title: Multiple Saline challenge

description: Sample 5

tag: genotype

value: multiple Saline challenge

value: control

value: Control


title: Multiple 8-oxoG challenge - 30 min

status: Public on Jul 03 2015

type: SRA

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

country: USA

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

description: Sample 6

library_source: transcriptomic

data_processing:
Base call conversion to sequence reads was done with Casava-1.8.2 software (Illumina).
Sequence data were analyzed with the Bowtie 2
Splice junction mapping was performed with TopHat
Assembly and estimation of abundance was perforemed with GFOLD
Genome_build: mm10
Supplementary_files_format_and_content: Sample*RPKM.txt tab-delimited text file includes RPKM values for the Sample.

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (Qiagen) followed by DNase I treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Balb/cJ

tag: tissue

value: Lung

tag: age

tag: gender

value: female

value: wild type

tag: treatment

value: multiple 8-oxoG challenge

tag: time

value: 30 min

tag: type of sample

value: Test


title: FLT3_ITD2_lane2_DNAse-Seq

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

description: H17606_sorted_from_ordered_tag_gff_bin1_bin10.wig

library_source: genomic

data_processing:
Base-calling (Illumina)
DNAse-seq reads were aligned to the hg18 genome assembly using Bowtie 1.00 to SAM output using --all --best --strata --v 2 -m 1 -S
Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. Nat Struct Mol Biol 2011.
Fixed-step 10bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. Nat Struct Mol Biol 2011
Peaks were called using CoCAS (Benoukraf et al. Bioinformatics 2009)
Genome_build: hg18
Supplementary_files_format_and_content: Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. Nat Struct Mol Biol 2011. Fixed-step 10bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. Nat Struct Mol Biol 2011. Peaks were called using CoCAS (Benoukraf et al. Bioinformatics 2009)

molecule: genomic DNA

organism: Homo sapiens

source_name: FLT3-ITD AML patient sample

growth_protocol: Patient and donor samples were obtained either from blood or bone marrow. Lymphoprep extraction of leukocytes was performed following 30 min no brake centrifugation. Enrichment for CD34 and CD117 were checked via FACS analysis. For CD14 samples, enricment for CD14 was controlled by FACS analysis. Where available, purification was performed using MACS columns following anti-CD34 bead conjugation to samples (anti-CD14 for CD14 samles).

extract_protocol:
Phenol-chloroform
Libraries of DNA fragments from chromatin immunoprecipitation or DNase I treatment were prepared from approximately 10 ng of DNA. Firstly, overhangs were repaired by treatment of sample material with T4 DNA polymerase, T4 PNK and Klenow DNA polymerase (all enzymes obtained from New England Biolabs UK) in a reaction also containing 50 mM Tris-HCl,10 mM MgCl2, 10 mM Dithiothreitol, 0.4 mM dNTPs and 1 mM ATP. Samples were purified after each step using Qiagen MinElute columns (according to the manufacturer’s guidelines). Adenosine bases were added to 3’ ends of fragments using Klenow Fragment (3´- 5´ exo-minus), allowing for subsequent ligation of adapter oligonucleotides (Illumina part #1000521) using Quick T4 DNA ligase. After a further column clean up to remove excess adaptors, fragments were amplified in an 18 cycle PCR reaction using adapter-specific primers (sequences 5’- CAAGCAGAAGACGGCATACGAGCTCTTCCGATC*T and 5’-AATGATACGGCGACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T).  The libraries were purified and adapter dimers removed by running PCR products on 2% agarose gels and excising gel slices corresponding to fragments approximately 200-300 bp in size, which were then extracted using the Qiagen gel extraction kit. Libraries were validated using quantitative PCR for known targets, and quality assessed by running 1 μl each sample on an Agilent Technologies 2100 Bioanalyser. Once prepared, DNA libraries were subject to massively parallel DNA sequencing on an Illumina Genome Analyzer. ETO, RUNX1, C/EBPα, PU.1, LMO2 ChIP and Kasumi-1 DNase I libraries were sequenced employing the Illumina Genome Analyzer GAIIx, by using 36 base pair single end reads.

treatment_protocol: To perform DNaseI accessibility assays with patient and donor samples, the optimal cell number and DNaseI (DPFF DNaseI, Worthington Biochemical Corporation) concentration was titrated for each sample. The DNA digestion extent was comparable in all the generated samples as measured by RT-PCR (5). Briefly, nuclei were isolated from 1-5 x 106 cells by detergent lysis and immediately digested for 3 min at 22 °C with DNaseI at 1-10 U/ml in a 1 mM CaCl2 supplemented buffer. Nuclear proteins were digested with 1 mg/ml Proteinase K overnight at 37 °C

tag: dnasei origin

value: Worthington


title: SOX10_ChIP_rep1

city: Bethesda

first: Laura

middle: L

last: Baxter

state: MD

address: 35A Convent Drive

department: NHGRI

institute: NIH

description: immortalized melanocyte cell line

data_processing:
ChIP-Seq peaks for each experimental replicate were called independently using the Model-based Analysis for ChIP-Seq (MACS v1.4.2) algorithm by applying default settings and a significance p-value threshold of 1.00e-05, except for H3K27me3 where the broad peak parameters were applied as follows: macs14 -t chip.bam -c input.bam -name = chip_output -format = BAM -gsize = mm -tsize = 50 -bw = 300 -mfold = 10,30 -nolambda -nomodel -shiftsize = 150 --pvalue=1.00e-05.
Only ChIP-Seq profiles that showed reproducible overlap between both experimental samples were used for downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS and scores represent tag pileup over each position; text files contain MACS output with called peak coordinates and scores.

source_name: melan-Ink4a-Arf-1 (melan-a)

growth_protocol: According to guidelines from Bennett et al. 1987 (PMID 3102392), cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibco), 200 nM 12-O-tetradecanoylphorbol 13-acetate (Sigma-Aldrich, St Louis, MO, USA) and 200 pM cholera toxin (Sigma- Aldrich, St Louis, MO, USA) at 37°C in humidified air with 10% CO2.

extract_protocol:
Approximately 2 x 10^7 cells were harvested and crosslinked at room temperature with 1% formaldehyde for 10 minutes. Crosslinking reaction was quenched with the addition of glycine to a final concentration of 125 mM for at least 15 minutes. Crosslinked cells were lysed on ice using 1 ml low-salt ChIP buffer (150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.5% NP-40, 1.0%Triton X-100) and sonicated using a Qsonica Sonicator Q500 (Newtown, CT 0647) with the following settings: 90% amplitude; 30 seconds on/30 seconds off cycles; total sonication time of 35 minutes. Sonicated samples were centrifuged and the soluble chromatin (supernatant) was used for chromatin immunoprecipiation reactions. Briefly, 200 µl of lysate (~ 2 x 106 cells) was incubated with each  antibody and immunoprecipitated chromatin was recovered using recombinant protein G beads or magnetic Dynabeads® (Invitrogen). ChIP samples were reverse crosslinked and DNA was purified using the phenol-chloroform extraction method.
Aliquots of input (total genome) and ChIP DNA obtained from two independent experiments per antibody were used for ChIP library construction and high-throughput sequencing, per Illumina protocols.

tag: source

value: Normal embryonic skin

tag: genotype/variation

value: Cdkn2a tm1RDp/tm1RDp mice

tag: developmental stage

value: embryo

value: skin

tag: cell type

value: melanocyte

tag: cell line

tag: chip antibody

value: SOX10 (sc-17342X; Santa Cruz Biotechnology)


title: VCaP-siPIAS1-ChIPseq-SUMO2-C-rep1

status: Public on Jul 02 2015

city: Kuopio

first: Einari

middle: A

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description:
ChIP-seq
processed data file: VCaP_siPIAS1_SUMO2_C.bedGraph.gz

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
Reads were aligned against human genome hg19 with Bowtie software (0.12.7) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19.
BedGraph files were done using HOMER software (V 4.6; http://homer.salk.edu/homer/) by combining two replicates and normalizing total number of reads to 10 million. GROseq signal is divided between plus- and minus-strand signals in separate files.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq signal intensities as bedGraph files.

source_name: VCaP cells

growth_protocol: VCaP cells were grown in DMEM medium supplemented with 10% feta bovine serum and 1% penicillin/streptomycin antibiotics at 37 degree C temperature incubator with 5% CO2.

extract_protocol:
Nuclei from approximately 10 million formaldehyde crosslinked (1%; 10min at room temperature for VCaP cells, and 8min. at room temperature for K562 cells)  cells were isolated and chromatin was fragmented using sonicator (bioruptor). Lysates were cleared and protein-DNA complexes were isolated using target specific antibodies and protein-A/G magnetic beads.
DNA fragments were purified and libraries were prepared accorcing to standard Illumina protocol. Samples were sequenced at BGI Tech Solutions (Shenzhen, China) or at the Gene Core in EMBL (Heidelberg, Germany).

treatment_protocol:
Heat shock for ChIP-seq samples was done at 43 degree C incubator for 30min.
Silencing for VCaP cells was done by transfecting siRNA for UBE2I (siUBE2I samples), PIAS1 (siPIAS1 samples) or non-targeting control siRNA (siNON samples) using lipofectamine RNAiMAX transfection reagent (life technologies).
RNA polymerase II inhibitors TRP (triptolide; 1 micromolar) and DRB (5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside, 100 micromolar) were applied to VCaP cells 3h before collecting.

value: VCaP

value: control (37 degree C)

value: PIAS1 silenced (siPIAS1 transfected)

value: anti-SUMO-2/3 (MBL, catalog# M114-3, lot# 024)


title: VCaP-TRP-ChIPseq-SUMO2-rep2

description:
ChIP-seq
processed data file: VCaP_TRP_SUMO2.bedGraph.gz

value: Triptolide (1 micromolar, 3h)


title: VCaP-siPIAS1-ChIPseq-SUMO2-C-rep2


title: VCaP-siNON-ChIPseq-SUMO2-C-rep2

description:
ChIP-seq
processed data file: VCaP_siNON_SUMO2_C.bedGraph.gz

value: control for siPIAS1 (control siRNA transfected)


title: VCaP-siPIAS1-ChIPseq-SUMO2-HS-rep1

description:
ChIP-seq
processed data file: VCaP_siPIAS1_SUMO2_HS.bedGraph.gz

value: heat shock (30min at 43 degree C)


title: VCaP-siPIAS1-ChIPseq-SUMO2-HS-rep2


title: VCaP-siNON-ChIPseq-SUMO2-C-rep1


title: VCaP-DRB-ChIPseq-SUMO2-rep2

description:
ChIP-seq
processed data file: VCaP_DRB_SUMO2.bedGraph.gz

value: 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB, 100 micromolar, 3h)


title: VCaP-TRP-ChIPseq-SUMO2-rep1


title: VCaP-siNON-ChIPseq-SUMO2-HS-rep2

description:
ChIP-seq
processed data file: VCaP_siNON_SUMO2_HS.bedGraph.gz


title: RNA sequencing ccRCC3

city: Rochester

first: Jeff

last: Nie

state: MN

address: 200 First St. SW

institute: Mayo Clinic

description:
RNA sequencing ccRCC3
s_5620_L4

data_processing:
Illumina Casava1.9 software used for basecalling.
Paired-end reads are aligned by TopHat 2.0.6 (3) against the hg19 genome build using the bowtie1 aligner option.
Gene counts are generated using HTseq software (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) and gene annotation files are obtained from Illumina.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited text files include raw tagcount and RPKM values for each Sample ...

