title: ES.2

city: Beijing

first: Runsheng

last: Chen

address: 15 Datun Road, Chaoyang District

department: CAS Key Laboratory of RNA Biology

institute: Institute of Biophysics, Chinsese Academy of Sciences

data_processing:
Reads were trimmed by Trimmomatic-0.36
Then reads were aligned to mouse reference genome mm10 by STAR
Cufflinks was used to assemble transcripts and calculate the abundances
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: mouse embryonic stem cell

growth_protocol: Mouse ESCs were grown on C57/BL6 mouse MEFs treated with mitomycin C. mESCs were cultured in DMEM supplemented with 15% FBS (Invitrogen, USA), 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 1 mM nucleotide, 0.1 mM non-essential amino acids and 103 units/ml mouse leukemia inhibitory factor (LIF). MEFs were isolated from E14.5 embryos of C57/BL6 mice and cultured in DMEM supplemented with 15% FBS (Invitrogen, USA) and 2 mM L-glutamine .

extract_protocol:
RNA was harvested using Trizol reagent.VAHTS Total RNA-seq Library Prep Kit (CatNR603) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols.

treatment_protocol: LIF were induced from ESCs by LIF withdrawal for 2 days. EBs were induced from ESCs by LIF withdrawal for 5 days.


title: LIF

status: Public on Jan 12 2017

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: LIF; induced from ESCs by LIF withdrawal for 2 days

tag: strain

tag: cell type


title: B1_mel

city: Leipzig

first: Edith

last: Willscher

address: Haertelstraße 16-18

country: Germany

institute: IZBI

description:
single cell
processed data file: GSE81383_data_melanoma_scRNAseq_BT_2015-07-02.txt.gz, GSE81383_data_melanoma_scRNAseq_BT_Mel.txt.gz

data_processing:
Raw reads were processed using a custom script and aligned to a Bowtie2 (Langmead and Salzberg, 2012) indexed human genome (grch38 sourced from ENSEMBL) using TopHat (Trapnell et al., 2009) with default settings.
Transcript levels were quantified as fragments per kilobase of mapped reads (FPKM) generated by Cufflinks (Trapnell et al., 2010) using gencode protein coding genes (grch38 v22 Havana).
We excluded cells that did express neither of two housekeeping genes ACTB and GAPDH. Ninety-two single cells remained for the transcriptome analysis.
Genome_build: grch38 sourced from ENSEMBL
Supplementary_files_format_and_content: FPKM values. The file GSE81383_data_melanoma_scRNAseq_BT_Mel.txt.gz contains the FPKM values for all samples. GSE81383_data_melanoma_scRNAseq_BT_2015-07-02.txt.gz contains the FPKM values for GSM2151479 - GSM2151570.

organism: Homo sapiens

source_name: subcutaneous metastasis

growth_protocol: melanoma short-term culture Ma-Mel-123

extract_protocol:
Single melanoma cells from short-term cultures were captured on an integrated fluidic circuit RNA-seq chip (Fluidigm, Hamburg, Germany) using the Fluidigm C1 system. Cells were loaded onto the chip at a concentration of 200 cells/μL and imaged by phase-contrast. Cell capture, cell lysis, reverse transcription, and cDNA amplification were performed on the chip as described (Camp et al., 2015).
Illumina libraries were constructed using the Illumina Nextera XT DNA Sample Preparation kit using the protocol supplied by Fluidigm. Ninety-six libraries were pooled (3 µL each) and purified with SPRI beads. Library concentration and size distribution were assessed on an Agilent Bioanalyzer and with Qubit dsDNA HS Assay kits and a Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Invitrogen, Darmstadt).  Each cell was paired-end sequenced (100 base reads) on an Illumina HiSeq 2500 to a depth of 2–5 million reads and base-calling, adaptor trimming, and de-multiplexing were performed as described (Renaud et al., 2013; Renaud et al., 2015).

tag: tissue

value: skin (melanoma metastasis)

tag: culture

value: melanoma short-term culture Ma-Mel-123

tag: melanoma genetic conditions

value: double-negative for BRAF and NRAS mutations


title: B6_mel


title: EB

source_name: embryoid body; induced from ESCs by LIF withdrawal for 5 days


title: A12_mel


title: A7_mel


title: A10_mel


title: A6_mel


title: ES.1


title: A8_mel


title: A9_mel


title: A4_mel


title: A5_mel


title: B7_mel


title: A3_mel


title: A1_mel


title: A2_mel


title: B2_mel


title: PB119_input

city: Salt Lake CIty

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

country: USA

institute: University of Utah

library_source: genomic

data_processing:
Sequence reads in fastq format were aligned to mm10 using bowtie with the following parameters: -m 1 -t --best -q -S -l 32 -e 80 -n 2
Sam alignments were converted to sorted bams using samtools
Peaks were called with MACS2 using a p-value cutoff of 1e-10 and the mfold parameter bounded between 15 and 100
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files inlcude peak calls in xls format from MACS2

molecule: genomic DNA

extract_protocol:
20 million cells per ChIP were crosslinked in 1% formaldehyde for 10 minutes at room temperature.  Crosslinking was stopped with 125 mM Glycine and nuclei were extracted.
Chromatin was sonicated using an Epishear Probe Sonicator (Active Motif) for 4 minutes at 40% power. c-MYC (D3N8F) antibody (Cell Signaling Technology) was used for immunoprecipitation and an input sample for each cell line served as the control. Libraries were constructed using a standard Illumina library construction protocol.

