10_REP1_131

description:
CL0613_H3K27me3_PAR_10_REP1_131
processed data file: H3K27me3_PAR_10.rpkm.bedgraph

source_name: H3K27me3 PAR P10


title: ChIP_RNAPII_10min

value: RNAPII N20 (Santa Cruz, sc-899)


title: ChIP_Myc_20min


title: RNA_labeled_2h_rep3


title: CL0624_H3K27me3_MUT_10_REP2_133

description:
CL0624_H3K27me3_MUT_10_REP2_133
processed data file: H3K27me3_MUT_10.rpkm.bedgraph


title: RNA_labeled_1_5h_rep3


title: CL0318_H3K4me3_MUT_40_REP1_136

description:
CL0318_H3K4me3_MUT_40_REP1_136
processed data file: H3K4me3_MUT_40.rpkm.bedgraph

source_name: H3K4me3 MUT P40


title: CL0313_H3K4me3_PAR_10_REP1_131

description:
CL0313_H3K4me3_PAR_10_REP1_131
processed data file: H3K4me3_PAR_10.rpkm.bedgraph

source_name: H3K4me3 PAR P10


title: CL0000_H3K9me3_OFF_M70_REP_001

description:
CL0000_H3K9me3_OFF_M70_REP_001
processed data file: H3K9me3_OFF_M70.rpkm.bedgraph

source_name: H3K9me3 OFF M70

value: off dox 40P (wild-type)


title: RNA_total_12h_rep3

description:
[processed data files:]
counts_labeled_exons.txt
counts_labeled_introns.txt
counts_total_exons.txt
counts_total_introns.txt
rpkms_labeled_exons.txt
rpkms_labeled_introns.txt
rpkms_total_exons.txt
rpkms_total_introns.txt


title: CL0222_H3K9me3_PAR_10_REP1_131

description:
CL0222_H3K9me3_PAR_10_REP1_131
processed data file: H3K9me3_PAR_10.rpkm.bedgraph

source_name: H3K9me3 PAR P10


title: CL0324_H3K4me3_MUT_10_REP2_133

description:
CL0324_H3K4me3_MUT_10_REP2_133
processed data file: H3K4me3_MUT_10.rpkm.bedgraph

source_name: H3K4me3 MUT P10


title: CL0236_H3K9me3_MUT_40_REP2_136

description:
CL0236_H3K9me3_MUT_40_REP2_136
processed data file: H3K9me3_MUT_40.rpkm.bedgraph

source_name: H3K9me3 MUT P40


title: CL0131_INPUT_PAR_10_REP1_NA

source_name: INPUT PAR P10

value: INPUT


title: CL0618_H3K27me3_MUT_40_REP1_136

description:
CL0618_H3K27me3_MUT_40_REP1_136
processed data file: H3K27me3_MUT_40.rpkm.bedgraph

source_name: H3K27me3 MUT P40


title: CL0627_H3K27me3_MUT_40_REP2_136

description:
CL0627_H3K27me3_MUT_40_REP2_136
processed data file: H3K27me3_MUT_40.rpkm.bedgraph


title: CL0234_H3K9me3_PAR_40_REP2_134

description:
CL0234_H3K9me3_PAR_40_REP2_134
processed data file: H3K9me3_PAR_40.rpkm.bedgraph


title: CL0616_H3K27me3_PAR_40_REP1_134

description:
CL0616_H3K27me3_PAR_40_REP1_134
processed data file: H3K27me3_PAR_40.rpkm.bedgraph


title: CL0610_H3K27me3_PAR_02_REP1_128

description:
CL0610_H3K27me3_PAR_02_REP1_128
processed data file: H3K27me3_PAR_02.rpkm.bedgraph

source_name: H3K27me3 PAR P2


title: CL0315_H3K4me3_MUT_10_REP1_133

description:
CL0315_H3K4me3_MUT_10_REP1_133
processed data file: H3K4me3_MUT_10.rpkm.bedgraph


title: RNA_total_12h_rep2


title: RNA_labeled_10min_rep3

description:
labeled RNA
[processed data files:]
counts_labeled_exons.txt
counts_labeled_introns.txt
counts_total_exons.txt
counts_total_introns.txt
rpkms_labeled_exons.txt
rpkms_labeled_introns.txt
rpkms_total_exons.txt
rpkms_total_introns.txt


title: RNA_labeled_0min_rep3


title: CL0221_H3K9me3_MUT_02_REP1_130

description:
CL0221_H3K9me3_MUT_02_REP1_130
processed data file: H3K9me3_MUT_02.rpkm.bedgraph

source_name: H3K9me3 MUT P2


title: RNA_labeled_1h_rep3


title: RNA_labeled_30min_rep3

tag: labeling time


title: RNA_labeled_20min_rep3


title: CL0322_H3K4me3_PAR_10_REP2_131

description:
CL0322_H3K4me3_PAR_10_REP2_131
processed data file: H3K4me3_PAR_10.rpkm.bedgraph


title: CL0136_INPUT_MUT_40_REP1_NA

source_name: INPUT MUT P40


title: CL0621_H3K27me3_MUT_02_REP2_130

description:
CL0621_H3K27me3_MUT_02_REP2_130
processed data file: H3K27me3_MUT_02.rpkm.bedgraph

source_name: H3K27me3 MUT P2


title: CL0224_H3K9me3_MUT_10_REP1_133

description:
CL0224_H3K9me3_MUT_10_REP1_133
processed data file: H3K9me3_MUT_10.rpkm.bedgraph

source_name: H3K9me3 MUT P10


title: RNA_total_4h_rep2


title: CL0612_H3K27me3_MUT_02_REP1_130

description:
CL0612_H3K27me3_MUT_02_REP1_130
processed data file: H3K27me3_MUT_02.rpkm.bedgraph


title: RNA_total_2h_rep2


title: CL0133_INPUT_MUT_10_REP1_NA

source_name: INPUT MUT P10


title: CL0219_H3K9me3_PAR_02_REP1_128

description:
CL0219_H3K9me3_PAR_02_REP1_128
processed data file: H3K9me3_PAR_02.rpkm.bedgraph

source_name: H3K9me3 PAR P2


title: RNA_total_1_5h_rep2

description:
[processed data files:]
counts_labeled_exons.txt
counts_labeled_introns.txt
counts_total_exons.txt
counts_total_introns.txt
rpkms_labeled_exons.txt
rpkms_labeled_introns.txt
rpkms_total_exons.txt
rpkms_total_introns.txt

source_name: embryonic fibroblasts, E13.5


title: CL0230_H3K9me3_MUT_02_REP2_130

description:
CL0230_H3K9me3_MUT_02_REP2_130
processed data file: H3K9me3_MUT_02.rpkm.bedgraph


title: RNA_total_1h_rep2


title: CL0622_H3K27me3_PAR_10_REP2_131

description:
CL0622_H3K27me3_PAR_10_REP2_131
processed data file: H3K27me3_PAR_10.rpkm.bedgraph

source_name: H3K27me3 PAR P10


title: RNA_total_16h_rep2


title: CL0231_H3K9me3_PAR_10_REP2_131

description:
CL0231_H3K9me3_PAR_10_REP2_131
processed data file: H3K9me3_PAR_10.rpkm.bedgraph


title: CL0227_H3K9me3_MUT_40_REP1_136

description:
CL0227_H3K9me3_MUT_40_REP1_136
processed data file: H3K9me3_MUT_40.rpkm.bedgraph


title: RNA_total_8h_rep2


title: CL0619_H3K27me3_PAR_02_REP2_128

description:
CL0619_H3K27me3_PAR_02_REP2_128
processed data file: H3K27me3_PAR_02.rpkm.bedgraph


title: CL0319_H3K4me3_PAR_02_REP2_128

description:
CL0319_H3K4me3_PAR_02_REP2_128
processed data file: H3K4me3_PAR_02.rpkm.bedgraph

source_name: H3K4me3 PAR P2


title: CL0316_H3K4me3_PAR_40_REP1_134

description:
CL0316_H3K4me3_PAR_40_REP1_134
processed data file: H3K4me3_PAR_40.rpkm.bedgraph

source_name: H3K4me3 PAR P40


title: CL0228_H3K9me3_PAR_02_REP2_128

description:
CL0228_H3K9me3_PAR_02_REP2_128
processed data file: H3K9me3_PAR_02.rpkm.bedgraph


title: CL0321_H3K4me3_MUT_02_REP2_130

description:
CL0321_H3K4me3_MUT_02_REP2_130
processed data file: H3K4me3_MUT_02.rpkm.bedgraph

source_name: H3K4me3 MUT P2


title: CL0128_INPUT_PAR_02_REP1_NA

source_name: INPUT PAR P2


title: CL0233_H3K9me3_MUT_10_REP2_133

description:
CL0233_H3K9me3_MUT_10_REP2_133
processed data file: H3K9me3_MUT_10.rpkm.bedgraph


title: TS0303_H3K4me3_TS_667_REP1_TS121

source_name: H3K4me3 TS667

value: glioma tumorsphere

value: wild-type


title: CL0130_INPUT_MUT_02_REP1_NA

source_name: INPUT MUT P2


title: RNA_total_0min_rep2

value: 3T9 fibroblasts

value: c-mycflox/flox; in vitro infected with MycER


title: RNA_labeled_16h_rep2

description:
labeled RNA
[processed data files:]
counts_labeled_exons.txt
counts_labeled_introns.txt
counts_total_exons.txt
counts_total_introns.txt
rpkms_labeled_exons.txt
rpkms_labeled_introns.txt
rpkms_total_exons.txt
rpkms_total_introns.txt


title: RNA_total_30min_rep2


title: RNA_total_20min_rep2


title: RNA_labeled_12h_rep2


title: CL0325_H3K4me3_PAR_40_REP2_134

description:
CL0325_H3K4me3_PAR_40_REP2_134
processed data file: H3K4me3_PAR_40.rpkm.bedgraph


title: RNA_total_10min_rep2


title: TS0301_H3K4me3_TS_543_REP1_TS119

source_name: H3K4me3 TS543


title: RNA_labeled_8h_rep2


title: TS0302_H3K4me3_TS_603_REP1_TS120

source_name: H3K4me3 TS603


title: TS0120_INPUT_TS_603_REP1_NA

source_name: INPUT TS603


title: TS0121_INPUT_TS_667_REP1_NA

source_name: INPUT TS667


title: CL0009_H3K36me3_MUT_40_REP1_127

description:
CL0009_H3K36me3_MUT_40_REP1_127
processed data file: H3K36me3_MUT_40.rpkm.bedgraph