source_name: RNA sequencing ccRCC

extract_protocol:
RNA extraction using conventional protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue type

value: kidney

tag: tissue subtype

value: renal cell carcinoma (RCC)

tag: tag

value: ActiveMotif #61101


title: RNA sequencing ccRCC2

description:
RNA sequencing ccRCC2
s_5574_L6


title: VCaP-siNON-ChIPseq-SUMO2-HS-rep1


title: VCaP-DRB-ChIPseq-SUMO2-rep1


title: RNA sequencing ccRCC1

description:
RNA sequencing ccRCC1
s_4036_L2


title: RNA sequencing Uninvolved Kidney 3

description:
RNA sequencing Uninvolved Kidney 3
s_5621_L5

source_name: RNA sequencing Uninvolved Kidney

value: uninvolved kidney


title: Multiple 8-oxoG challenge - 60 min

description: Sample 7

tag: strain

value: Balb/cJ

value: Lung

value: female

tag: genotype

value: wild type

value: multiple 8-oxoG challenge

value: 60 min

value: Test


title: RNA sequencing Uninvolved Kidney 2

description:
RNA sequencing Uninvolved Kidney 2
s_5575_L1


title: H3K36me3 ChIP ccRCC3 Input

description: H3K36me3 ChIP ccRCC3 Input

data_processing:
bcl2fastq 2.15.0 is used for basecalling
Data was processed with Mayo chip-seq pipeline-- HiChIP (http://www.biomedcentral.com/1471-2105/15/280).
Paired_end reads are aligned to genome with BWA. Duplicated reads are filtered out with picard. Peak calling is performed with Sicer
Genome_build: hg19
Supplementary_files_format_and_content: Peak file is in bed fromat with header of  chr,peak_start,peak_end,peak_raw_count,INPUT_raw_count,raw_p_value and FDR

source_name: H3K36me3 ChIP ccRCC Input

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Nephrectomy samples underwent gross macrodissection to ensure that they contained >60% to 70% tumor, with verification by a mirror slide stained with hematoxylin-eosin. The frozen tissues were cut and divided into 50-mg aliquots and stored in 1.5-mL centrifuge tubes at -70°C. The frozen tissues were homogenized on ice for 15–30 seconds in 500 μL 1X PBS using a tissue grinder (ACTGene). Tissue homogenates were cross-linked to final 1% formaldehyde for 10 min and quenched with 125 mM glycine for 5 min at room temperature and washed once with TBS. The pellets were resuspended in cell lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. The lysates were divided into two aliquots and washed with MNase digestion buffer (20 mM Tris-HCl, pH 7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2). After resuspending in 500 μL MNase digestion buffer containing a proteinase inhibitor cocktails (ActiveMotif 37491), the lysates were incubated in the presence of 1,000 gel units of MNase (NEB M0247S) at 37 °C for 20 min with continuous mixing in a thermal mixer. After adding the same volume of sonication buffer (100 mM Tris-HCl, pH 8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), the lysates were sonicated for 15 min (30 seconds on / 30 seconds off) using Bioruptor Twin (Diagenode, model UCD-400) and centrifuged at 21,130 x g for 10 min. The cleared supernatant equivalent to 10–20 mg of tissue was incubated with 2 micrograms rabbit polyclonal anti-H3K36me3 antibody (Active Motif  61101) on a rocker overnight. After adding 30 microliters of protein G-agarose beads, the reactions were further incubated for 3 hours. The beads were extensively washed with ChIP buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl2 buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl2, 0.5% NP-40, 0.5% Sodium deoxycholate, 1 mM EDTA), and TE buffer. Bound chromatin were eluted and reverse-crosslinked at 65 °C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen 28004) after the treatment of RNase A and proteinase K.

tag: sample type

value: Nephrectomy sample

tag: tissue

value: tumor


title: RNA sequencing Uninvolved Kidney 1

description:
RNA sequencing Uninvolved Kidney 1
s_4037_L3


title: H3K36me3 ChIP ccRCC2 Input

description: H3K36me3 ChIP ccRCC2 Input


title: H3K36me3 ChIP ccRCC3

description: H3K36me3 ChIP ccRCC3

source_name: H3K36me3 ChIP ccRCC

value: Histone H3K36me3 antibody (pAb)

tag: chip antibody vendor

value: ActiveMotif

tag: chip antibody cat. #

tag: chip antibody lot#

value: Lot# 1


title: Laublab_BglII_HiC_NA1000_IsceI_enzyme_absence

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

data_processing:
library strategy: chromosome conformation capture coupled with deep sequencing (Hi-C)
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
We mapped reads in each FASTQ file back to the genome of Caulobacter CB15N (NA1000) independently by Bowtie version 2. All the processing steps afterwards were performed using public-availabe scripts as reported previously in Le et al., 2013 (PMID: 24158908) and in Imakaev et al., 2012 (PMID: 22941365)
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices.

organism: Caulobacter vibrioides NA1000

source_name: C. crecentus_control

growth_protocol: Caulobacter crescentus were grown as described previously in Skerker et al., 2005 (PMID: 16176121). When appropriate, media were supplemented with antibiotics at the following concentrations (liquid/solid media) [ug/ml]): chloramphenicol (1/2), kanamycin (5/25), oxytetracycline (1/2), spectinomycin (25/100). Synchronizations were performed on mid-exponential phase cells using Percoll (GE Healthcare) and density gradient centrifugation as described previously in Jones et al., 2001 (PMID: 11283290).

extract_protocol:
Hi-C experiments were performed using BglII restriction enzyme according to previous publications (Le et al., 2013 PMID: 24158908)
Standard library construction for Illumina Hiseq2000 sequencing platform

treatment_protocol: Caulobacter cells were depleted of DnaA for 1.5 h before synchronization. Swarmer cells were then released into DnaA depleting conditions (without IPTG)  for 1 h without addition of vanillate.

value: G1-arrested cells

value: IsceI site 33kb from oriC  and Isce-encoding gene at van locus

tag: restriction enzyme

value: BglII


title: H3K36me3 ChIP ccRCC1 Input

description: H3K36me3 ChIP ccRCC1 Input

value: kidney


title: H3K36me3 ChIP Uninvolved Kidney1 Input

description: H3K36me3 ChIP Uninvolved Kidney 1 Input

source_name: H3K36me3 ChIP Uninvolved Kidney Input

value: uninvolved kidney


title: H3K36me3 ChIP Uninvolved Kidney3

description: H3K36me3 ChIP Uninvolved Kidney 3

source_name: H3K36me3 ChIP Uninvolved Kidney


title: H3K36me3 ChIP Uninvolved Kidney3 Input

description: H3K36me3 ChIP Uninvolved Kidney 3 Input


title: H3K36me3 ChIP Uninvolved Kidney2 Input

description: H3K36me3 ChIP Uninvolved Kidney 2 Input


title: H3K36me3 ChIP ccRCC1

description: H3K36me3 ChIP ccRCC1


title: H3K36me3 ChIP Uninvolved Kidney1

description: H3K36me3 ChIP Uninvolved Kidney 1


title: VCaP-ChIPseq-Pol2-Re-rep2

description:
ChIP-seq
processed_data_file: VCaP-Pol2-Re.bedGraph.gz

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
Reads were aligned against human genome hg19 with Bowtie software (0.12.7) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19.
BedGraph files were done using HOMER software (V 4.6; http://homer.salk.edu/homer/) by combining two replicates and normalizing total number of reads to 10 million. GROseq signal is divided between plus- and minus-strand signals in separate files.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq and GRO-seq signal intensities as bedGraph files.

treatment_protocol: Heat shock for ChIP-seq samples was done at 43 degree C incubator for 30min.

value: VCaP

value: heat shock and recovery (30min at 43 degree C followed by 1h at 37 degree C)

value: anti-Pol2, clone:8WG16 (Covance, catalog# MMS-126R, lot# E12CF00481)


title: H3K36me3 ChIP Uninvolved Kidney2

description: H3K36me3 ChIP Uninvolved Kidney 2


title: 129_eWAT_LFDrosi_4 [RNA-seq]

city: Philadelphia

first: Mitchell

last: Lazar

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

description:
processed data file: 2b-RNA_seq_EDGEM_eWAT_LFD_Rosi.txt
RSR_065

data_processing:
Alignment of RNA-seq data was done using RUM
Differential expression analysis was carried out using EDGE-M
BigWig files for GRO-seq were generated using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: txt files containing fold change, p-values and RPKM normalized tag counts generated using EDGE-M

extract_protocol:
RNA was isolated with Trizol reagent followed with Qiagen's RNeasy Kit (#74104) from either tissue bead homogenized or cells directly treated with Trizol.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation (Part# 2001-2002).  The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Drug rosiglitazone (Cayman Chemicals) was incorporated into low fat diet D12450B by Research Diets at 36mg/kg of diet. Mice received control low fat diet for 10 weeks (age 6-16 weeks), and the rosiglitazone-containing diet versus control diet for the final 2 weeks (until sacrifice at 18 weeks)

tag: diet

value: rosiglitazone-incorporated low fat diet

value: epididymal White Adipose Tissue

tag: molecule subtype

value: mRNA

tag: experiment #


title: 129_eWAT_LFDrosi_3 [RNA-seq]

description:
processed data file: 2b-RNA_seq_EDGEM_eWAT_LFD_Rosi.txt
RSR_064


title: 129_eWAT_LFDrosi_1 [RNA-seq]

description:
processed data file: 2b-RNA_seq_EDGEM_eWAT_LFD_Rosi.txt
RSR_062


title: C57_eWAT_LFDrosi_3 [RNA-seq]

description:
processed data file: 2b-RNA_seq_EDGEM_eWAT_LFD_Rosi.txt
RSR_056


title: B6_eWAT_LFD_groseq [GRO-seq]

description: Sample A

data_processing:
Alignment of RNA-seq data was done using RUM
Differential expression analysis was carried out using EDGE-M
BigWig files for GRO-seq were generated using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: txt files containing fold change, p-values and RPKM normalized tag counts generated using EDGE-M
Genome Build:
negative_groseq.bw: mm9
positive_groseq.bw: mm9

value: LFD

value: pre-mRNA


title: VCaP-ChIPseq-Pol2-C-rep2

description:
ChIP-seq
processed_data_file: VCaP-Pol2-C.bedGraph.gz

value: control (37 degree C)


title: VCaP-ChIPseq-Pol2-HS-rep2

description:
ChIP-seq
processed_data_file: VCaP-Pol2-HS.bedGraph.gz

value: heat shock (30min at 43 degree C)


title: VCaP-ChIPseq-Pol2-C-rep1


title: 129_eWAT_LFDrosi_2 [RNA-seq]

description:
processed data file: 2b-RNA_seq_EDGEM_eWAT_LFD_Rosi.txt
RSR_063


title: H3K36me3 ChIP ccRCC2

description: H3K36me3 ChIP ccRCC2

value: Nephrectomy sample

value: tumor

value: Histone H3K36me3 antibody (pAb)

value: ActiveMotif


title: C57_eWAT_LFDrosi_1 [RNA-seq]

description:
processed data file: 2b-RNA_seq_EDGEM_eWAT_LFD_Rosi.txt
RSR_054


title: VCaP-ChIPseq-PIAS1-Re-rep2

description:
ChIP-seq
processed_data_file: VCaP-PIAS1-Re.bedGraph.gz

value: anti-PIAS1 (Abcam, catalog# ab77231, lot# YI122105C)


title: C57_eWAT_LFDrosi_2 [RNA-seq]

description:
processed data file: 2b-RNA_seq_EDGEM_eWAT_LFD_Rosi.txt
RSR_055


title: VCaP-ChIPseq-PIAS1-HS-rep2

description:
ChIP-seq
processed_data_file: VCaP-PIAS1-HS.bedGraph.gz


title: C57_eWAT_LFDrosi_4 [RNA-seq]

description:
processed data file: 2b-RNA_seq_EDGEM_eWAT_LFD_Rosi.txt
RSR_057


title: VCaP-ChIPseq-PIAS1-HS-rep1


title: 129_iWAT_12w_LFD_4 [RNA-seq]

description:
processed data file: 4-RNA_seq_EDGEM_iWAT_LFD.txt
RSR_045

value: control low fat diet (Research Diet D12450B)

value: inguinal White Adipose Tissue


title: VCaP-ChIPseq-SUMO2-Re-rep1

description:
ChIP-seq
processed_data_file: VCaP-SUMO2-Re.bedGraph.gz

value: VCaP

value: anti-SUMO-2/3 (MBL, catalog# M114-3, lot# 024)


title: VCaP-ChIPseq-SUMO2-Re-rep2

value: heat shock and recovery (30min at 43 degree C followed by 1h at 37 degree C)


title: 129_iWAT_12w_LFD_2 [RNA-seq]

description:
processed data file: 4-RNA_seq_EDGEM_iWAT_LFD.txt
RSR_043


title: VCaP-ChIPseq-SUMO2-HS-rep2

description:
ChIP-seq
processed_data_file: VCaP-SUMO2-HS.bedGraph.gz


title: K562-shSCR-ChIPseq-SUMO2-HS-rep2

description:
ChIP-seq
processed_data_file: K562-shSCR-SUMO2-HS.bedGraph.gz

source_name: K562 cells

growth_protocol: K562 cells were grown in RPMI1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin antibiotics and 2mM l-glutamine at 37 degree C temperature incubator with 5% CO2.