tag: antibody


title: PB120_input


title: A11_mel


title: PB120_Myc_ChIP-seq

value: c-MYC (D3N8F, Cell Signaling Technology)


title: PB115_Myc_ChIP-seq


title: PB119_Myc_ChIP-seq


title: Latrunculin B, actin destabilization or DMSO

city: Geneva

first: Pauline

last: Gosselin

address: Science II, 30 quai Ernest-Ansermet

department: Molecular Biology

country: Switzerland

institute: University of Geneva

description:
drug+DMSO treated samples are combined in each library
lib5
library strategy: Custom procedure, details in the manuscript

data_processing:
Conversion to FASTA
The luciferase 3’ UTR was clipped away starting from the XbaI site, isolating the 3’ end of the barcode. [Clipping Adapter: TCTAGAGTCG] FASTX-toolkit.
Clipped FASTA files were demultiplexed using the barcode splitter tool: on the 5’, the identifier sequence (index) was used to assign every read to its original sample. Barcode splitter (allowed mismatches: 2; allowed deletions: 2) I found that it works better when I give a bigger sequence to retrieve: NNNNNNCAAGATCGCC, where NNNNNN is my index (FASTX-toolkit).
demultiplexed FASTA files were trimmed from position 27 to 46 to isolate the barcode region. (FASTX-toolkit) Trimming: first base to keep 27; last base to keep: 46. This is done for each split. If every thing works properly I should have now 20 bp reads that are my barcodes.
trimmed barcodes were counted using FASTA collapse, converted to tabular, and joined together in a table containing the barcode sequence in the first column and the barcode counts for each sample in the other columns
Genome_build: na
Supplementary_files_format_and_content: [.tabular] text tabulated files containing the barcode sequence in the first column and the barcode counts for each sample in the other columns. The data are measures of promoter activity in response to the different drugs at various timepoints.
Columns in lib3, 7, 5, 4 are:  1.drug T0; 2.drug T0,5h; 3.drug T1h; 4.drug T2h; 5.drug T4h; 6.drug T8h; 7.DMSO T0; 8.DMSO T1h; 9.DMSO T2h; 10.DMSO T8h.
Columns in lib 8 are:  1.DMSO T0; 2.DMSO T1h; 3.DMSO T2h; 4.DMSO T4h; 5.DMSO T8h; 6.Jasp T0; 7.Jasp T1h; 8.Jasp T2h; 9.Jasp T4h; 10.Jasp T8h; 11.Vb T0; 12.Vb T1h; 13.Vb T2h; 14.Vb T4h; 15.Vb T8h

source_name: U2OS cells transfected with synthetic library, drug-treated

growth_protocol: Cells were cultivated in standard DMEM supplemented with 10% FBS

extract_protocol:
RNA was extracted by Trizol, and purified by LiCl precipitation
RNA corresponding to STAR-PROM luciferase was reverse transcribed and the barcode region amplified by PCR

treatment_protocol: After 24h serum starvation, cells were treated with either DMSO or the drug

tag: cell line

value: osteosarcoma U2OS cell line

tag: drug

value: Latrunculin B or DMSO


title: Vinblastine, tubulin destabilization or DMSO

description:
drug+DMSO treated samples are combined in each library
lib3
library strategy: Custom procedure, details in the manuscript

value: Vinblastine or DMSO


title: Biological duplicate Jasplakinolide and Biological duplicate Vinblastine or DMSO

description:
drug+DMSO treated samples are combined in each library
lib8
library strategy: Custom procedure, details in the manuscript

value: Jasplakinolide or Vinblastine or DMSO


title: adult_Lgr5-ISCs_rep3

status: Public on Jan 11 2017

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

institute: Institute of Molecular Biology, Mainz

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with STAR_2.3.1z13_r470 onto the iGenomes mm9 reference
Secondary alignments were filtered with samtools 1.2
Counts for every gene were calculated with HTSeq-0.6.1p1 using the gene model provided with the iGenomes mm9 reference from 2013-03-06
Counts were normalized and modeled with DESeq2_1.6.3
Genome_build: mm9
Supplementary_files_format_and_content: tab separated file containing counts per gene

molecule: polyA RNA

source_name: Lgr5+ adult intestinal stem cells_P60

extract_protocol:
250 EpCAM+, Lgr5+EpCAM+, EpCAM- (mesenchymal) embryonic intestinal cells and Lgr5-EGFPhigh ISCs were isolated by FACS directly in 7ml of lysis buffer (Clontech) supplemented with 5% RNase inhibitor and stored at -80°C. For each replicate, RNA was isolated from either single embryos (E11.5) or pools of 6–12 embryos (E13.5). PolyA+ mRNA was used for cDNA synthesis using SMARTer v3.0 kit (Clontech) according to manufacturer’s instructions. Amplification was performed for 15 cycles.
After cDNA fragmentation (Covaris), libraries were prepared using Ovation Ultralow Library System (NuGEN) according to manufacturer’s instructions.
RNA-seq, single end 50 bp

value: mixed C57BL/6 CD1

value: small intestine

tag: developmental stage

value: post natal day 60


title: adult_Lgr5-ISCs_posterior_Id2KO_rep1

source_name: Lgr5+ adult intestinal stem cells_P60 posterior third of the small intestine from Id2KO