source_name: H3K36me3 MUT P40


title: RNA_labeled_4h_rep2


title: CL0007_H3K36me3_PAR_40_REP1_125

description:
CL0007_H3K36me3_PAR_40_REP1_125
processed data file: H3K36me3_PAR_40.rpkm.bedgraph

source_name: H3K36me3 PAR P40


title: CL0609_H3K27me3_MUT_40_REP1_127

description:
CL0609_H3K27me3_MUT_40_REP1_127
processed data file: H3K27me3_MUT_40.rpkm.bedgraph

source_name: H3K27me3 MUT P40


title: CL0327_H3K4me3_MUT_40_REP2_136

description:
CL0327_H3K4me3_MUT_40_REP2_136
processed data file: H3K4me3_MUT_40.rpkm.bedgraph

source_name: H3K4me3 MUT P40


title: RNA_labeled_2h_rep2


title: RNA_labeled_1h_rep2


title: CL0607_H3K27me3_PAR_40_REP1_125

description:
CL0607_H3K27me3_PAR_40_REP1_125
processed data file: H3K27me3_PAR_40.rpkm.bedgraph

source_name: H3K27me3 PAR P40


title: RNA_labeled_1_5h_rep2

source_name: embryonic fibroblasts, E13.5


title: CL0603_H3K27me3_MUT_02_REP1_121

description:
CL0603_H3K27me3_MUT_02_REP1_121
processed data file: H3K27me3_MUT_02.rpkm.bedgraph

source_name: H3K27me3 MUT P2


title: CL0134_INPUT_PAR_40_REP1_NA

source_name: INPUT PAR P40


title: CL0606_H3K27me3_MUT_10_REP1_124

description:
CL0606_H3K27me3_MUT_10_REP1_124
processed data file: H3K27me3_MUT_10.rpkm.bedgraph

source_name: H3K27me3 MUT P10


title: RNA_labeled_30min_rep2


title: CL0601_H3K27me3_PAR_02_REP1_119

description:
CL0601_H3K27me3_PAR_02_REP1_119
processed data file: H3K27me3_PAR_02.rpkm.bedgraph

source_name: H3K27me3 PAR P2


title: CL0006_H3K36me3_MUT_10_REP1_124

description:
CL0006_H3K36me3_MUT_10_REP1_124
processed data file: H3K36me3_MUT_10.rpkm.bedgraph

source_name: H3K36me3 MUT P10


title: CL0004_H3K36me3_PAR_10_REP1_122

description:
CL0004_H3K36me3_PAR_10_REP1_122
processed data file: H3K36me3_PAR_10.rpkm.bedgraph

source_name: H3K36me3 PAR P10


title: CL0604_H3K27me3_PAR_10_REP1_122

description:
CL0604_H3K27me3_PAR_10_REP1_122
processed data file: H3K27me3_PAR_10.rpkm.bedgraph

source_name: H3K27me3 PAR P10


title: RNA_labeled_10min_rep2


title: CL0307_H3K4me3_PAR_40_REP1_125

description:
CL0307_H3K4me3_PAR_40_REP1_125
processed data file: H3K4me3_PAR_40.rpkm.bedgraph

source_name: H3K4me3 PAR P40


title: RNA_labeled_0min_rep2


title: RNA_labeled_20min_rep2


title: CL0306_H3K4me3_MUT_10_REP1_124

description:
CL0306_H3K4me3_MUT_10_REP1_124
processed data file: H3K4me3_MUT_10.rpkm.bedgraph

source_name: H3K4me3 MUT P10


title: CL0304_H3K4me3_PAR_10_REP1_122

description:
CL0304_H3K4me3_PAR_10_REP1_122
processed data file: H3K4me3_PAR_10.rpkm.bedgraph

source_name: H3K4me3 PAR P10


title: CL0303_H3K4me3_MUT_02_REP1_121

description:
CL0303_H3K4me3_MUT_02_REP1_121
processed data file: H3K4me3_MUT_02.rpkm.bedgraph

source_name: H3K4me3 MUT P2


title: CL0003_H3K36me3_MUT_02_REP1_121

description:
CL0003_H3K36me3_MUT_02_REP1_121
processed data file: H3K36me3_MUT_02.rpkm.bedgraph

source_name: H3K36me3 MUT P2


title: TS0119_INPUT_TS_543_REP1_NA

source_name: INPUT TS543


title: CL0301_H3K4me3_PAR_02_REP1_119

description:
CL0301_H3K4me3_PAR_02_REP1_119
processed data file: H3K4me3_PAR_02.rpkm.bedgraph

source_name: H3K4me3 PAR P2


title: RNA_total_12h_rep1

description:
[processed data files:]
counts_labeled_exons.txt
counts_labeled_introns.txt
counts_total_exons.txt
counts_total_introns.txt
rpkms_labeled_exons.txt
rpkms_labeled_introns.txt
rpkms_total_exons.txt
rpkms_total_introns.txt


title: CL0218_H3K9me3_MUT_40_REP2_127

description:
CL0218_H3K9me3_MUT_40_REP2_127
processed data file: H3K9me3_MUT_40.rpkm.bedgraph

source_name: H3K9me3 MUT P40


title: RNA_total_8h_rep1


title: CL0216_H3K9me3_PAR_40_REP2_125

description:
CL0216_H3K9me3_PAR_40_REP2_125
processed data file: H3K9me3_PAR_40.rpkm.bedgraph

source_name: H3K9me3 PAR P40


title: RNA_total_4h_rep1

source_name: embryonic fibroblasts, E13.5


title: RNA_total_16h_rep1


title: CL0215_H3K9me3_MUT_10_REP2_124

description:
CL0215_H3K9me3_MUT_10_REP2_124
processed data file: H3K9me3_MUT_10.rpkm.bedgraph

source_name: H3K9me3 MUT P10


title: RNA_total_2h_rep1


title: CL0213_H3K9me3_PAR_10_REP2_122

description:
CL0213_H3K9me3_PAR_10_REP2_122
processed data file: H3K9me3_PAR_10.rpkm.bedgraph

source_name: H3K9me3 PAR P10


title: CL0210_H3K9me3_PAR_02_REP2_119

description:
CL0210_H3K9me3_PAR_02_REP2_119
processed data file: H3K9me3_PAR_02.rpkm.bedgraph

source_name: H3K9me3 PAR P2


title: RNA_total_1_5h_rep1


title: RNA_total_1h_rep1


title: CL0309_H3K4me3_MUT_40_REP1_127

description:
CL0309_H3K4me3_MUT_40_REP1_127
processed data file: H3K4me3_MUT_40.rpkm.bedgraph

source_name: H3K4me3 MUT P40


title: CL0212_H3K9me3_MUT_02_REP2_121

description:
CL0212_H3K9me3_MUT_02_REP2_121
processed data file: H3K9me3_MUT_02.rpkm.bedgraph

source_name: H3K9me3 MUT P2


title: CL0209_H3K9me3_MUT_40_REP1_127

description:
CL0209_H3K9me3_MUT_40_REP1_127
processed data file: H3K9me3_MUT_40.rpkm.bedgraph


title: RNA_total_20min_rep1


title: RNA_total_30min_rep1


title: CL0207_H3K9me3_PAR_40_REP1_125

description:
CL0207_H3K9me3_PAR_40_REP1_125
processed data file: H3K9me3_PAR_40.rpkm.bedgraph


title: CL0204_H3K9me3_PAR_10_REP1_122

description:
CL0204_H3K9me3_PAR_10_REP1_122
processed data file: H3K9me3_PAR_10.rpkm.bedgraph


title: RNA_total_10min_rep1


title: CL0203_H3K9me3_MUT_02_REP1_121

description:
CL0203_H3K9me3_MUT_02_REP1_121
processed data file: H3K9me3_MUT_02.rpkm.bedgraph


title: 4121 NSTC

first: Briana

last: Prager

address: 9500 Euclid Ave.

data_processing:
fastq files were cleaned and processed using SOAP
Alignment was performed using Tophat
Transcripts were reconstructed and normalized using Cufflinks and Cuffcompare
Genome_build: USCS hg19
Supplementary_files_format_and_content: format is .txt, content is FPKM values processed using cufflinks

source_name: patient-derived GBM

growth_protocol: GSCs were grown in suspension as spheres in neurobasal complete media

extract_protocol:
total RNA was extracted with trizol using a Qiagen RNA extraction kit
Samples were rRNA and polyA-RNA depleted to emphasize lncRNA sequencing and libraries were prepared using standard illumina protocols

treatment_protocol: NSTCs were dervied from GSC lines grown in DMEM + 10% FBS

tag: tissue

value: glioblastoma

value: non-stem tumor cell


title: RNA_labeled_12h_rep1

description:
labeled RNA
[processed data files:]
counts_labeled_exons.txt
counts_labeled_introns.txt
counts_total_exons.txt
counts_total_introns.txt
rpkms_labeled_exons.txt
rpkms_labeled_introns.txt
rpkms_total_exons.txt
rpkms_total_introns.txt


title: RNA_labeled_16h_rep1


title: CL0206_H3K9me3_MUT_10_REP1_124

description:
CL0206_H3K9me3_MUT_10_REP1_124
processed data file: H3K9me3_MUT_10.rpkm.bedgraph


title: RNA_total_0min_rep1


title: 4121 GSC

value: glioblastoma stem cell


title: CL0018_H3K36me3_MUT_40_REP2_127

description:
CL0018_H3K36me3_MUT_40_REP2_127
processed data file: H3K36me3_MUT_40.rpkm.bedgraph

source_name: H3K36me3 MUT P40


title: CL0201_H3K9me3_PAR_02_REP1_119

description:
CL0201_H3K9me3_PAR_02_REP1_119
processed data file: H3K9me3_PAR_02.rpkm.bedgraph


title: 3691 NSTC


title: 3565 GSC


title: CL0016_H3K36me3_PAR_40_REP2_125

description:
CL0016_H3K36me3_PAR_40_REP2_125
processed data file: H3K36me3_PAR_40.rpkm.bedgraph

source_name: H3K36me3 PAR P40


title: CL0015_H3K36me3_MUT_10_REP2_124

description:
CL0015_H3K36me3_MUT_10_REP2_124
processed data file: H3K36me3_MUT_10.rpkm.bedgraph

source_name: H3K36me3 MUT P10


title: CL0013_H3K36me3_PAR_10_REP2_122

description:
CL0013_H3K36me3_PAR_10_REP2_122
processed data file: H3K36me3_PAR_10.rpkm.bedgraph

source_name: H3K36me3 PAR P10


title: 3565 NSTC


title: RNA_labeled_2h_rep1


title: 3691 GSC


title: RNA_labeled_4h_rep1


title: RNA_labeled_1_5h_rep1


title: RNA_labeled_1h_rep1


title: CUTLL ICN1 2 [lncRNA]