treatment_protocol:
Heat shock for ChIP-seq samples was done at 43 degree C incubator for 30min.
Silencing  was done by transfecting short hairpin RNA for HSF1 (shHSF1 samples) or scrambled sequence (shSCR samples) to K562 cells with electroporation.

value: control for HSF1 silencing (shSCR transfection)


title: VCaP-ChIPseq-SUMO2-HS-rep1


title: K562-shSCR-ChIPseq-SUMO2-HS-rep1


title: VCaP-ChIPseq-PIAS1-Re-rep1


title: VCaP-ChIPseq-Pol2-Re-rep1

description:
ChIP-seq
processed_data_file: VCaP-Pol2-Re.bedGraph.gz

value: anti-Pol2, clone:8WG16 (Covance, catalog# MMS-126R, lot# E12CF00481)


title: B6_iWAT_12w_LFD_3 [RNA-seq]

description:
processed data file: 4-RNA_seq_EDGEM_iWAT_LFD.txt
RSR_028

value: mRNA


title: B6_iWAT_12w_LFD_1 [RNA-seq]

description:
processed data file: 4-RNA_seq_EDGEM_iWAT_LFD.txt
RSR_026


title: B6_iWAT_12w_LFD_2 [RNA-seq]

description:
processed data file: 4-RNA_seq_EDGEM_iWAT_LFD.txt
RSR_027


title: 129_iWAT_12w_LFD_1 [RNA-seq]

description:
processed data file: 4-RNA_seq_EDGEM_iWAT_LFD.txt
RSR_042


title: K562-shSCR-ChIPseq-SUMO2-C-rep1

description:
ChIP-seq
processed_data_file: K562-shSCR-SUMO2-C.bedGraph.gz


title: B6_iWAT_12w_LFD_4 [RNA-seq]

description:
processed data file: 4-RNA_seq_EDGEM_iWAT_LFD.txt
RSR_029


title: 129_eWAT_12w_LFD_4 [RNA-seq]

description:
processed data file: 3-RNA_seq_EDGEM_eWAT_LFD.txt
RSR_037

value: epididymal White Adipose Tissue


title: K562-shSCR-ChIPseq-SUMO2-C-rep2


title: C4_eWAT_LFD-12w [RNA-seq]

description:
processed data file: 3-RNA_seq_EDGEM_eWAT_LFD.txt
RSR_004


title: C5_eWAT_LFD-12w [RNA-seq]

description:
processed data file: 3-RNA_seq_EDGEM_eWAT_LFD.txt
RSR_005


title: K562-shHSF1-ChIPseq-SUMO2-HS-rep2

description:
ChIP-seq
processed_data_file: K562-shHSF1-SUMO2-HS.bedGraph.gz

value: HSF1 silenced (shHSF1 transfection)


title: K562-shHSF1-ChIPseq-SUMO2-HS-rep1


title: K562-shHSF1-ChIPseq-SUMO2-C-rep2

description:
ChIP-seq
processed_data_file: K562-shHSF1-SUMO2-C.bedGraph.gz

value: control (37 degree C)


title: 129_eWAT_12w_LFD_3 [RNA-seq]

description:
processed data file: 3-RNA_seq_EDGEM_eWAT_LFD.txt
RSR_036


title: 129_eWAT_12w_LFD_2 [RNA-seq]

description:
processed data file: 3-RNA_seq_EDGEM_eWAT_LFD.txt
RSR_035


title: K562-ChIPseq-SUMO2-HS-rep2

description:
ChIP-seq
processed_data_file: K562-SUMO2-HS.bedGraph.gz

value: heat shock (30min at 43 degree C)


title: K562-GROseq-Hs-rep2

description:
nascent RNA
GRO-seq
processed_data_file: K562-GROseq-HS-plus.bedGraph.gz; K562-GROseq-HS-minus.bedGraph.gz

data_processing:
Library strategy: GRO-Seq
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
Reads were aligned against human genome hg19 with Bowtie software (0.12.7) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19.
BedGraph files were done using HOMER software (V 4.6; http://homer.salk.edu/homer/) by combining two replicates and normalizing total number of reads to 10 million. GROseq signal is divided between plus- and minus-strand signals in separate files.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq and GRO-seq signal intensities as bedGraph files.

extract_protocol:
Nuclei were extracted from 5-10 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight.
Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified on a denaturing 10% polyacrylamide TBE-urea gel. The recovered cDNA was circularized, linearized, amplified for 11-14 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000.

treatment_protocol: Heat shock for GRO-seq was done in 43 degree water bath for 30min. Recovery was done by incubating cells at 37 degree C for 1h after heat shock.


title: K562-ChIPseq-input-HS

description:
sequencing of fragmented chromatin
processed_data_file: K562-Input-HS.bedGraph.gz

value: input control for HS samples (30min at 43 degree C)

value: none (input)


title: K562-shHSF1-ChIPseq-SUMO2-C-rep1


title: K562-GROseq-HS-rep1


title: K562-GROseq-C-rep2

description:
nascent RNA
GRO-seq
processed_data_file: K562-GROseq-C-plus.bedGraph.gz; K562-GROseq-C-minus.bedGraph.gz


title: 129_eWAT_LFDcontrol_4 [RNA-seq]

description:
processed data file: 2-RNA_seq_EDGEM_eWAT_LFD_control.txt
RSR_061

value: LFDcontrol


title: K562-ChIPseq-SUMO2-HS-rep1


title: 129_eWAT_LFDcontrol_1 [RNA-seq]

description:
processed data file: 2-RNA_seq_EDGEM_eWAT_LFD_control.txt
RSR_058


title: 129_eWAT_12w_LFD_1 [RNA-seq]

description:
processed data file: 3-RNA_seq_EDGEM_eWAT_LFD.txt
RSR_034


title: K562-GROseq-C-rep1


title: C3_eWAT_LFD-12w [RNA-seq]

description:
processed data file: 3-RNA_seq_EDGEM_eWAT_LFD.txt
RSR_003


title: K562-ChIPseq-SUMO2-C-rep2

description:
ChIP-seq
processed_data_file: K562-SUMO2-C.bedGraph.gz


title: C2_eWAT_LFD-12w [RNA-seq]

description:
processed data file: 3-RNA_seq_EDGEM_eWAT_LFD.txt
RSR_002


title: C57_eWAT_LFDcontrol_4 [RNA-seq]

description:
processed data file: 2-RNA_seq_EDGEM_eWAT_LFD_control.txt
RSR_053


title: RS_051

description:
processed data file: peakfile_universe_HAR_62188.bed
processed data file: 47893_all4.ucsc.bedGraph.gz

data_processing:
Alignment of ChIP-seq data was done using GSNAP version 2014-07-04(mouse) and bowtie2-v2.2.3(human)
Peak calls and subsequent analysis of ChIP-seq data was done using HOMER v4.7.2
Genome_build: mm9, hg19
Supplementary_files_format_and_content: bed files generated using HOMER;

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

tag: experiment type

value: PPARG ChIP-seq

tag: subject#

value: SQ White Adipose Tissue

value: anti-PPARγ antibody

value: Santa Cruz Biotechnologies


title: K562-ChIPseq-input

description:
sequencing of fragmented chromatin
processed_data_file: K562-Input-C.bedGraph.gz

tag: cell line

value: input control (37 degree C)

tag: chip antibody


title: C1_eWAT_LFD-12w [RNA-seq]

description:
processed data file: 3-RNA_seq_EDGEM_eWAT_LFD.txt
RSR_001

value: control low fat diet (Research Diet D12450B)


title: C57_eWAT_LFDcontrol_3 [RNA-seq]

description:
processed data file: 2-RNA_seq_EDGEM_eWAT_LFD_control.txt
RSR_052


title: RS_053


title: C57_eWAT_LFDcontrol_2 [RNA-seq]

description:
processed data file: 2-RNA_seq_EDGEM_eWAT_LFD_control.txt
RSR_051


title: RS_052


title: K562-ChIPseq-SUMO2-C-rep1

value: anti-SUMO-2/3 (MBL, catalog# M114-3, lot# 024)


title: RS_024


title: C57_eWAT_LFDcontrol_1 [RNA-seq]

description:
processed data file: 2-RNA_seq_EDGEM_eWAT_LFD_control.txt
RSR_050


title: RS_055_2

description:
processed data file: peakfile_universe_HAR_62188.bed
processed data file: 125S_all3.ucsc.bedGraph.gz


title: 129_eWAT_LFDcontrol_3 [RNA-seq]

description:
processed data file: 2-RNA_seq_EDGEM_eWAT_LFD_control.txt
RSR_060


title: F1 - 4_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_024

value: standard rodent chow diet


title: 129_iWAT_12w_LFD_3 [RNA-seq]

description:
processed data file: 4-RNA_seq_EDGEM_iWAT_LFD.txt
RSR_044

value: inguinal White Adipose Tissue


title: F1 - 5_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_025

value: mRNA


title: RS_055_1


title: F1 - 3_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_023

value: epididymal White Adipose Tissue


title: F1 - 2_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_022


title: RS_072_2

description:
processed data file: peakfile_universe_HAR_62188.bed
processed data file: 124S_all3.ucsc.bedGraph.gz


title: F1 - 1_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_021


title: 129_eWAT_LFDcontrol_2 [RNA-seq]

description:
processed data file: 2-RNA_seq_EDGEM_eWAT_LFD_control.txt
RSR_059


title: RS_032


title: 129 - 4_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_019


title: 129 - 5_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_020


title: RS_072_1


title: RS_006


title: RS_070_2

description:
processed data file: peakfile_universe_HAR_62188.bed
processed data file: 120S_all3.ucsc.bedGraph.gz


title: RS_070_1


title: 129 - 2_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_017


title: RS_028


title: C57 - 3_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_013


title: 129 - 3_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_018


title: 129 - 1_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_016


title: C57 - 2_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_012


title: RS_022

description:
processed data file: peakfile_universe_HAR_62188.bed
processed data file: 114S_all3.ucsc.bedGraph.gz


title: C57 - 1_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_011


title: B6_eWAT_chow_GR

description: processed data file: peakfile_universe_GR_80944.bed

value: GR ChIP-seq

value: anti-GR antibody

tag: chip antibody vendor/cat. #

value: Santa Cruz Biotechnologies, sc-1004 (6 ug)

value: Affinity BioReagents, PA1-511A (3 ug)


title: B6_iWAT_chow_GR


title: 129_iWAT_chow_GR


title: input_F1_iWAT_gsnap


title: 129_eWAT_chow_GR


title: input_B6_iWAT_gsnap


title: RS_056_1


title: 129_iWAT_chow

description: processed data file: peakfile_universe_PPARG_35226.bed


title: F1_iWAT_chow


title: B6_iWAT_chow


title: F1_eWAT_chow_a

description:
processed data file: peakfile_universe_PPARG_35226.bed
processed data file: F1_eWAT_chow_ab_gsnap.ucsc.bedGraph.gz