title: adult_Lgr5-ISCs_rep1


title: adult_Lgr5-ISCs_rep4


title: adult_Lgr5-ISCs_anterior_Id2KO_rep1

source_name: Lgr5+ adult intestinal stem cells_P60 anterior third of the small intestine from Id2KO


title: adult_Lgr5-ISCs_rep2


title: Jasplakinolide, actin stabilization or DMSO

description:
drug+DMSO treated samples are combined in each library
lib4
library strategy: Custom procedure, details in the manuscript

value: Jasplakinolide or DMSO


title: adult_Lgr5-ISCs_posterior_wt_rep2

source_name: Lgr5+ adult intestinal stem cells_P60 posterior third of the small intestine


title: adult_Lgr5-ISCs_middle_Id2KO_rep1

source_name: Lgr5+ adult intestinal stem cells_P60 middle third of the small intestine from Id2KO


title: adult_Lgr5-ISCs_middle_wt_rep2

source_name: Lgr5+ adult intestinal stem cells_P60 middle third of the small intestine


title: adult_Lgr5-ISCs_middle_wt_rep1


title: SEM_2umEPZ5676_Rep1

city: Oxford

first: Thomas

last: Milne

address: John Radcliffe Hospital

department: Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

description: processed data file: EPZ5676_rpkm.txt

data_processing:
ChIP-seq reads were aligned to the hg18 genome using bowtie version 1.1.2 with following parameters: p1 m2 best strata sam
Peaks were called using SeqMonk version 0.24.1
Nascent RNA-seq reads were aligned to the hg18 genome using STAR
Read counts were determined using featureCounts (Subread package)
Genome_build: hg18
Supplementary_files_format_and_content: bed files were generated from text files outputted directly from SeqMonk; Rpkm tables (.txt) were generated using edgeR

source_name: Leukemia cell line (SEM)

growth_protocol: SEM cells were continuously grown in IMDM with 10-20% FBS, split when they reached a density of 1-2X10e6 down to 5X10e5; all other cell lines were grown in a similar manner in RPMI 1640.

extract_protocol:
ChIP-seq: Fixed cells were lysed in 1% SDS lysis buffer. Samples were sonicated and protein-DNA complexes were isolated with antibody.
Nascent RNA-seq: 108 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
Libraries were prepared according to Illumina's protocol accompanying the DNA Library Prep Master Mix Set (Part# E6040) or Ultra RNA Library Prep Master Mix Set (Part# E7530).

value: Leukemia cell line; SEM

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

tag: treated with

value: 2µM EPZ-5676 for 7 days

tag: molecule subtype

value: nascent RNA


title: adult_Lgr5-ISCs_anterior_wt_rep1

source_name: Lgr5+ adult intestinal stem cells_P60 anterior third of the small intestine


title: adult_Lgr5-ISCs_posterior_wt_rep1


title: adult_Tomato+Lgr5-ISCs_posterior_Id2KO_rep2

source_name: Tomato+Lgr5+ adult intestinal stem cells_P60 posterior third of the small intestine from Id2KO


title: adult_Tomato+Lgr5-ISCs_posterior_Id2KO_rep1


title: Paclitaxel (Taxol), tubulin stabilization or DMSO

description:
drug+DMSO treated samples are combined in each library
lib7
library strategy: Custom procedure, details in the manuscript

value: Paclitaxel (Taxol) or DMSO


title: adult_Lgr5-ISCs_posterior_Id2KO_rep2


title: adult_Lgr5-ISCs_middle_Id2KO_rep2


title: PB115_input


title: EpCAM+_E13.5_intestinal epithelium_rep4

source_name: EpCAM+ embryonic intestinal epithelial cells_E13.5

value: embryonic day 13.5


title: adult_Lgr5-ISCs_anterior_Id2KO_rep2


title: EpCAM+_E13.5_intestinal epithelium_rep3


title: EpCAM+_E13.5_intestinal epithelium_rep2


title: Lgr5-EGFP+EpCAM+_E13.5_intestinal epithelium_rep4

source_name: Lgr5-EGFP+EpCAM+ embryonic intestinal epithelial cells_E13.5


title: adult_Lgr5-ISCs_anterior_wt_rep2


title: Lgr5-EGFP+EpCAM+_E13.5_intestinal epithelium_rep3


title: Lgr5+EpCAM+_E11.5_intestinal epithelium_Id2KO_rep3

source_name: Lgr5-EGFP+EpCAM+ embryonic intestinal epithelial cells_E11.5 from Id2KO