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

description:
genes_10495_rpkm.txt
lncRNA_12606.txt

data_processing:
Sequence reads were aligned to the hg19 genome using TopHat or Trinity
lncRNA expression levels were identified using Trinity
Genome_build: hg19
Supplementary_files_format_and_content: [lncRNA_12606.txt] lncRNA expression RPKM table processed with Trinity

source_name: CUTLL ICN1

growth_protocol: Human T-LL cell line CUTLL1 cells were maintained in RPMI1640 medium complement with 10% fetal bovine serum, 1X Penicillin-Streptomycin-Glutamine (PSG).

extract_protocol:
Total RNA was extracted with RNAeasy kit,
and after ribosomal RNA depletion, stranded RNA libraries were prepared following the instruction of Truseq library preparation guide (Illunima # 15031048). Quality control was assessed by BioA analysis (Agilent Technologies) prior to library construction and again prior to sequencing

treatment_protocol: Cells transduced with ICN1 and R1984A were maintained in the presence of gamma-secretase inhibitor GSI ((S)-2-[2-(3,5-difluorophenyl)-acetylamino]-N-((S)-5-methyl-6-oxo-6,7-dihydro-5H-dibenzo[b,d]azepin-7-yl)-propionamide, DBZ) at the concentration of 1µM.

value: T-ALL cell line containing a t(7;9) rearrangement and aberrant NOTCH1 activation


title: CUTLL R1984A 2 [lncRNA]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt

source_name: CUTLL R1984A


title: RNA_labeled_20min_rep1


title: CL0125_INPUT_PAR_40_REP1_NA

source_name: INPUT PAR P40


title: CL0121_INPUT_MUT_2_REP1_NA

source_name: INPUT MUT P2


title: CL0124_INPUT_MUT_10_REP1_NA

source_name: INPUT MUT P10


title: RNA_labeled_30min_rep1


title: RNA_labeled_0min_rep1


title: CL0122_INPUT_PAR_10_REP1_NA

source_name: INPUT PAR P10


title: CL0012_H3K36me3_MUT_02_REP2_121

description:
CL0012_H3K36me3_MUT_02_REP2_121
processed data file: H3K36me3_MUT_02.rpkm.bedgraph

source_name: H3K36me3 MUT P2


title: CUTLL DMSO 2 [lncRNA]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt

source_name: CUTLL DMSO

value: mig


title: CUTLL GSI 2 [lncRNA]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt

source_name: CUTLL GSI


title: CUTLL R1984A 1 [lncRNA]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt


title: RNA_labeled_8h_rep1

source_name: embryonic fibroblasts, E13.5

value: 10 minutes


title: IDH1 KI MPP

city: Toronto

first: Alan

last: Tseng

state: ON

address: 610 University Avenue

country: Canada

institute: The Campbell Family Cancer Research Institute

data_processing:
Fastq files were trimmed to read length 50 bases
Reads were aligned to mm10 reference genome using Bismark v0.10.0 with the following options: --directional -q -n 1 -k 2 --best --chunkmbs 512
SAM files were sorted and converted to BAM format using SAMtools v1.0
SAM files were sorted and used as input for methylKit R package v0.9.1
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing CpG methylation calls from methylKit v0.9.1

source_name: Bone marrow

extract_protocol:
As previously published in Gu et al. Nat Protoc. 2011 Apr;6(4):468-81 with slight modifications
Enhanced RRBS (eRRBS) was performed on 10 ng DNA purified from LT-HSC, ST-HSC, or MPP isolated from aged male Vav-IDH1-KI mice and control littermates (WT) (n=6/group) using a FACS Aria instrument (Beckton Dickenson). For ligation, methylated adapters from TruSeq Kit (Illumina) were diluted 1:4 and 1.5 μl were used in the reaction. After bisulfite conversion and before fragment selection, gels were cut between 150-400 bp for fragment size selection. Final libraries were purified using Agencourt AMpure XP magnetic beads (Beckman Coulter) according to the manufacturer’s protocol. Libraries were sequenced at the Princess Margaret Genomics Centre using a HiSeq2000 instrument. Five libraries per lane were multiplexed and 30% PhiX was added to increase library complexity.

value: Multipotent progenitor cells (Lin- Sca+ Kit+ CD150-)

tag: strain

value: IDH1+/lsl VavCre+

tag: age

value: 7-10 months


title: IDH1 KI ST-HSC

value: Short term hematopoietic stem cells (Lin- Sca+ Kit+ CD150+ CD48+)


title: CL0127_INPUT_MUT_40_REP1_NA

source_name: INPUT MUT P40

value: immortalized human astrocytes

value: IDH1 R132H


title: RNA_labeled_10min_rep1


title: CL0119_INPUT_PAR_2_REP1_NA

source_name: INPUT PAR P2

value: parental

value: INPUT


title: CL0118_H4K20me3_MUT_40_REP2_127

description:
CL0118_H4K20me3_MUT_40_REP2_127
processed data file: H4K20me3_MUT_40.rpkm.bedgraph

source_name: H4K20me3 MUT P40


title: CUTLL GSI 1 [lncRNA]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt


title: IDH1 KI LT-HSC

value: Long term hematopoietic stem cells (Lin- Sca+ Kit+ CD150+ CD48-)


title: CL0116_H4K20me3_PAR_40_REP2_125

description:
CL0116_H4K20me3_PAR_40_REP2_125
processed data file: H4K20me3_PAR_40.rpkm.bedgraph

source_name: H4K20me3 PAR P40


title: Control MPP

value: IDH1+/+ VavCre+


title: CUTLL DMSO 1 [lncRNA]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt


title: Control LT-HSC


title: CL0110_H4K20me3_PAR_02_REP2_119

description:
CL0110_H4K20me3_PAR_02_REP2_119
processed data file: H4K20me3_PAR_02.rpkm.bedgraph

source_name: H4K20me3 PAR P2


title: CL0115_H4K20me3_MUT_10_REP2_124

description:
CL0115_H4K20me3_MUT_10_REP2_124
processed data file: H4K20me3_MUT_10.rpkm.bedgraph

source_name: H4K20me3 MUT P10


title: CL0109_H4K20me3_MUT_40_REP1_127

description:
CL0109_H4K20me3_MUT_40_REP1_127
processed data file: H4K20me3_MUT_40.rpkm.bedgraph


title: CL0107_H4K20me3_PAR_40_REP1_125

description:
CL0107_H4K20me3_PAR_40_REP1_125
processed data file: H4K20me3_PAR_40.rpkm.bedgraph


title: CL0113_H4K20me3_PAR_10_REP2_122

description:
CL0113_H4K20me3_PAR_10_REP2_122
processed data file: H4K20me3_PAR_10.rpkm.bedgraph

source_name: H4K20me3 PAR P10


title: CUTLL ICN1 1 [genes]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt

data_processing:
Sequence reads were aligned to the hg19 genome using TopHat or Trinity
Coding gene expression levels were called using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: [genes_10495_rpkm.txt] gene expression RPKM table processed with Cufflinks

source_name: CUTLL ICN1


title: CUTLL R1984A 2 [genes]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt

source_name: CUTLL R1984A


title: CL0104_H4K20me3_PAR_10_REP1_122

description:
CL0104_H4K20me3_PAR_10_REP1_122
processed data file: H4K20me3_PAR_10.rpkm.bedgraph


title: CUTLL R1984A 1 [genes]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt


title: CL0106_H4K20me3_MUT_10_REP1_124

description:
CL0106_H4K20me3_MUT_10_REP1_124
processed data file: H4K20me3_MUT_10.rpkm.bedgraph


title: CUTLL ICN1 1 [lncRNA]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt


title: Control ST-HSC


title: CUTLL GSI 2 [genes]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt


title: CL0112_H4K20me3_MUT_02_REP2_121

description:
CL0112_H4K20me3_MUT_02_REP2_121
processed data file: H4K20me3_MUT_02.rpkm.bedgraph

source_name: H4K20me3 MUT P2


title: CUTLL DMSO 1 [genes]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt


title: CUTLL DMSO 2 [genes]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt


title: CL0103_H4K20me3_MUT_02_REP1_121

description:
CL0103_H4K20me3_MUT_02_REP1_121
processed data file: H4K20me3_MUT_02.rpkm.bedgraph


title: R1984A_H3K27ac

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie with default parameters.
BigWig traces were generated using MACS2 with default parameters.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: BigWig files containing genomic wiggle traces.

source_name: CUTLL1, R1984A, H3K27ac ChIP

extract_protocol:
Lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to New England BioLabs instructions accompanying the DNA Sample Prep Master Mix Set 1 (NEB E6040S).

value: T-cell lymphoma cell line

tag: notch

value: dimer-mutant


title: CUTLL GSI 1 [genes]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt


title: R1984A_input

source_name: CUTLL1, R1984A, input


title: CL0101_H4K20me3_PAR_02_REP1_119

description:
CL0101_H4K20me3_PAR_02_REP1_119
processed data file: H4K20me3_PAR_02.rpkm.bedgraph


title: ICN1_H3K27ac

source_name: CUTLL1, ICN1, H3K27ac ChIP

value: wild-type


title: CL0010_H3K36me3_PAR_02_REP2_119

description:
CL0010_H3K36me3_PAR_02_REP2_119
processed data file: H3K36me3_PAR_02.rpkm.bedgraph

source_name: H3K36me3 PAR P2


title: CL0001_H3K36me3_PAR_02_REP1_119

description:
CL0001_H3K36me3_PAR_02_REP1_119
processed data file: H3K36me3_PAR_02.rpkm.bedgraph


title: CUTLL ICN1 2 [genes]

description:
genes_10495_rpkm.txt
lncRNA_12606.txt


title: KO - ChIP Tcf1

city: Lausanne

first: Paolo

last: Angelino

address: Quartier Sorge, Bâtiment Génopode

department: BCF

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

data_processing:
Base calling- Illumina v1.82
Alignment to mm10/GRCm38 using Bowtie (version 2.1.0)
Peak Calling - MACS (version 1.4)
Peak annotation with R package ChIPpeakAnno (version 3.8.5)
Genome_build: GRCh37
Supplementary_files_format_and_content: List of peaks annotated with nearby Transcription Start Sites in a comma separated value text file

source_name: IL-2 activated Splenic NK cells, Tcf7-/-

growth_protocol: NK cells were cultured with IL-2 (500ng/mL) for five days.