title: C57 - 4_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_014


title: RS_056_2


title: B6_eWAT_chow_b

description:
processed data file: peakfile_universe_PPARG_35226.bed
processed data file: B6_eWAT_chow_ab_gsnap.ucsc.bedGraph.gz


title: input_129_iWAT_gsnap


title: F1_eWAT_chow_b


title: C57 - 5_eWAT_chow [RNA-seq]

description:
processed data file: 1-RNA_seq_EDGEM_eWAT_chow.txt
RSR_015


title: 129_eWAT_12wLFD_2

description:
processed data file: peakfile_universe_PPARG_35226.bed
processed data file: 129_eWAT_12wLFD_12_gsnap.ucsc.bedGraph.gz

value: control low fat diet


title: B6_eWAT_chow_a


title: 129_eWAT_chow_a

description:
processed data file: peakfile_universe_PPARG_35226.bed
processed data file: 129_eWAT_chow_ab_gsnap.ucsc.bedGraph.gz


title: 129_eWAT_12wLFD_1


title: B6_eWAT_12wLFD_3b

description:
processed data file: peakfile_universe_PPARG_35226.bed
processed data file: B6_eWAT_12wLFD_2b3b_gsnap.ucsc.bedGraph.gz


title: B6_eWAT_12wLFD_2b


title: KO_GFP_hr03

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
After demultiplexing, the data was mapped to the D. discoideum genome with bowtie version 0.12.7. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
Peak calling was done on 5-kb genomic regions using partially overlapping (50% overlap), sliding windows of 200 bp. For each window, we calculated the log-ratio of the scaled coverage (scaled by number of mapped reads) between IP+ and control ChIP-seq experiments while permitting a maximum of five mapped reads to share the same genomic coordinates. At each time point, we identified peaks as genomic regions preferentially associated with the TF (GtaC) in the sample compared to control (enrichment > 4-fold; FDR < 0.01; read support > 50). In the proximity of candidate peaks, we accounted for shifts (up to 200 bp) in the distributions of reads mapping to positive and negative strands (Jothi et al. 2008) and enforced similar read support on either strand (absolute log-ratio < 0.5). We also used MACS (Zhang et al. 2008) to identify peaks (parameters: shiftsize=150, bw=200, slocal=5000) and only used peaks identified in both methods. At each time point, ChIP-seq performed on the null strain (carrying GFP), was considered to be the control.
supplementary_files_format_and_content: Processed ChIP-seq files contain the genomic coordinates of predicted peaks and the enrichment of coverage in the IP+ compared to the control ChIP-seq experiments within each region.
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.

organism: Dictyostelium discoideum

source_name: gtaCKO 3h developing ; replicate 1

growth_protocol: Wild-type and the different gtaC alleles strains were cultured axenically in HL5 supplemented with antibiotics.

extract_protocol:
ChIP-seq: After cellular fixation, we isolated nuclei and prepared nuclear extract by sonication. We used precleared nulcear extract for ChIP experiment with anti-GFP antibodies (Roche, clones 7.1 and 13.1 mixture). After stringent wash, we performed reverse-crosslinking treatment and purified the ChIP DNA.
We prepared Illumina multiplexed libraries. We prepared 15 (or 20) individual libraries separately (one from each sample) and added a unique barcode to each library at the final step of PCR amplification. We pooled equal amounts of DNA from each library and sequenced one pool per lane of a flow cell on Illumina Genome Analyzer II using the manufacturer's recommended pipeline (versions 1.2 and 1.3, read length = 50 bases)

treatment_protocol: ChIP-seq: development on nitrocellulose filters placed on a buffer-soaked filter paper pad, cells were washed twice with potassium phosphate buffer (KK2) and deposited on nitrocellulose filter 3.3x106 cells/cm10

value: GFP/gtaC-

tag: replicate

tag: developmental time


title: 3T3L1

value: PPARG ChIP-seq

tag: strain


title: KO_GFP_hr09

source_name: gtaCKO 9h developing ; replicate 1

treatment_protocol: ChIP-seq: development on nitrocellulose filters placed on a buffer-soaked filter paper pad, cells were washed twice with potassium phosphate buffer (KK2) and deposited on nitrocellulose filter 3.3x106 cells/cm11

tag: genotype


title: KO_GFP_hr01

source_name: gtaCKO 1h developing ; replicate 1

treatment_protocol: ChIP-seq: development on nitrocellulose filters placed on a buffer-soaked filter paper pad, cells were washed twice with potassium phosphate buffer (KK2) and deposited on nitrocellulose filter 3.3x106 cells/cm9


title: CS_NtermGFP_hr09

source_name: GtaCC-S-GFP 9h developing ; replicate 1

treatment_protocol: ChIP-seq: development on nitrocellulose filters placed on a buffer-soaked filter paper pad, cells were washed twice with potassium phosphate buffer (KK2) and deposited on nitrocellulose filter 3.3x106 cells/cm8

value: GFP-GtaCC-S/gtaC-


title: CM_NtermGFP_hr10

source_name: GtaC-GFP 9h developing ; replicate 1

treatment_protocol: ChIP-seq: development on nitrocellulose filters placed on a buffer-soaked filter paper pad, cells were washed twice with potassium phosphate buffer (KK2) and deposited on nitrocellulose filter 3.3x106 cells/cm6

value: GFP-GtaC/gtaC-


title: CS_NtermGFP_hr03

source_name: GtaCC-S-GFP 3h developing ; replicate 1

treatment_protocol: ChIP-seq: development on nitrocellulose filters placed on a buffer-soaked filter paper pad, cells were washed twice with potassium phosphate buffer (KK2) and deposited on nitrocellulose filter 3.3x106 cells/cm7


title: CM_NtermGFP_hr04

source_name: GtaC-GFP 3h developing ; replicate 1

treatment_protocol: ChIP-seq: development on nitrocellulose filters placed on a buffer-soaked filter paper pad, cells were washed twice with potassium phosphate buffer (KK2) and deposited on nitrocellulose filter 3.3x106 cells/cm4


title: CM_CtermGFP_hr02

source_name: GtaC-GFP 1h developing ; replicate 2

treatment_protocol: ChIP-seq: development on nitrocellulose filters placed on a buffer-soaked filter paper pad, cells were washed twice with potassium phosphate buffer (KK2) and deposited on nitrocellulose filter 3.3x106 cells/cm3


title: 129_eWAT_chow_b

tag: tissue

value: anti-PPARγ antibody

value: Santa Cruz Biotechnologies


title: CSrep2_hr03

data_processing:
After demultiplexing, the data was mapped to the D. discoideum genome with bowtie version 0.12.7. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable).
supplementary_files_format_and_content: Processed gene expression files have two columns: the first containing gene names and the second its abundance (raw or normalized). Files ending with "_raw.txt" contain raw expression values while files ending with "_nor.txt" contain normalized expression values.
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.

source_name: GtaCC-S-GFP 2h developing ; replicate 2

extract_protocol:
RNA-seq: At each time point, we suspended the cells (5x107cells) with 1 mL of Trizol® (life technologies, CA, USA) and extracted total RNA according to the manufacturer’s recommended protocol. We purified mRNA by two rounds of poly-A selection and fragmented 100 ng of the resulting mRNA into approximately 200-bases fragments. We prepared cDNA and the second strand.
We prepared Illumina multiplexed libraries. We prepared 15 (or 20) individual libraries separately (one from each sample) and added a unique barcode to each library at the final step of PCR amplification. We pooled equal amounts of DNA from each library and sequenced one pool per lane of a flow cell on Illumina Genome Analyzer II using the manufacturer's recommended pipeline (versions 1.2 and 1.3, read length = 50 bases)

treatment_protocol: RNA-seq: development on non-nutrient agar, cells were washed with developmental buffer (DB) and plated on DB agar at a density of 5.2x105 cells/cm2


title: CM_NtermGFP_hr02

source_name: GtaC-GFP 1h developing ; replicate 1

treatment_protocol: ChIP-seq: development on nitrocellulose filters placed on a buffer-soaked filter paper pad, cells were washed twice with potassium phosphate buffer (KK2) and deposited on nitrocellulose filter 3.3x106 cells/cm2


title: CSrep1_hr09

source_name: GtaCC-S-GFP 8h developing ; replicate 1


title: CSrep1_hr03

source_name: GtaCC-S-GFP 2h developing ; replicate 1


title: CSrep2_hr01

source_name: GtaCC-S-GFP 0h developing ; replicate 2


title: CSrep2_hr02

source_name: GtaCC-S-GFP 1h developing ; replicate 2


title: CSrep1_hr01

source_name: GtaCC-S-GFP 0h developing ; replicate 1


title: CMrep2_hr09

source_name: GtaCGFP 8h developing ; replicate 2


title: KOrep1_hr09

source_name: gtaCKO 8h developing ; replicate 1

value: gtaC-


title: KOrep2_hr09

source_name: gtaCKO 8h developing ; replicate 2


title: WTrep1_hr09

source_name: AX2 8h developing ; replicate 1

value: wildtype


title: ChIP ESR1 preantral follicles

status: Public on Jul 01 2015

city: GIF SUR YVETTE

first: Adrien

last: Georges

address: CEA/SACLAY

country: France

institute: CNRS

description: DNA ChiPed with anti-ESR1 C-terminal antibody (Santa Cruz sc543)

data_processing:
Base calling, CASAVA-1.8.2
Adapter removal, cutadapt-1.2.1
Fastq conversion, Fastqc-0.10.1
Read alignment, Bowtie Galaxy version v1.1.2, Full list of parameters : Will you select a reference genome from your history or use a built-in index?:indexed;Select a reference genome:mm9female;Is this library mate-paired?:single;FASTQ file:1: Foxl2;Bowtie settings to use:full;Skip the first n reads (-s):0;Only align the first n reads (-u):-1;Trim n bases from high-quality (left) end of each read before alignment (-5):0;Trim n bases from low-quality (right) end of each read before alignment (-3):0;Maximum number of mismatches permitted in the seed (-n):2;Maximum permitted total of quality values at mismatched read positions (-e):70;Seed length (-l):28;Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround):Round to nearest 10;Number of mismatches for SOAP-like alignment policy (-v):-1;Whether or not to try as hard as possible to find valid alignments when they exist (-y):Do not try hard;Report up to n valid alignments per read (-k):1;Whether or not to report all valid alignments per read (-a):Do not report all valid alignments;Suppress all alignments for a read if more than n reportable alignments exist (-m):1;Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max):False;Write all reads that could not be aligned to a file (--un):False;Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best):noBest;Maximum number of backtracks permitted when aligning a read (--maxbts):125;Override the offrate of the index to n (-o):-1;Seed for pseudo-random number generator (--seed):-1;Suppress the header in the output SAM file:False;
Unmapped reads removal, Filter SAM galaxy version 1.0.0
Peak calling, MACS Galaxy version 1.0.1, Full list of parameters : Tag size:50;Band width:160;Pvalue cutoff for peak detection:0,00001;Select the regions with MFOLD high-confidence enrichment ratio against background to build model:20;Parse xls files into into distinct interval files:False;Save shifted raw tag count at every bp into a wiggle file:wig;Extend tag from its middle point to a wigextend size fragment.:-1;Resolution for saving wiggle files:20;Use fixed background lambda as local lambda for every peak region:False;3 levels of regions around the peak region to calculate the maximum lambda as local lambda:1000,5000,10000;Build Model:create_model;Diagnosis report:no_diag;Perform the new peak detection method (futurefdr):True;
Genome_build: mm9
Supplementary_files_format_and_content: .bed file contain 5 columns : chr, peakStart, peakEnd, peakID and score
Supplementary_files_format_and_content: .wig file contain unnormalized read mapping abundancies (20bp digits)

source_name: cells from preantral follicles maintained for 9 days in vitro and treated for 45 minutes with 10-7M estradiol

growth_protocol: The ovaries of 20 8-week old female Swiss mice were dissected and digested in DMEM/F-12 medium (Gibco) containing 1mg/mL collagenase (Sigma-Aldrich), 0,5mg/mL BSA (Sidma-Aldrich) and 2000 U/mL DNase I (Thermo-Fisher), in a ratio of 500µL per ovary, at 37°C for 30 min. Ovaries were progressively dispersed during digestion using pipette tips of decreasing size to flush the organ debris. The mix was then diluted in 10 volumes of DMEM/F-12 medium, filtered using a 500 µm membrane, spinned at 300 g. The pellet was rinsed in cold PBS and spinned again, and the pelleted debris were resuspended in a PBS/Ficoll mix of density 1.10. A PBS/Ficoll gradient was made by depositing PBS/Ficoll layers of density 1.08, 1.07, 1.06, 1.05, 1.03 and 1. The gradient was spinned at 1500 g for 20min, and 1 mL fractions were collected and diluted in 5 mL culture medium (i.e. DMEM/F-12 supplemented with 4% FBS, 1% Insulin-Transferrin-Selenium-X supplement, 1% Penicillin-Streptomycine (Gibco) and 10-7M androstenedione (Sigma-Aldrich). We then manually collected intact preantral follicles, characterized by the presence of several layers of granulosa cells around the oocyte and the absence of antrum. They mainly migrated to the 1.07/1.06 and 1.06/1.05 interfaces. Follicles were then rinsed, transferred to culture plates and grown overnight. On day 1, they were dispersed using trypsin and then cultured in monolayers. Culture medium was changed on day 3, and cells were passed on days 5 and 7.