value: embryonic day 11.5


title: Mes_wt_E11.5_intestinal mesenchyme_rep2

source_name: intestinal mesenchyme_E11.5


title: Mes_wt_E11.5_intestinal mesenchyme_rep1


title: Mes_E11.5_intestinal mesenchyme_Id2KO_rep2

source_name: intestinal mesenchyme_E11.5 from Id2KO


title: Lgr5-EGFP+EpCAM+_E13.5_intestinal epithelium_rep2


title: Mes_E11.5_intestinal mesenchyme_Id2KO_rep3


title: Mes_wt_E11.5_intestinal mesenchyme_rep3


title: EpCAM+_E11.5_intestinal epithelium_wt_rep1

source_name: EpCAM+ embryonic intestinal epithelial cells_E11.5


title: Lgr5+EpCAM+_E11.5_intestinal epithelium_Id2KO_rep2


title: EpCAM+_E11.5_intestinal epithelium_wt_rep3


title: EpCAM+_E11.5_intestinal epithelium_wt_rep2


title: Lgr5+EpCAM+_E11.5_intestinal epithelium_Id2KO_rep1


title: Mes_E11.5_intestinal mesenchyme_Id2KO_rep1


title: Kc167_Hi-C_replicate

city: Houston

first: Kyle

last: Eagen

state: TX

address: 1 Baylor Plaza

department: Department of Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
Platforms: Illumina NextSeq 500, HiSeq X Ten
Platforms: Illumina NextSeq 500 (used to generate majority of raw files), HiSeq X Ten

data_processing:
Reads were mapped to dm3/BDGP Release 5 of the Drosophila melanogaster genome using BWA-MEM.
Reads were assigned to DpnII restriction fragments, duplicates removed, reads with a MAPQ < 30 removed, and intra-fragment reads removed.
Genome was then divided into equally spaced bins.
To account for the uncertainty in the location of the position of the cross-link within each restriction fragment,the read position was radnomized within the restriction fragment each read mapped to and the resulting contact was assigned to its respective genomic bin.
Hi-C contact maps were normalized by matrix balancing using the KR normalization algorithm (Durand et al., 2016; Knight and Ruiz, 2012; Rao et al., 2014).
Biological replicates combined after filtering, intrafragment read positions randomized as described above, and the combined contact map KR normalized.  All subsequent analysis was performed on the combined, KR normalized contact map.
TADs were identified using the previously described Arrowhead algorithm (Durand et al., 2016; Rao et al., 2014), with an additional post-processing step:  TADs were identified at 5 kb, 2 kb, 1 kb, and 500 bp resolution using the Arrowhead algorithm, merged into a single list sorted by decreasing corner score, and conflicts, defined as the boundary of one TAD being located within another TAD, resolved by using the greater corner score of any conflicting TADs.
Loops were annotated by visual identification of focal peaks of contact enrichment using Juicebox (Durand et al., 2016).
All of the above steps were performed using the previously described Juicer pipeline (Durand et al., 2016; Rao et al., 2014) and Juicebox visualization interface (Durand et al., 2016).
Genome_build: dm3
Supplementary_files_format_and_content: *.hic file of Hi-C contacts in compressed format.  Readable by open-source Juicebox software (http://aidenlab.org/juicebox/).
Supplementary_files_format_and_content: *_randomized.hic file of Hi-C contacts in compressed format after read positions were randomized within the restriction fragment to which each read was assigned.  Readable by open-source Juicebox software (http://aidenlab.org/juicebox/).
Supplementary_files_format_and_content: Kc167combined_TADs.txt file of TAD calls from combined biological replicates in Juicebox format.  The column headers x1 x2 y1 y2 represent the boundaries of the TAD in genomic coordinates.
Supplementary_files_format_and_content: Kc167combined_loops.txt file of loop calls from combined biological replicates in Juicebox format.  The column headers x1 x2 represent the position of the loop anchor closer to the start of the chromosome; y1 y2 represent the position of the loop anchor closer to the end of the chromosome.

organism: Drosophila melanogaster

source_name: Kc167 cultured cells

growth_protocol: Kc167 cells were obtained from the Drosophila Genomics Resource Center (Bloomington, IN).  Cells were grown in CCM3 media (HyClone) at 25° C following Drosophila Genomics Resource Center protocols.

extract_protocol:
Cross-linked chromatin was released by detergent lysis and Dounce homogenization.  Cross-linked proteins were then biotinylated at cysteine residues and the DNA digested with DpnII.  Digested chromatin was bound to streptavidin beads, thoroughly washed to remove uncross-linked DNA, DNA ends filled in with biotin-14-dATP, and free DNA ends ligated together.  DNA-protein cross-links were reversed, DNA purified, and biotinylated nucleotides marking unligated ends removed.
DNA sheared to a size of approximately 500 bp.  DNA was end-repaired and adaptor-ligated by following “NEBNext End Prep” and “Adaptor Ligation” in the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).  The biotinylated DNA was pulled down with streptavidin beads and PCR amplified by following "PCR Amplification" in the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: 1 billion Kc167 cells at a density of 4-6 x 10^6 cells/mL were washed with 20 mL CMM3 media and then cross-linked with 1% EM-grade paraformaldehyde.

value: embryonic


title: EpCAM+_E11.5_intestinal epithelium_Id2KO_rep2

source_name: EpCAM+ embryonic intestinal epithelial cells_E11.5 from Id2KO


title: EpCAM+_E11.5_intestinal epithelium_Id2KO_rep1


title: EpCAM+_E11.5_intestinal epithelium_Id2KO_rep3


title: Kc167_Hi-C_primary

description: Platforms: Illumina NextSeq 500 (used to generate majority of raw files), HiSeq X Ten


title: EpCAM+_E13.5_intestinal epithelium_rep1


title: Zfp407 transgenic sample 954

city: Cleveland

first: Alyssa

last: Charrier

state: OH

address: 2109 Adelbert RT400D

institute: Case Western Reserve University

description:
Sample_954
Processed data file: All_Genes_ZnfTG_Muscle_DESeq2_38.txt

data_processing:
Reads were aligned to the mouse genome (Ensembl GRCm38.82, GenBank Assembly ID GCA_000001635.6) using TopHat v2.1, SamTools v1.2 and Bowtie v2.2.6.
Gene expression count tables were generated using HTSeq v0.6.1.
Gene expression count tables were analyzed using DESeq2 v1.10.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: All_genes_ZnfTG_Muscle_DESeq2_38.txt: Tab-delimited text file containing RPKM values for wildtype or Zfp407 transgenic muscle samples.