extract_protocol:
DNA was purified using the MinElute PCR purification kit (Qiagen)
NEBNext Chip-Seq library Preparation from New England BioLabs
size selection to keep the inserts between 100bp and  400 bp

treatment_protocol: ChIP was performed according to the Upstate protocol, with slight modifications (see Materials and methods). Briefly, cross-linking was performed at 37°C for 10 min in 5 ml PBS with 1% formaldehyde, and quenched with 0.125 M glycine. Chromatin was incubated overnight either with a specific antibody or a control rabbit antibody, and immune complexes were precipitated. DNA was purified, amplified, and sequenced.

value: B6.129 Tcf7Tm1Cle

value: IL-2 activated NK cells

tag: antibody


title: KO - Input


title: KO - ChIP H3K4me3


title: DGM-12023-LA-BC

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: basal cells cultured from airway epithelium samples

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using the human reference genome build GRCh37/hg19, STAR (2.3.1z13_r470) for aligning reads, RefSeq gene definitions (2014-06-02) and Cufflinks (v2.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM).
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent STAR results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged STAR output to produce a file with FPKM values for each sample
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM text files include unique ID with gene ID and location, gene ID, transcript start site, location and the FPKM values for all samples

source_name: airway basal cells

growth_protocol: Pure populations of nonsmoker derived large airway basal cells (BC) were obtained and characterized using detailed protocols as previously described (PMID:1572528). Both primary and immortalized (BCi-NS1.1 cells) BC were maintained in Bronchial Epithelial Growth Media (BEGM, Lonza, Walkersville, MD) and passaged by seeding at a cell density of 3000 cells/cm2 in BEGM with fresh media changed every 2 days (PMID:24298994). RNA sequencing of primary (Passage 0) and immortalized BC was performed on cells once they had reached 70-80% confluence.

extract_protocol:
Total RNA from harvested nonsmoker basal cells was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA pu-rification kit to remove residual DNA
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIA-quick PCR purification kit (Qiagen, Valencia, CA)
Samples were loaded onto an Illumina flowcell for paired-end 125 x 2 sequencing reactions using the Illumina HiSeq 2500, using 4 samples multi-plexed per lane.

tag: individual

value: nonsmoker

value: primary BC


title: DGM-BCiNS1.1_P14

description: immortalized basal cell cultured from airway epithelium samples

source_name: airway basal cell line

value: immortalized (BCi-NS1.1 cells) BC


title: DGM-12251-LA-BC


title: DGM-BCiNS1.1_P20


title: E2F3a_SAL_4

first: Immanuel

last: Purushothaman

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Bowtie2 v.2.1.0 defaults
TopHat2 v.2.0.9 --no-novel-juncs --b2-very-sensitive
HTSeq v.0.6.0 -s no
Genome_build: mm10
Supplementary_files_format_and_content: TDF

molecule: polyA RNA

extract_protocol:
Mice were euthanized; brains were removed, coronally sliced and NAC tissues were rapidly dissected and frozen on dry ice. Tissue from 1 mouse was used for each sample for n=3-4 biological replicates for each brain region and phenotype. Total RNA was isolated with TriZol reagent (Invitrogen) and purified with RNAeasy micro kits from Qiagen.
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 protocol  with 300ng RNA (Illumina, San Diego, CA). Briefly, the cDNA was synthesized from poly-A-selected and then fragmented total RNA using random hexamers, followed by end-repair and ligation with   sequencing adaptors. The libraries were size selected and purified using AMPure XP beads (Beckman Coulter, Brea, CA). Barcode bases (6 bp) were introduced at one end of the adaptors during PCR amplification steps. Library size and concentration were measured by Bioanalyzer (Life Technologies, Grand Island, NY) before sequencing. Libraries were sequenced on the Illumina HiSeq 2500 System utilizing V4 chemistry with 125 base pair single-end reads by Beckman Coulter Genomics (now GeneWiz)

value: viral-mediated overexpression of E2F3a

tag: treated with

value: saline

value: brain

tag: brain region

value: Nucleus Accumbens


title: WT - ChIP Tcf1

source_name: IL-2 activated Splenic NK cells, Tcf7+/+

tag: cell type

tag: genotype


title: DGM-11956-LA-BC

tag: passage


title: E2F3a_SAL_5

tag: genotype/variation


title: Day 5 Undiff (D5ND)

city: Boston

first: Anaïs

last: Wanet

state: MA

address: 3 Blackfan circle

department: Hematology Oncology

institute: BIDMC

data_processing:
GenXPro provides the results of the digital gene expression analyses in tab-separated format (Wanet_annotated_raw_data.txt file). They used 50 bp reads of which 44 were made up the tag and 6 were used for the "TruQuant" PCR bias elimination. Sequencing platform was HiSeq 2500, Basecalling pipeline: HiSeq Control Software 2.0.12.0, RTA 1.17.21.3 and CASAVA 1.8.2.
Transcript per million normalization and tests for differential expression of mapped reads were performed in the statistical programming language R (www.rproject.org/) using the DEGexp function of the DEGseq package (Wang et al., 2010), after replacing the « 0 » counts by the arbitrary « 0.5 » value (Wanet_processed_data.txt file)
Genome_build: hg19
Supplementary_files_format_and_content: Wanet_annotated_raw_data.txt
Supplementary_files_format_and_content: Wanet_processed_data.txt contains transcript per million normalized (tpm) reads for each condition, as well as the log2 fold-change, p-value and q-value (calculated using the DEGexp function of the DEGseq package) for the comparisons D0 vs Exp, D3D vs Exp, D3D vs D0, D3D vs D3ND, D5D vs Exp, D5D vs D0, and D5D vs D5ND.

source_name: Bone marrow-derived mesenchymal stem cells, day 5 Undiff

growth_protocol: Cultures of human BM-MSCs were established as previously described (Najar et al., 2013) after informed consent from donors and the approbation of the local ethics committee of the Jules Bordet Institute (Belgium). BM-MSCs from healthy donors were expanded in Dulbecco's Modified Eagle Medium low glucose (DMEM-LG) supplemented with 1% penicillin-streptomycin mixture (Life Technologies, Carlsbad, CA, USA) and 10% fetal bovine serum (FBS, PAA/GE Healthcare, Piscataway, NJ, USA).

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit and Qiacube (Qiagen, Venlo, The Netherlands). For each condition, equal amounts of RNA isolated from 5 independent donor cell batches were pooled and submitted to MACE (GenXPro, Germany).
RNA libraries were prepared for sequencing using standard protocols for MACE (Massive analysis of cDNA ends) at GenXPro.

treatment_protocol: Prior to the hepatogenic induction, BM-MSCs were seeded on type-1 collagen (BD Biosciences, San Jose, CA) coated dishes and expanded till 95% confluency (« day 0 »). Hepatogenic induction was carried out by incubating BM-MSCs in Iscove's Modified Dulbecco's Medium (IMDM, Life Technologies) containing 1% penicillin-streptomycin mixture and supplemented with 20 ng/ml epidermal growth factor (EGF, PeproTech, Rocky Hill, NJ, USA) and 10 ng/ml basic-fibroblast growth factor (FGF-2, PeproTech) for 48 hours and then with 10 ng/ml FGF-2, 20 ng/ml hepatocyte growth factor (HGF, PeproTech), 0.61 mg/ml nicotinamide (Sigma-Aldrich, Saint-Louis, MO, USA) and insulin-transferrin-selenium (ITS) mixture 1X (Life Technologies) for 1 day ("Day 3 Diff") or 3 days ("Day 5 Diff"). Undifferentiated BM-MSCs were maintained in IMDM supplemented with 1% FBS and 1% penicillin-streptomycin mixture.

value: BM-MSC

tag: medium

value: IMDM + Pen/Strep + 1% FBS

tag: coating

value: Type 1 collagen-coated dishes

tag: confluency

tag: time

value: Day 5


title: WT- ChIP  H3K4me3


title: DGM-10500_M12-LA-BC


title: DGM-12535-LA-BC


title: E2F3a_SAL_2


title: GFP_SAL_5

value: viral-mediated overexpression of GFP


title: GFP_SAL_3


title: Day 5 Diff (D5D)

source_name: Bone marrow-derived mesenchymal stem cells, day 5 Diff

value: IMDM + Pen/Strep + differentiation cytokines


title: Day 3 Diff (D3D)

source_name: Bone marrow-derived mesenchymal stem cells, day 3 Diff

value: Day 3


title: ICN1_input

source_name: CUTLL1, ICN1, input

tag: cell line

value: T-cell lymphoma cell line

value: wild-type

tag: chip antibody


title: GFP_SAL_2

tag: strain

tag: tissue


title: Day 0 (D0)

source_name: Bone marrow-derived mesenchymal stem cells, day 0

value: DMEM + Pen/Strep + 10% FBS

value: Day 0


title: DGM-BCiNS1.1_P30

value: nonsmoker


title: GFP_SAL_1


title: Capsella rubellla Cr B x Cr A R2

city: Sentul

first: Marcelinus

middle: Rocky

last: Hatorangan

state: Jawa Barat

address: Cijayanti, Babakan Madang

department: Biotechnology

country: Indonesia

institute: PT SMART, Tbk.

data_processing:
excess index clean up: fastq-mcf -L 100 -l 25
additional adapter cleanup: trimmomatic PE ILLUMINACLIP:adapter.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
DNA sequencing reads were aligned to the C. rubella genome v1.0 (Phytozome) using Bowtie 1.0, -m 1 option, RNA sequencing were aligned using TopHat with -g 1 -N 2 --bowtie1 option
Genome SNP calling was done using Freebayes with -i -X -u --min-coverage 20 --min-alternate-total 10 -q 30 option
Nucleotide counting for RNA-seq was done by running a loop of igvtools.jar count -w 1
Allele spectrum ratio for imprinting analysis was done by using a custom R-script and is available by request, p-value for imprinting status was calculated using chi.test(). Parental genotype is represented using integer value of A = 1, T= 3, G = 9, C = 27. For example, genotype AT will be A(1) + T(3) = 4, and TC will be T(3) + C(27) = 30.
Genome_build: C. rubella genome v1.0 (Phytozome)
Supplementary_files_format_and_content: Aligned reads
---------------------------
RNA-Seq CSV files contain the following:
#LOCUS_NAME","#POS","#A_COUNT", "#C_COUNT ", "#G_COUNT ", " #T_COUNT ", " #N_COUNT "
#POS: position at the locus
#A_COUNT: Number of A bases found in particular locus
#C_COUNT: Number of C bases found in particular locus
#G_COUNT: Number of G bases found in particular locus
#T_COUNT: Number of T bases found in particular locus
#N_COUNT: Number of unknown bases found in particular locus

organism: Capsella rubella

source_name: Capsella rubella Cr75.2 x Cr48.21 endosperm

growth_protocol: All seeds were surface sterilized using 5 % Sodium Hypochloride solution under the fume hood. After sterilization seeds were plated on MS media containing 1% sucrose. After stratification for two days in the dark at 4°C seedlings were grown in a growth room under long-day photoperiod (16 hrs light and 8 hrs darkness) at 22°C light and 20°C darkness temperature and a light intensity of 110 µE. All seedlings were transferred to pots and plants were grown in a growth chamber at 60 % humidity and daily cycles of 16 hrs light at 21°C and 8hrs darkness at 18°C. ts were grown in a growth cabinet under long day photoperiods (16 h light and 8 h dark) at 22°C. After 10 days, seedlings were transferred to soil and plants were grown in a growth chamber at 60% humidity and daily cycles of 16 h light at 22°C and 8 h darkness at 18°C.