extract_protocol:
Cells grown to confluence in three 150-mm plates were fixed in situ with 1% Formaldehyde for 10 min at room temperature, fixation was then blocked with 125 mM glycine, cells were rinsed and scrapped in PBS. Cells were first lysed in Lysis buffer A (50 mM Hepes pH 7.5, NaCl 140 mM, EDTA 1 mM, glycerol 10% NP-40 0.5% and Triton X-100 0.25%), then spinned and rinsed in lysis buffer B (Tris 10 mM pH 7.5, NaCl 200 mM, EDTA 1 mM, EGTA 0.5 mM), centrifugated again and finally resuspended in lysis buffer C (Tris 10 mM pH 7.5, NaCl 100 mM, EDTA 1 mM, EGTA 0.5 mM, Na–deoxycholate 0.5%, N-lauryl sarcosine 0.5%). Chromatin was sheared in a Bioruptor sonicator, used at high power with 30/30 s cycles for 20 min, then 1% Triton X-100 was added to lysates, and cell debris were centrifugated. In parallel, 30 μg anti-FOXL2 or anti-ESR1 were incubated with 200 μl ProteinG Dynabeads for 4 h in PBS containing 0.1% BSA. Lysates were incubated with the beads overnight, beads were then washed five times in wash buffer (50 mM Hepes pH 7.6, 500 mM LiCl, 1 mM EDTA, 0.7% Na–deoxycholate, 1% NP-40) and once in TBS. DNA–protein complexes were then eluted in 10 mM Tris pH 8, 1 mM EDTA, 1% SDS at 65 °C for 15 min. Crosslinks were reversed at 65 °C overnight, then recovered DNA was treated with RNaseA, proteinase K and purified using phenol–chloroform. Input samples underwent to the same procedure.
Adapters were ligated using a SPRI-TE Nucleic Acid Extractor Robot with a SPRIworks Fragment Library Kit I and adapters from TruSeq DNA LT Sample Prep kit (Illumina). Ligated fragments were amplified with C and D primers(C primer :5’-AATGATACGGCGACCACCGAGATCTACAC-3’b and D primer : 5’-CAAGCAGAAGACGGCATACGAGAT-3’) using Phusion HF polymerase (Thermo Fisher Scientific) for 14 PCR cycles. 200 to 400 bp fragments were selected on gel and purified on a Qiagen column.

treatment_protocol: 45 minutes before fixation, cells were treated with 100nmol/L 17beta-estradiol (Sigma-Aldrich)

value: SWISS

tag: Sex

value: female

value: ovary

tag: age

tag: antibody


title: CSrep1_hr06

source_name: GtaCC-S-GFP 5h developing ; replicate 1


title: SKmel147-control-RNA

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

data_processing:
Read alignment preformed using TopHat, version 2.0.12 (--transcriptome-only). Transcriptome assemblies in FPKM (fragments per kilo-base per million reads). For each RNA sample two technical replicates were merged
Differential expression preformed using Cufflinks 2.2.1
bigWig file generated using genomeCoverageBed and bg2bw.sh
Genome_build: UCSC-hg19
Supplementary_files_format_and_content: txt files containg FPKM values for all samples.

source_name: SKmel147 melanoma cell line

growth_protocol: SK-mel147 were grown with DMEM media with 10%FBS and antibiotics. Melanocytes were cultured in Melanocyte Growth Media 254 supplemented with Human Melanocyte Growth Supplement (Life Technologies)

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
Sequencing libraries were prepared following the Illumina TruSeq Stranded Total RNA library prep protocol, with Ribo-Zero (RS-122-2201 or -2202), starting from 300-500ng of DNase I-treated total RNA, with the exception of 13 cycles of PCR amplification instead of 15. Amplified libraries were purified using AMPure beads, quantified by Qubit and qPCR, and visualized on an Agilent Bioanalyzer.

treatment_protocol: Cells were treated with 1µM of JQ1 or an enantiomer (control) for 6h

tag: cell type

value: melanoma cell line

tag: genotype/variation

value: NRAS mutant Q61R

tag: treated with

value: enantiomer (control) for 6h


title: CSrep2_hr06

source_name: GtaCC-S-GFP 5h developing ; replicate 2


title: Input preantral follicles

description: Input DNA submitted to same decrosslink and preparation as ChIPped DNA


title: Mel-RNA

source_name: Melanocytes

value: non tumorigenic (Melanocytes)

value: wild type


title: ChIP FOXL2 preantral follicles

description: DNA ChiPed with anti-FOXL2 C-terminal antibody (from lab)


title: lympho-directExtract

city: Durham

first: David

last: Reid

state: NC

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

institute: Duke University

data_processing:
Cutadapt
Trim AAGATCGGAAGAGCACACGTCT
cutadapt -a AAGATCGGAAGAGCACACGTCT --discard-untrimmed -m 20 DBA37-P.fastq -o trimDBA37-P.fastq
cutadapt 1.6 with Python 2.7.6
Bowtie
bowtie -p 7 -v 0 --norc database/chosenTranscripts reads/trimDBA37-P.fastq mapped/DBA37-P.map
Bowtie 1.1.1
Genome_build: NCBI v37
Supplementary_files_format_and_content: XLSX; RPKM values for all genes within the coding sequence

source_name: Lymphocytes

extract_protocol:
Cells lysed in 200 mM KOAC, 15 mM MgCl, 15 mM K-HEPES pH 7.2, 180 uM cycloheximide. Treated with 10 ug/ml Mnase for 30 min
NEB Directional Small RNA kit. Libraries purified by gel electrophoresis

tag: sample type

value: No ribosome purification

value: Lymphocytes


title: CSrep1_hr02

source_name: GtaCC-S-GFP 1h developing ; replicate 1


title: lympho-pelleted

value: With ribosome purification


title: hen1-2/heso1-2  Rep 2

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to TAIR10 whole genome using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each miRNA with trimmed mean of M values (TMM) normalization method. Robinson and Oshlack Genome Biology 2010.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is MicroRNA gene IDs and the second column is normalized reads counts

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: 16 hour light; 8 hour dark;  at 22 oC

extract_protocol:
Flower inflorescences were collected and total RNA was extracted by Trizol. Illumina TruSeq Small RNA Sample Prep Kits was used with 1 ug of total RNA for the construction of sequencing libraries.
Illumina small RNA library protocol

value: Landsberg erecta (Ler)

value: inflorescence


title: heso1-2 Rep1


title: hen1-2/heso1-2/urt1-3 Rep 2


title: heso1-2/utr1-3 Rep 1


title: VCaP-ChIPseq-Pol2-HS-rep1

description:
ChIP-seq
processed_data_file: VCaP-Pol2-HS.bedGraph.gz

source_name: VCaP cells

value: VCaP

value: heat shock (30min at 43 degree C)

value: anti-Pol2, clone:8WG16 (Covance, catalog# MMS-126R, lot# E12CF00481)


title: heso1-2 Rep2


title: hen1-2/heso1-2/urt1-3 Rep 1


title: CMrep1_hr09

source_name: GtaCGFP 8h developing ; replicate 1

value: GFP-GtaC/gtaC-


title: hen1-2/heso1-2  Rep 1


title: hen1-2 Rep 2


title: WTrep2_hr09

source_name: AX2 8h developing ; replicate 2

value: wildtype


title: Ler WT Rep1

value: WT Ler


title: hen1-2 Rep 1


title: Ler WT Rep 2


title: HP26695 ML B3 HS2 +TEX

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
Fastq quality trimming using FastX version 0.0.13 and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (READemption 0.3.5, Förstner et al., 2014)
Read mapping using segemehl version 0.1.7 (READemption 0.3.5, Förstner et al., 2014)
Coverage calculation and normalization (READemption 0.3.5, Förstner et al., 2014)
Coverage normalization by TSSpredator (http://it.inf.uni-tuebingen.de/TSSpredator)
Genome_build: NC_000915.1
Supplementary_files_format_and_content: wiggle

organism: Helicobacter pylori 26695

source_name: Helicobacter pylori 26695 wildtype

growth_protocol: Helicobacter pylori wild type strain 26695 (CSS-0065, kindly provided by D. Scott Merrell, Bethesda, MD) was grown on GC-agar (Oxoid) plates supplemented with 10% (V/V) donor horse serum (Biochrom AG), 1% (V/V) vitamin mix, 10 μg/ml vancomycin, 5 μg/ml trimethoprim, and 1 μg/ml nystatin. For liquid cultures, 15 or 50 ml Brain Heart Infusion medium (BHI, Becton, Dickinson and Company) supplemented with 10% (V/V) FBS (Biochrom AG) and 10 μg/ml vancomycin, 5 μg/ml trimethoprim, and 1 μg/ml nystatin were inoculated with H. pylori grown on plates to a final OD600 of 0.02 – 0.05 and grown under agitation at 140 rpm in 25 cm³ or 75 cm³ cell culture flasks (Corning). Bacteria were grown at 37°C in a HERAcell 150i incubator (Thermo scientific) in a microaerophilic environment (10% CO2, 5 % O2, and 85 % N2). When the cultures reached mid-log phase (OD600  ~0.6), culture volumes of cells corresponding to a total amount of 4 OD600, were mixed with 0.2 volumes of stop-mix (95% EtOH and 5% phenol, V/V), frozen in liquid N2 and stored at −80°C until RNA extraction. In total, three biological replicates of bacteria grown to mid-log phase (ML) were harvested: B1 which was grown separately from B2 and B3 which were grown on the same day.