source_name: Biceps femoris skeletal muscle, Zfp407 transgenic

extract_protocol:
Muscle was homogenized by rotor-stator in Trizol. RNA was isolated using Life Technologies PureLink RNA isolation kit with on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 5-week-old male mice were maintained on normal chow and fasted overnight for 16 hours.

tag: strain/background

tag: genotype/variation

value: Zp407 transgenic

value: biceps femoris skeletal muscle

tag: Sex

value: male

tag: age

value: 5 weeks


title: Wild type sample 955

description:
Sample_955
Processed data file: All_Genes_ZnfTG_Muscle_DESeq2_38.txt

source_name: Biceps femoris skeletal muscle, WT

value: wild type


title: Wild type sample 956

description:
Sample_956
Processed data file: All_Genes_ZnfTG_Muscle_DESeq2_38.txt


title: Zfp407 transgenic sample 914

description:
Sample_914
Processed data file: All_Genes_ZnfTG_Muscle_DESeq2_38.txt


title: Zfp407 transgenic sample 915

description:
Sample_915
Processed data file: All_Genes_ZnfTG_Muscle_DESeq2_38.txt


title: Wild type sample 927

description:
Sample_927
Processed data file: All_Genes_ZnfTG_Muscle_DESeq2_38.txt


title: Lgr5-EGFP+EpCAM+_E13.5_intestinal epithelium_rep1

value: mixed C57BL/6 CD1


title: Zfp407 transgenic sample 913

description:
Sample_913
Processed data file: All_Genes_ZnfTG_Muscle_DESeq2_38.txt


title: Wild type sample 912

description:
Sample_912
Processed data file: All_Genes_ZnfTG_Muscle_DESeq2_38.txt


title: Wild type sample 911

description:
Sample_911
Processed data file: All_Genes_ZnfTG_Muscle_DESeq2_38.txt


title: CB5 (input)

city: New York

first: Laura

last: Pasqualucci

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the human genome (UCSC hg19) for human GC B cells using the Bowtie2 aligner v2.1.0, allowing up to two mismatches. Duplicate reads (i.e. reads of identical length mapping to exactly the same genomic locations) were removed with samtools v0.1.19 using the rmdup option.
Reads were normalized to total reads aligned (counts per million). Peak detection was done using ChIPseeqer v2.0, enforcing a minimum fold change of 2 between ChIP and input reads, a minimum peak width of 100 bp, and a minimum distance of 100 bp between peaks.
The threshold for statistical significance of peaks was set at 10E-12 for CREBBP and 10E-15 for H3K27Ac
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files contain peak locations. Columns 1, 2, and 3 contain the chromosome, start, and end position of the peak respectively. The fourth column is the maximum peak height normalized per million mapped reads in each library.

source_name: germinal center B cells from human reactive tonsil

growth_protocol: Tonsillar germinal center B cells were isolated by  magnetic cell separation (CD38high, CD77+), as described in Klein et al, Proc Natl Acad Sci U S A, 2003.

extract_protocol:
Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200-500bp.
ChIP-seq libraries were constructed starting from 4ng of ChIP or Input DNA as reported in Blecher-Gonen et al., 2013, Nature protocol. Libraries were quantified using the KAPA SYBR FAST Universal qPCR Kit (KAPA Biosystems), normalized to 10nM, pooled and sequenced in an Illumina HiSeq 2500 instrument as single-end 101 bp reads, obtaining on average 25x10^6 reads/sample.

treatment_protocol: Purified cells were cross-linked with 1% formaldehyde for 10 min at room temperature, quenched by the addition of glycine to a final concentration of 0.125 M, and snap frozen. Two independent pools of GC cells, each comprising 3-5 donors, were used in the ChIP experiment

value: tonsil

value: germinal center B cell

tag: chip antibody


title: CB4 (input)


title: CB5_CREBBP

value: Santa Cruz-CBP Ab (A22)-sc369 (Rabbit polyclonal)


title: Zfp407 transgenic sample 928

description:
Sample_928
Processed data file: All_Genes_ZnfTG_Muscle_DESeq2_38.txt


title: S3: pA RNA Donor 1 CD3/CD28

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road

department: Biochemistry

institute: University of Iowa

data_processing:
Raw paired sequences were first trimmed to remove Illumina sequencing adapters and Bioo Scientific randomized 8-mer molecular indexes using Trim Galore! 0.4.1 (--quality 0 --illumina --paired --clip_R1 9 --clip_R2 9 --three_prime_clipR1 9 --three_prime_clipR2 9)
Trimmed paired sequences were aligned to hg19 using TopHat 2.1.0 (--library-type fr-firststrand --no-discordant --no-mixed)
PCR duplicates were removed by searching for identical fragments with identical randomized 8-mer molecular indexes (see Bioo Scientific product information)
For RNA-Seq tracks, aligned reads were compiled using bedtools 2.25.0 function genomecov (-split)
Resulting tracks were normalized by dividing the number of hg19-mapped reads within each sample by the average number of hg19-mapped reads across all nine samples
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files represent normalized stranded polyA RNA-Seq human-mapping reads and can be visualized over hg19.