extract_protocol:
For DNA-seq, 300 mg young fresh leaves were used as DNA source. For RNA-seq, dissected endosperm of 300-500 seeds per replicate was used. Seeds were harvested at 6 DAP and stored at -20oC in RNAlater® (Sigma-Aldrich, St Louis, USA). RNA extraction was done using RNAqueous® Kit with Plant RNA Isolation Aid (Life Technologies, Carlsbad, USA).
The RNA-sequencing libraries were prepared using TruSeq® RNA Sample Preparation Kit v2 (Illumina, San Diego, USA) according to the manufacturer's instructions.
DNA-seq and RNA-seq

treatment_protocol: For all crosses, designated female partners were emasculated, and the pistils were hand-pollinated 2 days after emasculation.

value: 6 DAP seed endosperm


title: Capsella rubellla Cr B x Cr A R1


title: Capsella rubellla Cr A x Cr B R2

source_name: Capsella rubella Cr48.21 x Cr75.2 endosperm


title: E2F3a_SAL_1

value: viral-mediated overexpression of E2F3a


title: GFP_COC_5

value: cocaine


title: WT - Input

value: IL-2 activated NK cells


title: Capsella rubellla Cr A x Cr B R1


title: Capsella rubellla B (Cr B)

source_name: Capsella rubella Cr75.2 leaves

value: leaves


title: Expansion (Exp)

source_name: Bone marrow-derived mesenchymal stem cells, expansion (Exp)

value: BM-MSC

value: no

value: control


title: fie_4D_seedling_5mC

city: Lyon

first: Daniel

last: Bouyer

address: 46 Allée d'Italie

department: ENS-Lyon/RDP

country: France

institute: CNRS

description: bisulfite converted gDNA

data_processing:
Bisulfite-Seq reads were mapped to reference genomes (TAIR 10) using the Bowtie2 alignment algorithm allowing one mismatch and  only uniquely mapped reads were used for further analysis
Bisulfite-Seq Analysis methylated regions (MRs) were defined by tiling the genome into 100 base pair bins and comparing the number of called Cs and Ts with the reference genome. Bins with absolute methylation difference of 0.4, 0.2, 0.1 for CG, CHG, CHH, respectively, and Benjamini-Hochberg corrected FDR < 0.01 (Fisher’s exact test) were selected. To avoid 100 bp bins with few cytosines, we selected for bins with at least 4 cytosines that are each covered by at least 10 reads in each sample.MRs within 100 bp of each other were merged.
sRNA of 21-22nt and 24nt reads were selected before mapping against the reference genomes (Release 10) using the Bowtie alignment algorithm allowing one mismatch
Genome_build: Arabidopsis thaliana (TAIR10)
Supplementary_files_format_and_content: bedGraph = Chromosome, START- and STOP-position, level of methylation for MRs; gff with normalized density for small RNA-seq

organism: Arabidopsis thaliana

source_name: 4 day old seedlings

growth_protocol: Seeds of Arabidopsis thaliana accession Columbia-0 grown in soil under long day conditions (16h light/8h dark) at 23°C were hand-dissected to extract the embryo. Mutants of fie at the mature embryonic stage were identified by their enhanced dormancy; genotyping verified homozygousity for the T-DNA insertion. Wild type Col0 and fie seedlings were grown on 1/2 MS media plates and harvested at the earliest stage allowing distinctinction between wild type and mutant (4 days after germination).

extract_protocol:
DNA extraction was performed using standard CTAB/Phe-Chloroform purification. Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturers instructions and its quality was validated using RNA 6000 NanoChip (Agilent).
1 ug of total DNA was shipped to BGI-genomics, Shenzen, China where samples where further treated for quality control, bisulfite conversion, library preparation and squencing. 1ug of total RNA was sent to Fasteris SA, Plan-les-Ouates, Switzerland, performing sRNA extracting, library production and sequencing.

tag: background strain

value: fie

tag: developmental stage

value: 4 day old seedlings


title: Capsella rubellla A (Cr A)

source_name: Capsella rubella Cr48.21 leaves


title: Day 3 Undiff (D3ND)

source_name: Bone marrow-derived mesenchymal stem cells, day 3 Undiff

value: IMDM + Pen/Strep + 1% FBS

value: Type 1 collagen-coated dishes


title: 387_dakar

first: Zhe

last: Zhu

address: 9500 Euclid Avenue NE3-201

department: Stem cell biology

institute: Cleveland clinic foundation

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultipler written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCh38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text MS Excel format

source_name: GSCs

growth_protocol: GBM tissues were obtained from excess surgical materials from patients at the Cleveland Clinic after neuropathology review with appropriate consent, in accordance with an IRB-approved protocol (2559). To prevent culture-induced drift, patient-derived subcutaneous xenografts were generated and maintained as a recurrent source of tumor cells for study. Upon xenografts removal, a papain dissociation system (Worthington Biochemical) was used to dissociate tumors according to the manufacturer’s instructions. Cells were then cultured in Neurobasal medium (Life Technologies) supplemented with 1x B27 without vitamin A (ThermoFisher), L-glutamine (ThermoFisher), sodium pyruvate (ThermoFisher), 10 ng/ml basic fibroblast growth factor (bFGF), and 10 ng/ml epidermal growth factor (EGF) (R&D Systems).

extract_protocol:
Total cellular RNA was isolated using the RNeasy kit (Qiagen, Venlo, Netherlands) and reverse transcribed into cDNA using qScript cDNA SuperMix (Quanta Biosciences, Gaithersburg, MD). mRNA levels were measured using an ABI-7900 system (Applied Biosystems, Carlsbad, CA).
Ribo-Zero Gold

treatment_protocol: GSCs were treated with ZIKV-Brazil/Dakar strains for 48 hours at MOI-5

tag: gsc

tag: infection

value: ZIKV-Brazil/Dakar strains


title: WT_10D_seedling_sRNA

description: sRNA

source_name: young seedling

value: wildtype

value: 10 day old seedling


title: 4121_cont


title: WT_4D_seedling_5mC

description: bisulfite converted gDNA


title: GFP_COC_4

value: viral-mediated overexpression of GFP

tag: treated with

value: brain

tag: brain region

value: Nucleus Accumbens


title: 4121_dakar


title: GFP_COC_2


title: WT_mature_embryo_5mC

description: bisulfite converted gDNA

source_name: mature embryos

tag: genotype

value: mature embryo


title: LNCaP_Bag1L_CMut_DHT_AR_ChIP

first: Laura

last: Cato

address: 450 Brookline Ave., D728

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
ChIP-seq reads were aligned to the hg19 genome using Bowtie
Peaks were called using MACS 2.0
Genome_build: hg19
Supplementary_files_format_and_content: bed and bw

source_name: LNCaP Bag-1L CMut cells

growth_protocol: Routinely cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100 μg/ml), streptomycin (100 units/ml) and L-glutamine (2 mM), at 37 °C with an atmosphere of 5% CO2. For experimental conditions, cells were grown under hormone-starvation conditions for 72 h using the same media composition, but substituting FBS for charcoal/dextran-treated FBS (CDT).

extract_protocol:
Crosslinked cells were lysed using a Sarkosyl-containing lysis buffer. Chromatin was isolated, sheared and subjected to immunoprecipitation with an anti-AR antibody.
Libraries were prepared using 5 ng ChIP DNA and the ThruPLEX DNA-seq kit (Rubicon Genomics) according to the manufacturer's instructions.
ChIP-seq. Libraries were sequenced on an Illumina NS500 Single-End 75 bp platform.

treatment_protocol: Cells were grown under hormone-starvation conditions  for 72 h using the same media composition as described above. Cells were then treated with vehicle (ETOH) or 10 nM DHT for 4 h.

tag: treatment

value: 10 nM DHT (4 h)

tag: phenotype

value: Bag-1L CMut

value: AR N-20 antibody (Santa Cruz Biotechnology; sc-816;  lot # I0215)


title: fie_mature_embryo_5mC

description: bisulfite converted gDNA


title: LNCaP_Bag1L_CMut_DHT_Input


title: 34 anaerobic

city: Freising

first: Elena

last: Ferrari

address: Weihenstephaner Berg 3

department: ZIEL, Department of Microbiology

country: Germany

institute: Technische Universität München

description: 18°C_down; 18°C_up; 34°C_down; 34°C_up

data_processing:
The Illumina output files (fastq files) were mapped to the genome of L. weihenstephanensis (NCBI RefSec CP011102) using Bowtie for Illumina implemented in the open-source platform Galaxy, with the commonly used settings (2 maximum number of mismatches permitted, seed length 28 nt).
The number of reads mapping on each gene were visualized and calculated in Artemis (version 15.0.0), using the GenBank file of the L. weihenstephanensis genome as reference.
The Bioconductor package edgeR was used to analyze the differential gene expression of the counts of all the coding genes. All genes with less than 1 count per million (cpm) were filtered. Genes with a false discovery rate (FDR) < 0,3 and p-value < 0.05 were at the end selected.
Genome_build: L. weihenstephanensis WS 4560 (=DSM 24698) (NCBI RefSec CP011102)
Supplementary_files_format_and_content: Excel files include gene tag, logFC, logCPM, PValue, FDR, product description and the normalized reads to the smallest library (18°C anaerobic) based on the coding genes for each gene and each condition.
Supplementary_files_format_and_content: logFC, logCPM, Pvalue,FDR, raw data normalized, gene abbreviation and product for all the genes at 18°C and 34°C

organism: Paenilisteria weihenstephanensis

source_name: water plant Lemna trisulca

growth_protocol: L. weihenstephanensis WS 4560 (=DSM 24698) was growth at 18°C and 34°C aerobically and anaerobically in Brain-Heart Infusion (=BHI) media.