extract_protocol:
Frozen cell pellets were thawed on ice and re-suspended in lysis solution containing 600 µl of 0.5 mg/ml lysozyme in TE buffer (pH 8.0) and 60 µl 10% SDS. Bacterial cells were lysed by incubating the samples for 1–2 minutes at 65°C. Afterwards, total RNA was extracted using the hot-phenol method described previously (Sharma et al. 2010, Bloomberg 1990, EMBO J). DNaseI (Fermentas) treatment was performed on total RNA according to manufacturer’s instruction. Afterwards, ~200 ng RNA samples were poly(A)-tailed using 2.5 U E.coli poly(A) polymerase (NEB) for 5 min at 37°C. Terminator exonuclease treatment (+TEX) and mock treatment without the enzyme (-TEX) were carried out after poly(A)-tailing. In brief, poly(A)-tailed RNA was denatured for 2 min at 90˚C, cooled on ice for 5 min and treated with 1.5U of Terminator Exonuclease (Epicentre) for 30 min at 30˚C.
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). At first, the 5'-PPP structures were removed using tobacco acid pyrophosphatase (TAP). TAP treatment was performed by incubating TEX-treated (+TEX) and untreated control (−TEX) samples with 5U TAP for 15 min at 37˚C.  Afterwards, an RNA adapter (5' Illumina sequencing adapter, 5'-UUUCCCUACACGACGCUCUUCCGAUCU-3') was ligated to the 5´-phosphate of the TAP-treated, poly(A)-tailed RNA for 30 min at 25°C. First-strand cDNA was synthesized by using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase (AffinityScript, Agilent) by incubation at 42°C for 20 min, ramp to 55°C followed by 55°C for 5 min. In a PCR-based amplification step using a high fidelity DNA polymerase (Herculase II Fusion DNA Polymerases, Agilent)  the cDNA concentration was increased to 10-20 ng/μl (initial denaturation at 95°C for 2 min, 10-15 cycles 95°C for 20 sec and 68°C for 2 min). The TruSeq index primers for PCR amplification were according to the instructions of Illumina. For all libraries the Agencourt AMPure XP kit (Beckman Coulter Genomics) was used to purify the DNA (1.8 x sample volume), and cDNA sizes were examined by capillary electrophoresis on a MultiNA microchip electrophoresis system (Shimadzu). A library-specific barcode for multiplex sequencing was included as part of a 3'-sequencing adapter.

tag: treatment

value: TEX treated


title: SKmel147-JQ1-RNA

value: melanoma cell line

value: 1µM of JQ1 for 6hrs


title: HP26695 ML B3 HS2 -TEX

treatment_protocol: When the cultures reached mid-log phase (OD600  ~0.6), culture volumes of cells corresponding to a total amount of 4 OD600, were mixed with 0.2 volumes of stop-mix (95% EtOH and 5% phenol, V/V), frozen in liquid N2 and stored at −80°C until RNA extraction.

value: untreated


title: HP26695 ML B2 HS2 +TEX


title: heso1-2/utr1-3 Rep 2


title: HP26695 ML B2 HS2 -TEX


title: LB mRNA biological replicate

city: Potsdam

first: Alexander

last: Bartholomaeus

address: Telegrafenberg C

department: Department 3 Geochemie

institute: Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences

description:
mRNA-Seq
biological replicate LB mRNA

data_processing:
Mapping using FANSe [Zhang et al. 2012, Nucleic Acids Res40, e83] allowing 3 mismatches and enabled indel detection
Read counting taking middle nucleotide (for even read length nucleotide to the right of the middle) of the each read and assigning it to ORFs identified by NCBI gene names (done by own scripts)
Reads in non-unique regions were assigned to the more closest unique region (done by own scripts)
rpkMd obtained by read count divided by gene length and median of samples read counts (done by own scripts)
Genome_build: E.coli K-12 MG1655 / U00096.2
Supplementary_files_format_and_content: *_rpkMd.txt containing gene names and rpkMd values, tab seperated

organism: Escherichia coli str. K-12 substr. MC4100

source_name: E. coli MC4100, LB

growth_protocol: E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.3 or 0.4)

extract_protocol:
To isolate mRNA-bound ribosome complexes we used a previously described approach[Cozzone et al. 1973, J Mol Biol76, 163-179] with some modifications. Exponentially growing cells were poured over crushed ice containing 100 µg/ml chloramphenicol and harvested by centrifugation at 5000xg for 5 min at 4°C. All subsequent operations were carried out on ice with pre-chilled buffers. To obtain polysomal profiles, the cell pellet from 100 ml culture was resuspended in 12 ml of ice-cold sucrose-buffer solution (16 mM Tris pH 8.1 supplemented with 0.5 M RNase-free sucrose, 50 mM KCl, 8.75 mM EDTA, 100 µg/ml chloramphenicol, 1.25 mg/ml lysozyme) and gently stirred for 5 min on ice. 0.3 ml of 1M MgCl2 was added to inhibit lysozyme and the suspension was spun at 6000xg for 10 min at 4°C. The pellet was resuspended in 0.7 ml freshly prepared lysis buffer (10 mM Tris pH 7.8 containing 50 mM NH4Cl, 0.01 M MgCl2, 0.2% triton X-100, 100 µg/ml chloramphenicol and 10 U DNase I (RNase-free, Fermentas)). The lysate was clarified by centrifugation at 10000xg for 10min at 4°C and frozen at -80°C if not analysed immediately. Up to 0.4 ml of clarified lysate was layered onto 15 to 50% (w/v) sucrose gradient (buffered in 10 mM Tris pH 7.8 supplemented with 50 mM NH4Cl, 10 mM MgCl2, 0.2% triton X-100, 100 µg/ml chloramphenicol) and centrifuged for 1.5 h at 35,000 rpm in SW 55Ti rotor (Beckman) at 4°C. The gradient was slowly pumped out from the bottom of the tubes with a flow rate set to 0.38 ml/min and the absorbance at 254 nm (A254) was recorded via a flow-through UV spectrophotometer cell (Pharmacia LKB-UV-M II). For the isolation of RPFs, an aliquot of 100 A260 units of ribosome-bound mRNA fraction (prior to ultracentrifugation in the sucrose gradients, see above) was subjected to nucleolytic digestion with 10 units/µl micrococcal nuclease (Fermentas) for 10 min at room temperature in buffer with pH 9.2 (10 mM Tris pH 11 containing 50 mM NH4Cl, 10 mM MgCl2, 0.2% triton X-100, 100 µg/ml chloramphenicol and 20 mM CaCl2). The monosomal fraction was separated by sucrose density gradient (15-50% w/v). The total RNA was isolated from the monosomes using the hot SDS/phenol method. The micrococcal nuclease also cleaved the rRNAs into fragments with a size similar to the RPFs. The sample was enriched predominantly in one rRNA fragment which was removed by subtractive hybridization at 70 0C using a 5’-biotin-5’-GCCTCGTCATCACGCCTCAGCC-3’ DNA oligonucleotide along with µMACS Streptavidin Kit (Myltenyi Biotec) to remove the biotin-labeled DNA/rRNA hybrids.
Total RNA was isolated from ~ 6 ml exponentially growing bacteria with GeneJET™ RNAPurification Kit (Fermentas). Prokaryotic mRNA is a minor fraction of the total cellular RNA, therefore mRNAs were enriched by removal of 16S and 23S rRNAs[He et al. 2010, Nat Methods7, 807-812] with a MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). 20 µl of the enriched mRNA was mixed with equal volume of 2x alkaline fragmentation solution (2 mM EDTA and 100 mM Na2CO3 pH 9.2) and incubated for 40 min at 95 °C. The reaction was stopped by adding 560 µl 300 mM NaOAc pH 5.5, followed by isopropanol precipitation[Ingolia et al. 2010, Methods Enzymol470, 119-142]. For quantification[Jiang et al. 2011, Genome Res21, 1543-1551], after the random fragmentation the RNA sample was spiked with an external 25-nt RNA standard (5’-AAUGAUAAUUCAAGAAUCAUAACGG-3’) which does not align anywhere in the E. coli genome. Typically, 10 ng of spike-in RNA were added to 25.5 µg total extracted RNA. The optimal time for fragmentation of the mRNA was determined using GAPDH mRNA (0.25 µg; Fermentas) and the spectra were recorded with BioAnalyzer (Agilent RNA 6000 Kit). RNA-size selection and generation of the cDNA libraries was performed as described in [Guo et al. 2010, Nature466, 835-840]

treatment_protocol: For heat stress, an aliquot of cells grown in LB medium was centrifuged for 4 min at 4000xg at room temperature, resuspended in LB medium preheated to 47°C and further incubated for 7 min at 47°C. Osmotic stress was exerted to an aliquot of cells grown in MM medium by adding NaCl to 0.3M (0.6 Osm) and further incubated for 20 min at 37°C.

tag: growth media

value: LB

tag: type of stress

value: no

tag: assayed molecule

value: mRNA


title: heat RPF

description:
mRNA-Seq of ribosome protected fragments (RPF)
an aliquot of cells grown in LB medium was centrifuged for 4 min at 4000xg at room temperature, resuspended in LB medium preheated to 47°C and further incubated for 7 min at 47°C

source_name: E. coli MC4100, heat

value: heat stress 7 min 47°C

value: mRNA (ribosome protected)


title: MM RPF

description: mRNA-Seq of ribosome protected fragments (RPF)

source_name: E. coli MC4100, MM

value: MM medium (12.8 g/l Na2HPO4×7H2O, 3 g/l KH2PO4, 1 g/l NH4Cl, 2 mM MgSO4, 0.1 mM CaCl2, 0.4% glucose)

value: No / MM medium


title: osm RPF

description:
mRNA-Seq of ribosome protected fragments (RPF)
an aliquot of cells grown in MM medium by adding NaCl to 0.3M (0.6 Osm) and further incubated for 20 min at 37°C

source_name: E. coli MC4100, osm

value: osmotic stress 20min


title: heat mRNA

description:
mRNA-Seq
an aliquot of cells grown in LB medium was centrifuged for 4 min at 4000xg at room temperature, resuspended in LB medium preheated to 47°C and further incubated for 7 min at 47°C


title: MM mRNA

description: mRNA-Seq


title: LB RPF


title: LB mRNA

description: mRNA-Seq


title: CSrep2_hr09

source_name: GtaCC-S-GFP 8h developing ; replicate 1

value: GFP-GtaCC-S/gtaC-


title: NTHi 86-028NPrpsL∆fur rep3

city: Columbus

first: Alistair

last: Harrison

state: OH

address: 700 Children's Drive

department: Center for Microbial Pathogenesis

institute: The Research Institute at Nationwide Children's Hospital

data_processing:
Base calls and initial quality scoring of data produced by the Illumina HiSeq2000 were performed using Illumina RTA 1.12.4
Base call files were converted to fastq files using Illumina CASAVA 1.8.2
Read alignment was performed using Burrows-Wheelr Aligner v0.78 allowing up to four mismatches with multiple aligned reads counted only once
Processing the read alignemnt file was done using samtools v0.1.19 with default parameters
Gene expression measurement was determiend using NGSUtlis v.0.55 with default parameters
Differential gene expression analysis was performed using edgeR v3.6.1
Genome_build: NC_007146
Supplementary_files_format_and_content: Processed data for all strains is contained in a matrix in an excel spreadsheet. For each gene expression comparision there is logCounts/million reads, fold change calculation of gene expression, an FDR calculation, and a P-value for the associated comparison. Additionally for each open reading frame and RNA annotation there are raw counts in each strain and their associated biological replicate used in comparison.

organism: Haemophilus influenzae

source_name: Bacterial cells

growth_protocol: All strains were grown in an RPMI-based defined iron source medium, DIS. Strains were plated onto Chocolate II agar plates (Fisher Scientific) overnight. Cells from plates were diluted into DIS medium for the purpose of iron depletion and grown statically at 37˚C, 5% CO2 for 12-13 hours. Iron-depleted cells were transferred to DIS supplemented with 10µg human hemoglobin/ml and grown at 37˚C with shaking at 50rpm to mid-logarithmic phase.

extract_protocol:
Total RNA was extracted via hot phenol once bacterial cultures were in mid-logarithmic phase.
cDNA libraries were prepared using the Illumina TruSeq RNA sample prep kit according to the manufacturers protocol.