source_name: Uninfected central memory T cells cultured from peripheral blood mononuclear cells from three separate donors

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen 15596) and polyadenylated RNA was enriched using NEXTflex Poly(A) Beads (Bioo Scientific 512980)
Stranded libraries were prepared using a NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific 5130-02D)

tag: treatment

value: 24 h antiCD3/CD28-coated beads


title: S1: pA RNA Donor 1 IL-2

description: BigWig files represent normalized stranded polyA RNA-Seq human-mapping reads and can be visualized over hg19.


title: S2: pA RNA Donor 1 HODHBt

value: 24 h IL-2 + 100 micromolar HODHBt


title: S4: pA RNA Donor 2 IL-2


title: CB4_CREBBP


title: CB5_H3K27Ac

value: Active Motif-Histone H3K27Ac (Rabbit polyclonal)


title: CB4_H3K27Ac


title: S6: pA RNA Donor 2 CD3/CD28


title: S5: pA RNA Donor 2 HODHBt


title: S7: pA RNA Donor 3 IL-2


title: S9: pA RNA Donor 3 CD3/CD28


title: S8: pA RNA Donor 3 HODHBt


title: AS: STAT5A ChIP DMSO/-

data_processing:
Raw paired sequences were aligned to hg19 using Bowtie 2.2.6 (--no-mixed --no-discordant --reorder)
Human-mapped reads were compiled using MACS 2.0.10 (--format BAMPE --bdg), normalized by dividing the number of hg19-mapped reads within each sample by the average number of hg19-mapped reads across all six samples, and converted into bigWigs for visualization on hg19
Unmapped sequences where both mates failed to map to hg19 (SAM flags 77 or 141) were paired-end aligned to the pNL4-3 HIV-1 genome using Bowtie 1.1.1 (-v 3 -m 2 --all --offbase 1 --maxins 2000) and unaligned sequences were saved (--un)
Sequences which failed to map to pNL4-3 were then trimmed from the 5' end to 36 bp and realigned to attempt to identify sequences whose 125 bp spanned both hg19 and HIV sequences (--trim5 90); hits were confirmed by manually querying BLASTn to both human- and HIV-mapping portions
Unmapped sequences whose mate aligned to hg19 (SAM flags 69 or 133) were also aligned to the pNL4-3 HIV-1 genome using Bowtie 1.1.1 and single-end settings
All HIV-aligned fragments within 90 bp of an LTR boundary (LTRs are 1-634 and 9076-9709) were checked to determine if they mapped concordantly and were under 2000 bp; fragments which could not be uniquely assigned to either 5' or 3' LTR are represented twice in the processed files (5' LTR is red; 3' LTR is blue)
The resulting HIV-aligned fragments were compiled into bigBeds whose chromosome fields are set to “chr1” to enable visualization on hg19 from 1-9709
Genome_build: hg19
Genome_build: HIV-1 pNL4-3
Supplementary_files_format_and_content: BigBed files represent fragments over the pNL4-3 HIV-1 genome and can be visualized over hg19 chr1:1-9709. BigWig files represent normalized human-mapping reads and can be visualized over hg19.

source_name: HIV-1 latently-infected central memory T cells cultured from uninfected primary T cells

extract_protocol:
Cells were crosslinked by adding 16% paraformaldehyde to a final concentration of 1% in media. Crosslinking was allowed to proceed for 15 min before Tris pH 7.6 addition to 1.33 M. Cells were pelleted, rinsed twice in PBS, decanted, and frozen at -80. Pellets containing 1.2 million cells were thawed and Dounce homogenized in 1 ml 0.2% Sarkosyl Buffer (20 mM Tris pH 7.6, 150 mM NaCl, 1 mM EDTA, 0.2% Sarkosyl), then sonicated, after which 100 microliters of 10% Triton X-100 was added. Sonicated samples were pelleted at 16000 x g for 15 min and supernatants were precleared with 50 microliters PBS-washed Protein A Dynabeads (Life Technologies 10001D) for 3 h at 4 degrees. In parallel, 50 microliters Protein A Dynabeads were PBS-washed, blocked in 50 microliters PBS containing 1 mg/ml BSA for 1 h at 4 degrees, washed again with PBS, and incubated with 15 micrograms anti-STAT5A (sc-1081). Antibody-beads were washed twice with 100 microliters Wash Buffer A (20 mM Tris pH 7.6, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), then resuspended with precleared sample and incubated overnight at 4 degrees. 1% of each precleared sample was set aside for input sequencing. Samples were washed once with 200 microliters Wash Buffer A, 200 microliters Wash Buffer B (20 mM Tris pH 7.6, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), and 200 microliters Wash Buffer C (20 mM Tris pH 7.6, 250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, and 0.1% SDS), then twice with 200 microliters Rinse Buffer (20 mM Tris pH 7.6, 50 mM NaCl, 1 mM EDTA). Beads were incubated with 200 microliters Elution Buffer (20 mM Tris pH 7.6, 1 mM EDTA, 1% SDS) for 2 h at 65 degrees to reverse crosslinks. Eluates were treated with 2 microliters RNase A for 30 min at 37 degrees, then 2 microliters Proteinase K for 30 min at 50 degrees. DNA was isolated using a MinElute PCR Purification Kit (QIAGEN 28004).
Libraries were prepared using a NEXTflex Rapid DNA-Seq Kit (Bioo Scientific 5144-03)

value: Untreated


title: CI: Input HODHBT/IL-2

description: BigBed files represent fragments over the pNL4-3 HIV-1 genome and can be visualized over hg19 chr1:1-9709. BigWig files represent normalized human-mapping reads and can be visualized over hg19.