extract_protocol:
Cell were pelleted and RNA was isolated from a 50ml culture, usinging a modified TRI Reagent protocol and addition of double DNA digestion and mRNA enrichment by RNeasy kit (Qiagen). rRNAs were removed by MICROBExpress kit (Life Technologies). RNA was fragmented to ~150nt fragments, dephosphorilated and phosphorilated and Illumina TruSeq small RNA Sample Prep Kit was used with 100 ng of total RNA for the construction of sequencing stranded libraries.
RNA libraries were prepared for sequencing using the Illumina protocols

tag: growth oxygen condition

value: anaerobiosis

tag: growth temperature

tag: od600 for pellet preparation


title: 34 aerobic

description: 18°C_down; 18°C_up; 34°C_down; 34°C_up

value: L. weihenstephanensis WS 4560 (=DSM 24698)

value: aerobiosis


title: 18 aerobic

description: 18°C_down; 18°C_up; 34°C_down; 34°C_up


title: 18 anaerobic

description: 18°C_down; 18°C_up; 34°C_down; 34°C_up


title: LNCaP_Bag1L_CMut_ETOH_AR_ChIP

value: ETOH (4 h)


title: LNCaP_Bag1L_CMut_ETOH_Input


title: LNCaP_Bag1L_WT_DHT_AR_ChIP

source_name: LNCaP Bag1L WT cells

value: Bag-1L WT


title: LgSi

city: LEXINGTON

first: Nadia

middle: Antoine

last: Ayoub

address: 204 West Washington Street

department: Biology

institute: Washington and Lee University

description:
Lgeo_Transcriptome.mRNA.normFPKM.tsv
Lgeo_Transcriptome.mRNA.RSEMcnts.tsv

data_processing:
For barcoded libraries (all those generated with the TruSeq kit) the illumina pipeline CASAVA 1.8.2 was used to de-multiplex.
Barcodes and low quality sequences were removed using Trimmomatic v0.32. Matches to arthropod ribosomal reads were also identified and removed. Both clean-up steps were performed by implementing a perl script available at: https://github.com/arensburger/RNAseq-clean
Transcript abundance was estimated by aligning each library to the transcriptome of its species using BOWTIE, and accounting for the possibility that some reads might align to more than one transcript using RSEM v1.1.20. The estimated read counts generated by RSEM can be found in the *.RSEMcnts.tsv files.
RSEM v1.1.20 was also used to calculate FPKM (fragments aligned per thousand base pairs of transcript per million total alignmen reads).
Estimated read counts were input into edgeR for each species separately.  Normalization factors were computed for each library within edgeR using the trimmed mean of M (TMM) method, under the statistical comparison of all silk gland libraries to all non-silk gland (cephalothoraxes, ovaries, venom glands) libraries. RSEM's FPKM values were multiplied by the TMM normalization factors to generate the data in *.normFPKM.tsv files.
Genome_build: GBJM00000000: Latrodectus geometricus transcriptome shotgun assembly accession used for aligning L. geometricus libraries. The associated bioproject accession is PRJNA256924
Genome_build: GBJN00000000: Latrodectus hesperus transcriptome shotgun assembly accession used for aligning L. hesperus libraries. The associated bioproject accession is PRJNA242358
Genome_build: GBJQ00000000: Steatoda grossa transcriptome shotgun assembly accession used for aligning S. grossa libraries. The associated bioproject accession is PRJNA256926
Supplementary_files_format_and_content: *.RSEMcnts.tsv are tab-delimited text files containing the estimated read counts generated by RSEM for each RNA-seq library for each species. *.normRPKM.tsv are tabe-delimited text files for each species containing RSEM's FPKM normalized by multiplying by the library-specific normalization factors calculated with edgeR. Lgeo = L. geometricus; Lhes = L. hesperus; Sgro = S. grossa

organism: Latrodectus geometricus

source_name: all silk glands combined

extract_protocol:
mRNA Sequencing Sample Preparation Kit (Illumina, San Diego, CA)
Total RNA was isolated from each sample by homogenizing tissue in TRIzol (Invitrogen) followed by further purification with the RNEasy Mini Kit (Qiagen). Potentially contaminating DNA was removed with TURBO DNase (Ambion).
One of two library construction kits were used to prepare RNA-seq libraries. These are listed for each SAMPLE above in the "Description: Library construction protocol" column.

treatment_protocol: Adult spiders were caught in the wild (San Diego or Riverside Counties, California, USA) or purchased from SpiderPharm (Yarnell, AZ). Each spider was fed one cricket in the lab and dissections were performed 2-3 days later. Tissues were snap frozen in liquid nitrogen and stored at -80 degrees C until RNA extraction.

tag: developmental stage and sex

value: adult female

tag: number of individuals combined


title: 387_cont.

value: control


title: LgCeph2

source_name: cephalothorax


title: LgVen2

source_name: venom glands

extract_protocol:
TruSeq RNA Sample Preparation Kit (Illumina)
Total RNA was isolated from each sample by homogenizing tissue in TRIzol (Invitrogen) followed by further purification with the RNEasy Mini Kit (Qiagen). Potentially contaminating DNA was removed with TURBO DNase (Ambion).
One of two library construction kits were used to prepare RNA-seq libraries. These are listed for each SAMPLE above in the "Description: Library construction protocol" column.


title: 3565_cont


title: LNCaP_Bag1L_WT_ETOH_Input


title: 3565_dakar

value: ZIKV-Brazil/Dakar strains


title: LgTub1

source_name: tubuliform silk glands


title: LNCaP_Bag1L_WT_ETOH_AR_ChIP

tag: chip antibody


title: LgVen1


title: LhSi

description:
Lhes_Transcriptome.mRNA.normFPKM.tsv
Lhes_Transcriptome.mRNA.RSEMcnts.tsv

organism: Latrodectus hesperus


title: LhVen2


title: SgVen2

description:
Sgro_Transcriptome.mRNA.normFPKM.tsv
Sgro_Transcriptome.mRNA.RSEMcnts.tsv

organism: Steatoda grossa


title: LhVen1


title: LnCaP_Bag1L_KO_Bag1L_Rescue_DHT_4h_AR_Input

source_name: LnCaP Bag-1L KO cells plus Bag-1L

extract_protocol:
Crosslinked cells were lysed using a Sarkosyl-containing lysis buffer. Chromatin was isolated, sheared and subjected to immunoprecipitation with an anti-AR antibody.
Libraries were prepared using 5 ng ChIP DNA and the ThruPLEX DNA-seq kit (Rubicon Genomics) according to the manufacturer's instructions.

tag: sample type

value: LnCaP Bag-1L KO cells plus Bag-1L


title: LgTub2


title: LnCaP_Bag1L_KO_Bag1L_Rescue_DHT_4h_AR_ChIP

value: AR (N-20) antibody (Santa Cruz, Catalog# sc-816, Lot# I0215)


title: LhTub2


title: SgVen1


title: LnCaP_Bag1L_KO_Bag1L_Rescue_Veh_AR_ChIP


title: LnCaP_Bag1L_KO_Bag1L_Rescue_Veh_AR_Input


title: LgOv1

source_name: ovaries with eggs


title: LnCaP_Bag1L_KO_EmptyVector_DHT_4h_AR_ChIP

source_name: LnCaP Bag-1L KO cells plus vector

value: LnCaP Bag-1L KO cells plus vector


title: LgMinor2

source_name: minor ampullate silk glands


title: SgTub2


title: LhTub1


title: LhPy2

source_name: pyriform silk glands


title: LNCaP_Bag1L_WT_DHT_Input


title: SgTub1


title: LnCaP_Bag1L_KO_EmptyVector_DHT_4h_AR_Input


title: LgMinor1


title: LgOv2


title: SgPy1


title: LhPy1


title: LnCaP_Bag1L_KO_EmptyVector_Veh_AR_Input


title: LgMale1

source_name: whole male

value: adult male


title: LnCaP_Bag1L_KO_EmptyVector_Veh_AR_ChIP


title: LgMale2


title: LgMaj2

source_name: major ampullate silk glands


title: LnCaP_Bag1L_KO_DHT_4h_ChIP_Reps1and2

source_name: LnCaP Bag-1L KO cells

value: LnCaP Bag-1L KO cells


title: LhOv1


title: SgMinor2


title: LnCaP_Bag1L_KO_DHT_4h_Input_Reps1and2


title: LgMaj1


title: SgMinor1


title: LhMinor2


title: LhOv2


title: LgAgA2

source_name: anterior aggregate silk glands


title: LnCaP_Bag1L_KO_Veh_AR_ChIP_Reps1and2


title: SgMale2


title: LgAgA1


title: LnCaP_Bag1L_KO_Veh_AR_Input_Reps1and2


title: LhMale2


title: SgMale1


title: LhMale1


title: LnCaP_Talen_Ctl_DHT_4h_ChIP_Reps1and2

source_name: LnCaP control cells

value: LnCaP control cells


title: LgCeph1


title: SgOv2


title: SgMaj2


title: SgOv1


title: LhMaj2


title: LgAgP2

source_name: posterior aggregate silk glands


title: LhMaj1


title: LnCaP_Talen_Ctl_DHT_4h_Input_Reps1and2

value: 10 nM DHT (4 h)


title: SgMaj1


title: LhAgA2


title: SgCeph1


title: LnCaP_Talen_Ctl_Veh_AR_Input_Reps1and2


title: LgAc+F

source_name: aciniform and flagelliform silk glands


title: LhMinor1


title: LhAgA1


title: Tfcp2l1 shRNA

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

country: China

institute: Anhui University

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from BGI company. 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 of BGI.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: HES_Tfcp2l1 shRNA