tag: strain background

tag: strain type

value: Nontypeable Haemophilus influenzae (NTHi)

value: isogenic fur mutant of 86-028NPrpsL


title: NTHi 86-028NPrpsL∆fur(pT-fur) rep1

value: complemented fur mutant strain


title: NTHi 86-028NPrpsL∆fur(pT-fur) rep2


title: NTHi 86-028NPrpsL∆fur rep2


title: NTHi 86-028NPrpsL∆fur(pT-fur) rep3


title: CSS rep2

city: Ithaca

first: Silin

last: Tang

address: Stocking Hall

department: Food Science

institute: Cornell University

description: Total RNA was treated with Ribo-ZeroTM rRNA Removal Reagents (Bacteria)-Low Input for removal of 16S and 23S ribosomal RNA

data_processing:
Raw data was generated by the Illumina pipeline software v1.8
the sequence reads were aligned to a H7858 pseudochromosome out using the Burrows-Wheeler Aligner (BWA), which allowed up to 2 mismatches per read. BWA parameters were set to include only perfect matches and map once reads, i.e., uniquely mapped reads are retained. The output was a SAM files for each sample. Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from BWA and convert them to BAM format. BAM files were converted to strand-specific base count files. Coverage at each base position along the chromosome was calculated by enumerating the number of reads that aligned to a given base for each DNA strand separately.
Differential expression of genes in different strains was statistically assessed using the BaySeq method implemented in the BaySeq 1.16.0 package available from Bioconductor. Genes were considered differentially expressed if they showed a false discovery rate (FDR) < 0.05 and a fold change (FC) ≥ 2.5 (meaning genes were upregulated on CSS) or FC ≤ 0.2 (meaning genes were downregulated on CSS).
Genome_build: H7858 pseudochromosome was constructed based on contigs available at NCBI Genbank under Accession: NZ_AADR00000000.1 / GI: 47094674
Supplementary_files_format_and_content:  Excel spreadsheet (.xlsx) file. Raw count data and normalized count data (from BaySeq output) for each coding gene in H7858. Locus names in H7858, F2365, EGD-e and 10403S are also provided as well as the function of the protein encoded. BaySeq result (likelihood of being differentially expressed and False Discovery Rate). Fold Changes (CSS/MBHIB) and whether the Fold Changes are above or below the thresholds (< 0.4 or > 2.5) are provided.

organism: Listeria monocytogenes

source_name: cold smoked slamon

growth_protocol: Defined media cultured L. monocytogenes was inoculated on cold smoked salmone (CSS) and in modified BHI broth (MBHIB) at approximately 1x106 CFU/ml or g and incubated for 7 days to late-log phase at 7oC before RNA extraction. Growth phase was determined by growth parameters generated by Buchannan model and growth curve information obtained from pilot growth experiments. Samples for RNA preparation were collected when the average cell density of collected L. monocytogenes samples were 8.17 ± 0.16 log(CFU/ml) for CSS and 8.28 ± 0.21 log(CFU/g) for MBHIB.

extract_protocol:
Total RNA was extracted by using RNA protect, proteinase K, and lysozyme, followed by Tri reagent with bead-beating. Total RNA was incubated with DNase in the presence of RNasin to remove remaining DNA.
Preparation of cDNA fragment libraries was performed using the ScriptSeqTM Complete Kit (Bacteria)-Low Input (Epicentre, Madison, WI), which is composed of Ribo-ZeroTM rRNA Removal Reagents (Bacteria)-Low Input, Magnetic Core Kit-Low Input, and ScriptSeqTM v2 RNA-Seq Library Preparation Kit.

tag: inoculated on

value: CSS

tag: growth stage

value: late log phase


title: CSS rep4

tag: strain


title: NTHi 86-028NPrpsL rep1

value: rpsL mutant of 86-028NP


title: NTHi 86-028NPrpsL∆fur rep1


title: NTHi 86-028NPrpsL rep2


title: NTHi 86-028NPrpsL rep3


title: MBHIB rep4

source_name: modified BHI broth

value: MBHIB


title: MBHIB rep3


title: LB RPF biological replicate

description:
mRNA-Seq of ribosome protected fragments (RPF)
biological replicate LB RPF


title: osm mRNA

description:
mRNA-Seq
an aliquot of cells grown in MM medium by adding NaCl to 0.3M (0.6 Osm) and further incubated for 20 min at 37°C


title: MBHIB rep1


title: PHH2_Diclofenac IonXpress_045

city: Basel

first: Jitao David

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

data_processing:
Base-calling, filtering, and alignment is handled automatically by IonTorrent Server Suite (version 4.0.2)
Amplicon coverage is reported by IonTorrent Server Suite (version 4.0.2) as a tab-delimited file, which was converted into GCT format by in-house scripts.
Genome_build: hg19
Supplementary_files_format_and_content: GCT

source_name: primary human hepatocytes

extract_protocol:
Cell were harvested 3h after test compound addition by removing the culture medium. Cell lysates in 50 µl RLT buffer (QIAGEN, Hombrechtikon, Switzerland) were immediately frozen and stored at -80°C.
10 ng of total RNA from each time point and biological replicate was reverse transcribed to cDNA and amplified by limited PCR according to the protocol supplied with the Ion AmpliSeq™ RNA Library Kit (Life Technologies, Carlsbad, USA, Catalog number 4482335). After primer digestion, adapters and barcodes were ligated to the amplicons followed by magnetic bead purification. The purified library was amplified, purified and stored at -20°C. Amplicon size and DNA concentration was measured using an Agilent High Sensitivity DNA Kit (Agilent Technologies, Waldbronn, Germany) according to the manufacturer's guide.

treatment_protocol: Cells were exposed to test compounds or vehicle (0.1% DMSO) after over-night pre-culture in William’s Medium E (Sigma-Aldrich, Buchs, Switzerland) supplemented with Penicillin/Streptomycin (Life Technologies, Zug, Switzerland).

tag: individual

value: primary human hepatocytes

value: Diclofenac

tag: rna conc

tag: library concentration


title: PHH2_Diclofenac IonXpress_043


title: PHH2_Compound_10uM IonXpress_042

value: Compound 10uM


title: PHH2_Compound_10uM IonXpress_040


title: PHH2_Compound_3uM IonXpress_039

value: Compound 3uM


title: PHH2_Diclofenac IonXpress_044


title: PHH2_Compound_1uM IonXpress_036

value: Compound 1uM


title: CSS rep3


title: PHH2_Compound_1uM IonXpress_035


title: CSS rep1


title: PHH2_Compound_10uM IonXpress_041


title: PHH2_Control IonXpress_031

value: Control


title: PHH2_Control IonXpress_032


title: PHH3_Compound_10uM IonXpress_026


title: PHH2_Compound_3uM IonXpress_037


title: PHH3_Diclofenac IonXpress_028


title: PHH3_Diclofenac IonXpress_029


title: PHH3_Compound_10uM IonXpress_027


title: PHH3_Compound_3uM IonXpress_023


title: PHH3_Control IonXpress_019


title: PHH3_Compound_1uM IonXpress_021


title: PHH2_Compound_1uM IonXpress_034


title: PHH3_Compound_1uM IonXpress_020


title: PHH3_Diclofenac IonXpress_030


title: PHH3_Compound_3uM IonXpress_022


title: MBHIB rep2


title: PHH3_Compound_10uM IonXpress_025


title: PHH3_Control IonXpress_018


title: PHH1_Diclofenac IonXpress_015


title: PHH1_Compound_10uM IonXpress_013


title: PHH3_Control IonXpress_017


title: PHH1_Compound_1uM IonXpress_010


title: PHH1_Compound_3uM IonXpress_012


title: PHH1_Compound_1uM IonXpress_009


title: PHH1_Control IonXpress_008


title: PHH1_Compound_3uM IonXpress_011


title: PHH2_Control IonXpress_033


title: PHH1_Control IonXpress_007


title: PHH1_Diclofenac IonXpress_005


title: HUVEC normoxia, rep3 [RNA-seq]

city: Hannover

first: Jan

last: Fiedler

address: Carl-Neuberg-Str. 1

department: Institute of Molecular and Translational Therapeutic Strategies (IMTTS), IFB-Tx

institute: Hannover Medical School

description:
Sample name: HUVEC-3
HUVECs cultured under normoxic condition for 24 h.
Processed data file: rawCountsLncipedia.txt
Processed data file: rawCountsEnsembl.txt

data_processing:
Reads were mapped on the hg19 genome via the STAR 2-pass method (version 2.3.0e_r291) with default parameters.
Potential splice junctions were extracted by the first mapping pass from all sequenced libraries and used to improve the second mapping pass.
Mapped reads were counted strand-specifically on the exon-level and subsequently summarized on the gene-level via featureCounts v1.4.3-p1 using the protein-coding genes of the EnsEMBL GRCh37 gene catalog for mRNA and the lncipedia 2.1 catalog for lncRNAs.
Genes were tested for differential expression using DESeq2 1.6.3, comparing fragment counts of the three hypoxia libraries to the three normoxia libraries.
Genes which resulted in Benjamini-Hochberg adjusted p-values < 0.05 were considered significant.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample.

source_name: Cell culture of HUVEC, normoxia

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVECs) were purchased from Lonza and cultured in EBM-2 (Lonza) supplemented with hEGF, hydrocortisone, VEGF, hFGF-B, R3-IGF-1, ascorbic acid, gentamicin/amphotericin-B and 10% FBS under standard cell culture conditions (37°C, 5% CO2).

extract_protocol:
rRNA was removed from the total RNA; RNA was fragmented into short fragments by the fragmentation buffer; cDNA was synthesized by random hexamer-primer; double-strand cDNA was purified with QiaQuick PCR extraction kit; sequencing adaptors were ligated to the fragments.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 24 h of normoxia or hypoxia (0.1-0.2%O2).

tag: culture condition

value: normoxia


title: HUVEC hypoxia, rep2 [RNA-seq]

description:
Sample name: HUVEC-5
HUVECs cultured under hypoxic condition for 24 h.
Processed data file: rawCountsLncipedia.txt
Processed data file: rawCountsEnsembl.txt

source_name: Cell culture of HUVEC, hypoxia

tag: cell type

value: Human Umbilical Vein Endothelial Cells (HUVECs)


title: PHH1_Compound_10uM IonXpress_004


title: PHH1_CPZ IonXpress_006

description:
IonXpress_006
Not used for the data analysis in the associated publication

value: CPZ


title: HUVEC normoxia, rep2 [RNA-seq]

description:
Sample name: HUVEC-2
HUVECs cultured under normoxic condition for 24 h.
Processed data file: rawCountsLncipedia.txt
Processed data file: rawCountsEnsembl.txt


title: HUVEC hypoxia, rep1 [RNA-seq]

description:
Sample name: HUVEC-4
HUVECs cultured under hypoxic condition for 24 h.
Processed data file: rawCountsLncipedia.txt
Processed data file: rawCountsEnsembl.txt


title: PHH1_Compound_3uM IonXpress_003


title: PHH1_Control IonXpress_001


title: PHH1_Compound_1uM IonXpress_002


title: SKmel147-xl-BRD2

data_processing:
ChIP-seq reads were analyzed with fastqc and the NGS-QC tool for quality control. All datasets passed the quality control tests.
Reads were aligned to the human genome assembly GRCh37/hg19 using Bowtie short read aligner 55 (version 0.12.7), with the following parameters: seed of 45 bp, maximum two mismatches, suppression (m)=20, --best option and reported alignments (k)=1.
Significant peak calling was performed using MACS2 (version 2.1.0) with a q- value cutoff of 1x10^-2, and the options --nomodel --extsize 300 were added.
Normalized read pileups were generated using MACS2 (version 2.0.10) peakcall tool (using --SPMR option) and fold enrichment over Input was calculated with MACS2 bdgcmp tool.
The number of reads within peaks was calculated using bedtools (version 2.17.0). The normalized number of reads within peaks or regions was calculated using DeepTools (version 1.5.7).
Genome_build: hg19
Supplementary_files_format_and_content: BED files include all the peaks calculated by MACS2
Supplementary_files_format_and_content: BigWig files include the RPKM fold enrichment of each sample over input.