value: 3 h IL-2 + 100 micromolar HODHBt


title: CS: STAT5A ChIP HODHBt/IL-2


title: BI: Input DMSO/IL-2

value: 3 h IL-2


title: BS: STAT5A ChIP DMSO/IL-2


title: no tag

city: Newcastle upon Tyne

first: Claudia

last: Schneider

address: Framlington Place

institute: Newcastle University

description:
total cross-linked RNA
5' barcode: GCGAGC

data_processing:
Library strategy: CRAC-seq
Basecalls performed using Illumina CASAVA version 1.8 (UTP23#2 and UTP23#4) or  Illumina CASAVA version 1.3 (no tag)
CRAC reads were mapped to the sacCer2 genome with Novoalign, using the following settings:-F STDFQ -aTGGAATTCTCGGGTGCCAAGG -f XXX_clipped_qf.fastq -r Random -h 150 -s > XXX.novo (except sample no tag for which -F ILMFQ was used)
Genome_build: SacCer2 (SGD)
Supplementary_files_format_and_content: Mapped coordinates were converted to wig format using custom perl scripts

organism: Saccharomyces cerevisiae

source_name: cells grown in SD (-TRP) medium

growth_protocol: Yeast cell cultures were grown in SD medium (OD600 ~0.5).

extract_protocol: Extracts from UV-crosslinked yeast cells were used to isolate RNAs cross-linked to a tagged protein in a 2-step purification protocol. Recovered RNAs are subjected to limited RNAse digest, linker ligation and cDNA amplification, and identified by Illumina sequencing (according to Granneman et al., PNAS, 2009).

treatment_protocol: To generate RNA-protein crosslinks, actively growing yeast cell cultures in SD medium were UV-irradiated in a 1.2 m metal tube for 100 sec at 254 nm (according to Granneman et al., EMBO J., 2011).

tag: strain

value: BY4741 (MATa; his3delta1; leu2delta0; met15delta0; ura3delta0)

tag: tagged protein

value: no tag


title: AI: Input DMSO/-


title: UTP23#2

description:
total cross-linked RNA
5' barcode: NNNGCGCAGC

source_name: cells grown in SD (-URA/-TRP) medium

value: Utp23-HTP (genomic)


title: mock mutant replicate 3_sRNA

city: Singapore

first: Chao

last: Wu

address: 21 Lower Kent Ridge Road

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

description: sRNA

data_processing:
Cut adaptor sequences by cutadapt
Filter by Trimmomatic
Remove low complexity via PRINSEQ
Align by Bowtie2 to Arabidopsis thaliana Reference Genome
Convert mapped Bam file to Fastq files via bedtools and convert to fasta format
Unique sequece Tag identify and align to miRBase via blastn
Genome_build: TAIR10
Supplementary_files_format_and_content: count file including miRBase accession ID and associated read counts

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: 22 degree Celcius with 18 hr light and 6 hr dark cycle

extract_protocol:
sRNA was purified from total RNA using miRcute miRNA Isolation Kit (TIANGEN Biotech)
Library construction was performed as per standard protocol of NEBNext® small RNA Library Prep Kit for Illumina

treatment_protocol: Nicotiana benthamiana leaves were inoculated with in vitro transcripts of pT1d1 to generate TCV virions for purification accordingly14. A total of 5 ug of purified TCV particles suspended in phosphate buffer containing 50 mM Na2HPO4 [pH 7.0] and 1% Celite were inoculated to a 4-weeks-old plant. For the mock plants, similar volume of phosphate buffer was inoculated. In order to minimize experimental variations, all leaf samples are consisted of pools of six leafs collected from three inoculated plants. All experiments were repeated at least three times with consistent results.

tag: ecotype

value: Columbia

tag: genotype

value: DCL1 homozygous mutant

tag: tissue

value: leaves

value: 4 weeks


title: TCV infected mutant replicate 1_sRNA

description: sRNA


title: mock mutant replicate 2_sRNA

description: sRNA


title: TCV infected mutant replicate 3_sRNA

description: sRNA


title: TCV infected mutant replicate 2_sRNA

description: sRNA


title: TCV infected wildtype replicate 2_sRNA

description: sRNA

value: wildtype


title: TCV infected wildtype replicate 3_sRNA

description: sRNA


title: mock mutant replicate 1_sRNA

description: sRNA


title: Uninfected splenic macrophage Rep 4

city: Galveston

first: Peter

middle: C

last: Melby

address: Marvin Graves Bldg, Rm. 4.210, Route 0435

department: Department of Microbiology and Immunology

institute: University of Texas Medical Branch

description:
Spleen harvested at 28 days after mock infection and splenic macrophages isolated from the collagenase-treated, mechanically disrupted spleen by adherence to a plastic culture flask for 4 hrs at 37C. RNA isolated from adherent macrohages immediately after removal of non-adherent cells by washing.
Sample_16