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. BGISEQ-500 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: human embryonic stem cells

tag: infected with

value: Tfcp2l1 knockdown lentivirus


title: SgAgA1


title: SgAgP1


title: LhAgP2


title: Scramble

value: scramble


title: SgAc+F


title: LhCeph2


title: LhVen3


title: LgAgP1 2


title: SgSi

source_name: all silk glands combined


title: HES2 hESCs_PB

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads (FPKM) were calculated using a standard protocol from BGI company. 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 of BGI.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HES2 hESCs_PB

value: human embryonic stem cell (ESC)

tag: genotype/variation

value: expressing PB


title: LhAc+F


title: LhCeph1

source_name: cephalothorax


title: SgCeph2


title: LgAgP1


title: NL4-3_L_ZAP-L_CLIP

status: Public on Aug 22 2017

first: Matthew

middle: A

last: Takata

address: 1230 York Ave

institute: The Rockefeller Univeristy

description: CLIP reads aligned to viral genome (bar code to demultiplex: GATGC)

data_processing:
The FASTX toolkit was used to process the reads from libraries before mapping. Briefly, reads that contained ambiguous nucleotides, did not contain the 3′ adapter sequence or were shorter than 15nt were discarded. The remaining reads were then separated based on their 5’ barcode sequences and collapsed to generate a set of unique sequences.
Reads were then aligned to the human genome (hg19) or to the HIV-1 genome(NL4-3 and NDK), with up to 2 mismatches allowed using the Bowtie algorithm. In the case of reads that mapped to the human genome, locations were only reported for those with the minimum number of observed mismatches for each read (Bowtie criteria: -m 10 -v 2 --best --strata for mapping to hg19, and - m 1 -v 2 for mapping to the viral genomes).
In the case of reads that mapped to the human genome, locations were only reported for those with the minimum number of observed mismatches for each read (Bowtie criteria: -m 10 -v 2 --best --strata for mapping to hg19, and - m 1 -v 2 for mapping to the viral genomes).
BEDTools was used to convert the mapped reads to unique CLIP tags.
Genome_build: hg19, NL4-3 wt (GenBank: AF324493.2) , NL4-3 L (GenBank: PENDING; GenBank Submission ID:  2041501)
Supplementary_files_format_and_content: Excel files report CLIP Reads aligned to viral genome

organism: Human immunodeficiency virus 1

source_name: 293T stable expression

growth_protocol: HEK293T cells stably expressing ZAP-L with an C-terminal HA tag were grown in 15-cm dishes and infected with NL4-3 HIV

extract_protocol:
UV-crosslinked cells were lysed, ZAP-RNA complexes were immunoprecipitatd and RNA was extracted for library construction. Libraries were prepared with sequential ligation of the following primers: 3' adapter: 5'adenylated/TCG TAT GCC GTC TTC TGC TTG-3'dideoxyC / 5' adapters containing the barcodes are as follows: rGUU CAG AGU UCU ACA GUC CGA CGA UC AGUGC rGUU CAG AGU UCU ACA GUC CGA CGA UC GAUGC rGUU CAG AGU UCU ACA GUC CGA CGA UC GUGGC rGUU CAG AGU UCU ACA GUC CGA CGA UC ACGGC rGUU CAG AGU UCU ACA GUC CGA CGA UC UAGGC rGUU CAG AGU UCU ACA GUC CGA CGA UC AUCGC
Once the extracted RNA had the appropriate adaptors ligated, a gene specific primer was used to create and cDNA library. The DNA library was further amplified by PCR and purified on a TBE-Urea gel.

treatment_protocol: For PAR-CLIP, one day following infection and 14 hours before harvesting cell, 100μM 40thiouridine (4SU) was added to the cell culture medium

tag: strain

value: NL4-3 L (CG High)

tag: viral expression

value: infection

tag: host cell line

tag: clip antibody

value: mouse anti-HA (Biolegend, Cat#:901502, Lot#:B218907)


title: NL4-3_wt_ZAP-L_CLIP

description: CLIP reads aligned to viral genome (bar code to demultiplex: AGTGC)

tag: genotype

value: NL4-3 wt (wildtype)


title: ThermococcusAtm3

city: La Jolla

first: Priya

last: Narasingarao

address: 8750 Biological Grade

institute: Scripps Institution of Oceanography

data_processing:
BaseCalls were performed with MiSeqReporter 2.4
Illumina reads were aligned to the updated Thermococcus sp. strain 175 genome, using Bowtie with up to 2 mismatches per read alignment FPKM values were calculated using Cufflinks
Functional RNA transcripts were excluded from FPKM determination .
Genome_build: 2545824513 Taxon ID on Integrated Microbial Genomes database (IMG).
Supplementary_files_format_and_content: ThermococcusIsoforms_exp.diff.xls in microsoft excel format. Contains FPKM values comparison for control and test data

organism: Thermococcus

source_name: Archeal culture

growth_protocol: Cells were grown to in an anaerobic rich media with sulfur as electron acceptor, incubated at 80C at either atmospheric pressure (ThermococcusAtm1,2,3) or at High pressure 80 to 90 MPa (ThermococcusHP1,2,3). 45ml of triplicates cultures were grown until mid-exponential phase (10 hours) at atmospheric pressure in serum vials and at high pressure (80 to 90MPa) in 60 ml syringes placed inside titanium pressures equilibrated to 80ºC

extract_protocol:
Cultures were fixed with 1/10th volume of 95%ethanol+5% Trizol mixture and placed on ice immediately. Cultures were centrifuged at 6000g for 5 minutes to collect the cells and RNA extraction was performed immediately on the pellets using a total RNA extraction kit (Life Technologies). Cell pellets were suspended in 10 mM Tris buffer pH7.5 and using a hand held mortar, cell wall was mechanically disrupted, followed by lysozyme and proteinase K treatment. Column purification was done and DNAase digestion was performed in the column as per manufacturer‘s instructions (Life Technologies). The total RNA eluted from the column was aliquoted and stored at -80ºC.
Paired-end, strand-specific RNA-seq was performed using the dUTP method.. rRNA was removed with Epicentre's Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion's RNA Fragmentation Reagents. cDNA was generated using Invitrogen's SuperScript III First-Strand Synthesis protocol with random hexamer priming

value: Strain 175

tag: treatment

value: atmospheric pressure


title: Hi-C in sap1-1mutant R2

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

data_processing:
Hi-C data were mapped, and reads were filtered. Corrected contact probability matrices at 10kb resolution were obtained using iterative correction. Both steps were performed using the hiclib library for python, publicly available at https://bitbucket.org/mirnylab/hiclib.
Paired-end sequencing reads were mapped independently using Bowtie 2.1.0 to the S. pombe reference genome (ASM294v2). Mapping with iteratively increasing truncation length was used to maximize yield of valid Hi-C interactions.Only read pairs where both reads uniquely aligned to the genome were considered for subsequent steps. Read pairs corresponding to repeat instances of the same DNA molecule were removed. based upon their HindIII restriction fragment assignments and orientations, read pairs were classified as valid Hi-C products, non-ligation, or self-ligation products. The following fragment-level filters were then applied which remove read pairs: with one end adjacent to the restriction site, from restriction fragments with very high or low counts, from very large or small restriction fragments, and separated by very few restriction fragments.
These data is then binned at 10 kB resolution. The bins with lowest 3% coverage are discarded (in addition to bins with zero counts). Remove the diagonal and neighboring diagonal (i.e. interactions < 20kB). Remove the standalone bins. Removed potential biases in raw Hi-C contact maps by normalizing coverage using an iterative procedure. Interpolate the singleton bins using neighboring bins. Normalize the sum = 1 along each row and column.
Genome_build: ASM294v2

organism: Schizosaccharomyces pombe

source_name: log. growing cells

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were first grown at 26˚C and then shifted to 33˚C for 6 hours.

extract_protocol:
Crosslinked cells were lysed by grinding in a cold mortar and pestle. Cell lysate was treated with 0.1% SDS for 10 min at 65˚C, and then quenched with 1% TritonX-100. Cell lysate was digested overnight with 100 U HindIII at 37˚C. The 5' overhang from the HindIII digestion was filled in using Klenow fragment in presence of biotin-14-dCTP and dATP, dGTP, and dTTP at 37˚C for 45 min. The reaction was terminated with 1.5% SDS. The DNA fragments were ligated by T4 DNA ligase in diluted conditions that favor the ligation between cross-linked DNA fragments in 16˚C for 8 hours (Hi-C DNA). The Hi-C DNA was reverse cross-linked at 65˚C overnight in the presence of proteinase K and purified by phenol/chrolorom extraction. Purified Hi-C DNA was treated with 1 mg/ml Rnase A for 30 min at 37˚C. Un-ligated biotin lablelled DNA was selectively removed by T4 DNA plymerase and reaction were purified by phenol/chloroform extraction.
Hi-C DNA was sheared by Covaris in the size range of <500 bp. The sheared Hi-C DNA was subjected to end-repair and 3' end adenylation. Hi-C DNA between 150 - 300 bp was selected with AMPure XP (Beckman-Coulter). The biotin-labled Hi-C DNA was selectively captured by Dynabeads Myone Streptavidin C1 (Invitrogen) and used for Illumina PE adapter ligation. Streptavidin beads containing bounds Hi-C DNA were used for the template for library amplification by PE-PCR primers (Illumina).

treatment_protocol: Cells (OD600 ~0.5) were fixed in 3% formaldehyde (Sigma) for 20 min at 26°C, and quenched with glycine for 5 min at 26°C.


title: ThermococcusAtm1


title: ThermococcusHP3

value: high pressure


title: ThermococcusHP2


title: ThermococcusHP1


title: ThermococcusAtm2


title: Hi-C in sap1-1mutant R1


title: HES2 hESCs_PB-Tfcp2l1deltaCP2

source_name: HES2 hESCs_PB-Tfcp2l1ΔCP2

value: expressing PB-Tfcp2l1{delta}CP2


title: control 3

city: Copenhagen

first: Rasmus

last: Hartmann-Petersen

address: Ole Maaloes Vej 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

data_processing:
BGI basecalling
Trimmomatic v0.32 (PE) used for adapter trimming with parameters: ILLUMINACLIP:./TruSeq3-PE-2.fa:2:30:10:8:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:0
Reads were aligned to the pombe genome with STAR v.2.3.0e with standard parameters except: MismatchNoverLmax=0.1, MismatchNmax=3, MatchNmin=18
Gene annotations in gtf format was downloaded from PomBase version 38 from October 2013
Gene count.txts based on the PomBase annotation were obtained from each STAR alignment file using htseq-count.txt with mode=union.
Genome_build: pombe.ASM294v2.21
Supplementary_files_format_and_content: Tab-delimited text files of raw ht-seq count.txt output

source_name: wild type, vector

growth_protocol: Growth at 29 C in EMM2 media.

extract_protocol:
Hot phenol total RNA extraction
Library construction protocol not provided.

value: wild type


title: control 5


title: bag101 overexpression 1

source_name: wild type, overexp. bag101

value: bag101 overexpression


title: control 2


title: bag101 overexpression 2


title: control 4


title: bag101 overexpression 3


title: bag101 overexpression 4


title: NoEndo_72hpf_E1

city: New Haven

first: Stefania

last: Nicoli

state: CT

address: 300 George street

department: Internal Medicine

institute: Yale University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Zv9 whole genome using STAR v2.3.0
Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM) were calculated using Cufflink software ( Annotation gtf for Zv9)
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Danio rerio

source_name: Endothelial cell

growth_protocol: Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee (# 2015-11473).