source_name: SKmel147 melanoma cell line

growth_protocol: SK-mel147 were grown in 15cm^2 cell culture dishes on DMEM media with 10%FBS and antibiotics. Melanocytes were cultured in Melanocyte Growth Media 254 supplemented with Human Melanocyte Growth Supplement (Life Technologies)

extract_protocol:
For BRD2 and E2F1, 1-3x10^7 cells (SK-mel147 and SK-mel147 stably expressing control or isoform-specific shRNAs) were cross-linked, with 1% formaldehyde for 10 min at 25°C. Cells were resuspended and lysed for 10min at 4°C with ChIP lysis buffer (50mM Hepes-KOH, pH7.6, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% Igepal, 0.25% TritonX), washed in ChIP wash buffer (10mM Tris-HCl, pH8, 200mM NaCl, 1mM EDTA, and 0.5mM EGTA) for 10min at 4°C and resuspended in ChIP shearing buffer (10mM Tris-HCl pH8, 100mM NaCl, 1mMEDTA, 0.5mM EGTA, 0.1% w/v deoxycholic acid, and 0.5% w/v Lauroylsarcosine). Cells were aliquoted in Covaris AFA microtubes (~6.6x10^6 cells in 130 ul per tube) and sonicated using a Covaris E220 (Intensity 2, DC 5%, CPB 200, duration 840sec). Fragment size (200-400bp) was evaluated using Agilent Bioanalyzer 2100. Samples were then diluted to 1.5ml, TritonX was added to a final concentration of 1%, and pre- cleared with 30ul of Dynal Magnetic beads for 20min at 4°C. The antibodies were coupled to the magnetic beads for 12 hours in blocking buffer (0.5% FBS in PBS), incubation was performed for 12- 16 hours. Beads were subsequently washed 5 times using RIPA buffer (50mM Hepes-KOH, pH7.6, 300mM LiCl, 1mM EDTA, 1% NP-40 (IGEPAL), 0.7% Na-Deoxycholate) and once with Tris-EDTA (TE) buffer (50mM NaCl). Precipitated chromatin was eluted in 200ul of Elution buffer (50mM Tris-HCl pH8, 10mM EDTA, and 1% SDS), after 2 hours incubation at 65°C. Reverse cross-linking was carried out for 12 hours at 65°C. Chromatin was then treated with RNase A, for 2 hours at 37°C, and Proteinase K, at 56°C for 4 hours. DNA was purified with phenol/chloroform extraction followed by Chloroform/H2O extraction and MiniElute PCR purification tubes.
Total of 25ng ChIPed DNA was processed for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3’ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the Hi-Seq 2000 illumina platform.

tag: cell line

value: melanoma cell line

tag: genotype/variation

value: NRAS mutant Q61R

tag: chip antibody

value: BRD2 antibody

value: Bethyl Laboratories

tag: chip antibody cat. #


title: Skmel147_H2AZ.1-GFP_GFP ChIP

data_processing:
library strategy: native ChIP-seq
ChIP-seq reads were analyzed with fastqc and the NGS-QC tool for quality control. All datasets passed the quality control tests.
Reads were aligned to the human genome assembly GRCh37/hg19 using Bowtie short read aligner 55 (version 0.12.7), with the following parameters: seed of 45 bp, maximum two mismatches, suppression (m)=20, --best option and reported alignments (k)=1.
Significant peak calling was performed using MACS2 (version 2.1.0). For H2A.Z the --broad option was used, and the options --nomodel --extsize 300 were added. H2A.Z peaks were called with a q- value cutoff of 5x10^-3
Normalized read pileups were generated using MACS2 (version 2.0.10) peakcall tool (using --SPMR option) and fold enrichment over Input was calculated with MACS2 bdgcmp tool.
The number of reads within peaks was calculated using bedtools (version 2.17.0). The normalized number of reads within peaks or regions was calculated using DeepTools (version 1.5.7).
Genome_build: hg19
Supplementary_files_format_and_content: BED files include all the peaks calculated by MACS2
Supplementary_files_format_and_content: BigWig files include the RPKM fold enrichment of each sample over input.

source_name: SKmel147_GFP ChIP

extract_protocol:
Chromatin from SK-mel147 cells and eGFP-H2A, eGFP-H2A.Z.1 or eGFP-H2A.Z.2-transduced cells was digested with micrococcal nuclease (MNase) and used for ChIP with H2A.Z and GFP Trap Beads (Chromotek), essentially as described (Hasson et al., 2013). Sequencing libraries were generated and barcoded for multiplexing as previously described (Hasson et al., 2013) and resulting libraries were submitted for 100-bp, single-end Illumina sequencing on a HiSeq 2000 instrument.
Total of 25ng MNase-ChIPed DNA was processed for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3’ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the Hi-Seq 2000 illumina platform.

treatment_protocol: Lentiviral infections with eGFP-fused complementary DNA (cDNAs) encoding H2A, H2A.Z.1 and H2A.Z.2.

value: stably expressing eGFP-H2A.Z.1

value: GFP Trap Beads (Chromotek)


title: HUVEC hypoxia, rep3 [RNA-seq]

description:
Sample name: HUVEC-6
HUVECs cultured under hypoxic condition for 24 h.
Processed data file: rawCountsLncipedia.txt
Processed data file: rawCountsEnsembl.txt


title: Melanocytes_H2AZ ChIP

source_name: melanocytes_H2AZ ChIP

value: non tumorigenic (Melanocytes)

value: wild type

value: H2A.Z (Abcam ab4174) lot GR16709-1


title: SKmel147-xl-E2F1

value: E2F-1 Antibody (C-20)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody lot #


title: SKmel147-xl-Input


title: Mj_V3 [miRNA-Seq]

city: Atlanta

first: Greg

last: Gibson

state: Georgia

address: North Ave NW

department: School of Biology

institute: Georgia Institute of Technology

data_processing:
Analysis of sequence reads was performed using miRExpress (http://mirexpress.mbc.nctu.edu.tw/) and reads per million counts were obtained.
Log2 transformed reads per million counts were normalized by the Supervised Normalization of Microarray (SNM) algorithm with a model fitting individual's age and BMI as the biological variable, and removing effects of RNA quality, gender and ethnicity
Supplementary_files_format_and_content: tab-delimited text file including SNM normalized log2 reads per million counts for all samples

source_name: Whole blood

extract_protocol:
Peripheral blood samples (10ml) were collected into EDTA tubes that were frozen for DNA preservation, and Tempus RNA tubes (Life Technologies, Grand Island NY) for preservation of RNA.
Total RNA was isolated from Tempus tubes using the Life Technologies Tempus Spin RNA Isolation Kit following manufacturer's protocols.
Small RNA libraries were prepared using Illumina TruSeq Small RNA Sample Prep kits from total RNA following the manufacturer’s protocols.

tag: tissue

value: Whole blood

tag: gender

value: Male

tag: ethnicity

value: Caucasian


title: Skmel147_H2A-GFP_GFP control ChIP

source_name: SKmel147_GFP control ChIP

value: stably expressing eGFP-H2A


title: Mj_V1 [miRNA-Seq]


title: Skmel147_H2AZ.2-GFP_GFP ChIP

value: stably expressing eGFP-H2A.Z.2


title: Melanocytes_Input control

source_name: melanocytes_Input control


title: Ml_V1 [miRNA-Seq]


title: Ml_V2 [miRNA-Seq]


title: Mk_V2 [miRNA-Seq]


title: SKmel147_Input_control

source_name: SKmel147_Input control


title: HUVEC normoxia, rep1 [RNA-seq]

description:
Sample name: HUVEC-1
HUVECs cultured under normoxic condition for 24 h.
Processed data file: rawCountsLncipedia.txt
Processed data file: rawCountsEnsembl.txt

value: Human Umbilical Vein Endothelial Cells (HUVECs)

value: normoxia


title: Ml_V3 [miRNA-Seq]


title: Mi_V2 [miRNA-Seq]


title: Mi_V1 [miRNA-Seq]


title: Mi_V3 [miRNA-Seq]


title: Ch_V3 [miRNA-Seq]

value: Female


title: Ch_V2 [miRNA-Seq]


title: Cg_V2 [miRNA-Seq]


title: Cg_V3 [miRNA-Seq]


title: Mk_V1 [miRNA-Seq]


title: Skmel147_H2AZ_ChIP

source_name: SKmel147_H2AZ ChIP

value: melanoma cell line

value: NRAS mutant Q61R


title: Cf_V2 [miRNA-Seq]


title: Cf_V1 [miRNA-Seq]


title: Ce_V3 [miRNA-Seq]


title: Ml_V1 [RNA-Seq]

data_processing:
All short reads were aligned to HuRef19 using the TopHat spliced-reads fast mapper in Cufflinks v2.0.1. FPKM (fragments per kilobase of exon per millions) values were obtained and log2 transformed.
Log2 transformed FPKM values were normalized by the Supervised Normalization of Microarray (SNM) algorithm with a model fitting individual's age and BMI as the biological variable, and removing effects of RNA quality, gender and ethnicity
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including SNM normalized log2 FPKM values for all samples

extract_protocol:
Peripheral blood samples (10ml) were collected into EDTA tubes that were frozen for DNA preservation, and Tempus RNA tubes (Life Technologies, Grand Island NY) for preservation of RNA.
Total RNA was isolated from Tempus tubes using the Life Technologies Tempus Spin RNA Isolation Kit following manufacturer's protocols.
Unstranded TruSeq cDNA libraries were prepared using Illumina TruSeq RNA Sample Prep kits (Set A, v2) from total RNA following the manufacturer’s protocols.


title: Ce_V2 [miRNA-Seq]


title: Ml_V3 [RNA-Seq]


title: Cf_V3 [miRNA-Seq]


title: Mj_V2 [miRNA-Seq]


title: Ad_V2 [miRNA-Seq]

value: African American


title: Mk_V3 [RNA-Seq]


title: Ad_V3 [miRNA-Seq]


title: Ce_V1 [miRNA-Seq]


title: Ab_V3 [miRNA-Seq]


title: Mk_V2 [RNA-Seq]


title: Ac_V2 [miRNA-Seq]


title: Mk_V1 [RNA-Seq]


title: Mj_V2 [RNA-Seq]


title: CM_CtermGFP_hr04

source_name: GtaC-GFP 3h developing ; replicate 2

treatment_protocol: ChIP-seq: development on nitrocellulose filters placed on a buffer-soaked filter paper pad, cells were washed twice with potassium phosphate buffer (KK2) and deposited on nitrocellulose filter 3.3x106 cells/cm5

tag: genotype

value: GFP-GtaC/gtaC-

tag: replicate

tag: developmental time


title: Mj_V3 [RNA-Seq]


title: Ab_V1 [miRNA-Seq]


title: Cg_V1 [miRNA-Seq]


title: Aa_V3 [miRNA-Seq]


title: Aa_V1 [miRNA-Seq]


title: Mj_V1 [RNA-Seq]


title: Ab_V2 [miRNA-Seq]


title: Mi_V2 [RNA-Seq]


title: Mi_V1 [RNA-Seq]


title: Ch_V3 [RNA-Seq]


title: Mi_V3 [RNA-Seq]


title: Ch_V2 [RNA-Seq]


title: Ch_V1 [RNA-Seq]


title: Cg_V3 [RNA-Seq]


title: Cf_V1 [RNA-Seq]


title: Cg_V1 [RNA-Seq]


title: Cf_V2 [RNA-Seq]


title: Cf_V3 [RNA-Seq]


title: Ce_V3 [RNA-Seq]


title: Ce_V2 [RNA-Seq]


title: Ad_V3 [RNA-Seq]


title: Ce_V1 [RNA-Seq]


title: Ad_V2 [RNA-Seq]


title: Ac_V3 [RNA-Seq]


title: Ac_V2 [RNA-Seq]


title: Ab_V3 [RNA-Seq]


title: Ac_V1 [RNA-Seq]


title: Aa_V3 [RNA-Seq]


title: Ab_V1 [RNA-Seq]


title: Aa_V2 [RNA-Seq]