extract_protocol:
Transgenic fish were treated with Liberase to disociate the cells. After FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

tag: tissue

value: Endothelial

tag: stain

value: GFP


title: NoEndo_6dpf_E1


title: NoEndo_24hpf_E1


title: Endo_72hpf_E2


title: Endo_72hpf_E1


title: Endo_6dpf_E1


title: bag101 overexpression 5


title: Endo_48hpf_E2


title: 24hpf_E1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Zv9 whole genome using STAR v2.3.0
Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM) were calculated using Cufflink software ( Annotation gtf for Zv9)
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

extract_protocol:
Transgenic fish were treated with Liberase to dissociate the cells. After FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 24 hpf


title: HLF_L21 IL5IgG#2

city: Madison

first: Yury

last: Bochkov

state: WI

address: 600 Highland Ave, K4/945 CSC

department: Pediatrics

institute: University Of Wisconsin-Madison

data_processing:
RNA-seq (1x100 bases; 25 million reads per sample) was carried out using Illumina HiSeq 2500 platform.
SeqMan Ngen (v.13) and ArrayStar with Qseq module (v.13) software packages (DNAStar, Madison, WI) were used to map sequence reads to human reference genome (GRCh38) and perform gene expression analysis.
Genome_build: Human reference genome, version GRCh38
Supplementary_files_format_and_content: Normalized log2 transformed RPKM (Reads Per Kilobase per Million mapped reads) values are presented in the processed data file

source_name: Fibroblast (HLF)_L21 IL5IgG#2

growth_protocol: HLF were grown in maintenance media composed of DMEM/10% FBS, 2 mM L-glutamine, 100 units/ml streptomycin, 250 ng/ml amphotericin B, 100 units/ml penicillin, and 10 µg/ml ciprofloxacin.

extract_protocol:
Total RNA was extracted from HLF using the RNeasy Mini Kit (Qiagen, Valencia, CA) and treated with DNase (RNase-free DNase kit, Qiagen). RNA samples were submitted to the University of Wisconsin-Madison Biotechnology Center (Madison, WI) for RNA quality and integrity evaluation via Agilent 2100 Bioanalyzer platform (Agilent Technologies)
The sequencing library from mRNA was prepared using TruSeq Stranded mRNA Library Preparation Kit (Illumina; San Diego, CA, USA)

treatment_protocol:
1) Preparation of eosinophil conditioned media: Peripheral blood eosinophils were cultured at 1 million cells/ml in medium (RPMI 1640 plus 10% fetal bovine serum (FBS)) with IL-3 (2 ng/ml) or IL-5 (4 ng/ml) for 20h. After 20 h stimulation with cytokines, eosinophils were washed and suspended at 1 million cells/ml in fresh medium (no cytokine), and 1 ml was added to a 24-well plate, which had been coated overnight with Heat-aggregated (HA-IgG; 10µg/ml; 350µl/well) and saturated with 0.1 % gelatin for 30 min at 37°C.  Heat aggregation of human IgG (HA-IgG) was performed in PBS for 30 min at 63°C . After a 6 h incubation, the 3 type of supernatant fluids (conditioned media) were harvested and stored at -80°C before their use to activate fibroblasts (HLF).
2) Activation of HLF: HLF were treated for 24 h in 1:1 dilution of maintenance media (DMEM (no FBS), 2 mM L-glutamine, and antibiotics ) and eosinophil-conditioned media. The 2 types of eosinophil-conditioned media described above (IL-3 on HA-IgG (IL3IgG) and IL-5 on HA-IgG (IL5IgG)) were obtained from 2 different blood donors. Controls included HLF cultured in medium only (RPMI with 5% FBS) and HLF cultured with 1 ng/ml plus 0.5 µg/ml of HA-IgG (rhIL3IgG). This latter control was used to account for potential release of intracellular IL-3 during IL-3-activated eosinophil degranulation, and any release of coated HA-IgG during the 6 h degranulation period. HLF were harvest with RLT extraction buffer from Qiagen for total RNA extraction.

value: Lung-derived fibroblasts

tag: passages

tag: phenotype

value: non-fibrotic

value: IL5IgG from blood donor #2


title: 6dpf_E1

value: 6 dpf


title: Endo_48hpf_E1


title: Endo_24hpf_E1


title: 48hpf_E1

value: 48 hpf


title: control 1


title: NoEndo_72hpf_E2


title: HLF_L21 IL5IgG#1

source_name: Fibroblast (HLF)_L21 IL5IgG#1

value: IL5IgG from blood donor #1


title: HLF_L21 IL3IgG#2

source_name: Fibroblast (HLF)_L21 IL3IgG#2

value: IL3IgG from blood donor #2


title: HLF_L21 IL3IgG#1

source_name: Fibroblast (HLF)_L21 IL3IgG#1

value: IL3IgG from blood donor #1


title: HLF_L20 rhIL3IgG

source_name: Fibroblast (HLF)_L20 rhIL3IgG


title: HLF_L20 IL3IgG#2

source_name: Fibroblast (HLF)_L20 IL3IgG#2


title: HLF_L21 medium

source_name: Fibroblast (HLF)_L21 medium

value: medium


title: HLF_L21 rhIL3IgG

source_name: Fibroblast (HLF)_L21 rhIL3IgG


title: NoEndo_48hpf_E2


title: NoEndo_48hpf_E1


title: HLF_L20 IL5IgG#1

source_name: Fibroblast (HLF)_L20 IL5IgG#1


title: HLF_L20 IL5IgG#2

source_name: Fibroblast (HLF)_L20 IL5IgG#2


title: HLF_L20 medium

source_name: Fibroblast (HLF)_L20 medium


title: HLF_L20 IL3IgG#1

source_name: Fibroblast (HLF)_L20 IL3IgG#1


title: 40911432 input

city: Singapore

first: Xiaosai

last: Yao

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Sequencing reads were trimmed (10bp from front and back) and mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm. Only reads with mapQ >10 and with duplicates removed by rmdup were used in the subsequent analysis.
Significant peaks were called using MACS2 (q-value < 0.01).
Genome_build: hg19
Supplementary_files_format_and_content: bed format for ucsc genome browser, including 5 columns: "chromosome"  "start of region" "end of region" "peak name" "peak enrichment"

source_name: ccRCC cell line

growth_protocol: 786-O cells were grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Gibco). Cells were maintained in a 5% CO2-humidified incubator at 37°C.

extract_protocol:
For each transcription factor, ~3x107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Chromatin was extracted and sonicated to ~500bp (Vibra cell, SONICS). The total volume of immunoprecipitation was 1.5 ml and the amount of antibody used was 15 µg. The input DNA was precleared with protein G Dynabeads (LifeTechnologies) for 2 hr at 4°C and then incubated with antibodies conjugated protein G beads overnight at 4°C. The beads were washed 6 times with wash buffer at room temperature.
Amplified DNA was used with NEBNext ChIP-Seq library prep reagent set (NEB)

tag: transcription factor

value: Input

tag: chip antibody

tag: source

value: patient tumor derived cell line


title: 40911432 HIF2A ChIP-seq

value: HIF2A (NB100-122, Novus Bio, lot# BY-6)


title: 786-O HIF2A siRNA control input

data_processing:
Sequencing reads were trimmed (10bp from front and back) and mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm. Only reads with mapQ >10 and with duplicate removed by rmdup were used in the subsequent analysis
H3K27ac and H3K4me1 ChIP-seq were called with CCAT whereas H3K27me3 ChIP-seq were called with MACS2
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq peaks are in bed format, including 5 columns: "chromosome"  "start of region" "end of region" "peak name" "peak enrichment"

extract_protocol:
One million cells were fixed in 1% formaldehyde/PBS buffer for 10 min at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Cells were washed 3 times with TBSE buffer.  Pelleted cells were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode). Sonicated DNA was normalized for each pair of cells with and without wildtype VHL before immuno-precipitation. The total volume of immunoprecipitation was 1 ml and the amount of antibody used was 2 µg. The input DNA was precleared with protein G Dynabeads (Life Technologies) for 1 hr at 4°C and then incubated with antibodies conjugated protein G beads overnight at 4°C. The beads were washed 3 times with cold wash buffer.
Whole-genome-amplification was performed on ChIP DNA and input using the WGA4 kit (Sigma-Aldrich).  The amplified DNA was used with NEBNext ChIP-Seq library prep reagent set.

treatment_protocol: 786-O cells stably expressing RC3 empty vector (VHL-) or wildtype VHL (VHL+) were kindly provided by Dr. Michael Ohh (University of Toronto). Whole-genome H3K27ac ChIP-seq was performed on these two isogenic cell lines.

tag: histone

value: HIF2A siRNA (Dharmacon L-004814-00)


title: 72hpf_E1

value: 72 hpf


title: 40911432 HIF1A ChIP-seq


title: 786-O HIF2A siRNA H3K27ac ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: 786-O non-targeting control input

value: Non-targeting control (Dharmacon, D-001810-01)


title: LnCaP_Talen_Ctl_Veh_AR_ChIP_Reps1and2

source_name: LnCaP control cells

tag: sample type

value: LnCaP control cells

value: ETOH (4 h)

value: AR (N-20) antibody (Santa Cruz, Catalog# sc-816, Lot# I0215)


title: 786-O non-targeting control H3K27ac ChIP-seq


title: 40911432 empty vector input rep2

value: Patient derived ccRCC cell line


title: 40911432 empty vector H3K27ac ChIP-seq rep2


title: 40911432 empty vector input rep1


title: 40911432 wt VHL H3K27ac ChIP-seq rep2


title: 40911432 empty vector H3K27ac ChIP-seq rep1


title: 40911432 wt VHL input rep1


title: 12364284 wt VHL input rep2


title: 12364284 wt VHL input rep1


title: 12364284 empty vector input rep2


title: 12364284 wt VHL H3K4me1 ChIP-seq rep2

value: H3K4me1 (ab8895, Abcam)


title: 12364284 empty vector H3K27ac ChIP-seq rep2


title: 12364284 empty vector H3K4me1 ChIP-seq rep2


title: 12364284 wt VHL H3K27ac ChIP-seq rep2


title: 12364284 wt VHL H3K27me3 ChIP-seq rep1

value: H3K27me3 (07-449, Millipore)


title: 12364284 wt VHL H3K27ac ChIP-seq rep1


title: 12364284 wt VHL H3K27me3 ChIP-seq rep2


title: 12364284 empty vector input rep1


title: 12364284 wt VHL H3K4me1 ChIP-seq rep1


title: 12364284 empty vector H3K27me3 ChIP-seq rep1