data_processing:
assemble de novo transcripts using the software Trinity (r2012-06-08) and BRANCH (v1.8.1)
blast (v 2.2.28+) each transcripts from BRANCH against Rattus norvegicus (Rnor_5.0.73) and Mus musculus (GRCm38.73) genomes to identified genes for assembled transcripts
align non-Leishmania-like raw sequencing reads to assembled transcripts using bowtie2 (v2.1.0)
measure expression abundance using the software eXpress (v1.1.1)
ran differential expression analysis using edgeR (v3.4.0)
Supplementary_files_format_and_content: raw counts, edgeR output

organism: Mesocricetus auratus

source_name: Splenic macrophage

extract_protocol:
Total RNA was isolated from fresh (unfrozen) samples using RNAqueus kit (Ambion-Life Technologies, CA) following the manufacturers protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Outbred

tag: tissue / cells

value: Splenic macrophage

tag: infectious agent

tag: gender

value: female

value: 10-12 weeks


title: TCV infected wildtype replicate 1_sRNA

description: sRNA


title: mock wildtype replicate 3_sRNA

description: sRNA


title: Uninfected splenic macrophage Rep 3

description:
Spleen harvested at 28 days after mock infection and splenic macrophages isolated from the collagenase-treated, mechanically disrupted spleen by adherence to a plastic culture flask for 4 hrs at 37C. RNA isolated from adherent macrohages immediately after removal of non-adherent cells by washing.
Sample_15


title: mock wildtype replicate 2_sRNA

description: sRNA


title: mock wildtype replicate 1_sRNA

description: sRNA


title: TCV infected mutant replicate 3

data_processing:
Clean data
Align by Tophat to Arabidopsis thaliana Reference Genome
Manipulate Bam by SAMtools
Calculate gene expression level by HTSeq
Genome_build: TAIR10
Supplementary_files_format_and_content: count file including Reference Sequencing ID and associated read counts

extract_protocol:
mRNA was enriched from total RNA by Oligo (dT) beads and rRNA was removed by the Ribo-Zero rRNA Removal Kit (Plant Leaf) kit (Illumina)
Library construction was performed as per standard protocol of NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina


title: Infected splenic macrophage Rep 2

description:
Spleen harvested at 28 days post-infection and splenic macrophages isolated from the collagenase-treated, mechanically disrupted spleen by adherence to a plastic culture flask for 4 hrs at 37C. RNA isolated from adherent macrohages immediately after removal of non-adherent cells by washing.
Sample_10

value: Leishmania donovani (MHOM/SD/001S-2D)


title: Uninfected splenic macrophage Rep 1

description:
Spleen harvested at 28 days after mock infection and splenic macrophages isolated from the collagenase-treated, mechanically disrupted spleen by adherence to a plastic culture flask for 4 hrs at 37C. RNA isolated from adherent macrohages immediately after removal of non-adherent cells by washing.
Sample_13


title: Infected splenic macrophage Rep 4

description:
Spleen harvested at 28 days post-infection and splenic macrophages isolated from the collagenase-treated, mechanically disrupted spleen by adherence to a plastic culture flask for 4 hrs at 37C. RNA isolated from adherent macrohages immediately after removal of non-adherent cells by washing.
Sample_12


title: Uninfected splenic macrophage Rep 2

description:
Spleen harvested at 28 days after mock infection and splenic macrophages isolated from the collagenase-treated, mechanically disrupted spleen by adherence to a plastic culture flask for 4 hrs at 37C. RNA isolated from adherent macrohages immediately after removal of non-adherent cells by washing.
Sample_14


title: Infected splenic macrophage Rep 3

description:
Spleen harvested at 28 days post-infection and splenic macrophages isolated from the collagenase-treated, mechanically disrupted spleen by adherence to a plastic culture flask for 4 hrs at 37C. RNA isolated from adherent macrohages immediately after removal of non-adherent cells by washing.
Sample_11


title: UTP23#4

description:
total cross-linked RNA
5' barcode: NNNTAAGC


title: TCV infected mutant replicate 1


title: TCV infected mutant replicate 2


title: mock mutant replicate 2


title: Infected splenic macrophage Rep 1

description:
Spleen harvested at 28 days post-infection and splenic macrophages isolated from the collagenase-treated, mechanically disrupted spleen by adherence to a plastic culture flask for 4 hrs at 37C. RNA isolated from adherent macrohages immediately after removal of non-adherent cells by washing.
Sample_9


title: Uninfected spleen Rep 3

description:
RNA isolated immediately from spleen harvested 28 days after mock infection
Sample_7

source_name: Spleen

value: Spleen


title: TCV infected wildtype replicate 3


title: HFD, rep3

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

description:
5 mg of liver tissue were homogenized using UltraThorax and RNA was purified using TRIzol-RNA lysis reagent (ThermoFisher) according to manufacturer’s instructions. Sample was prepared for sequencing using polydT-enriched cDNA synthesis.
GH1216

data_processing:
Illumina Casava 1.8 software was used for basecalling and alignment.
Areas of enrichment were identified using DNase2Hotspots software(htrceforge.net/projects/dnase2hotspots/) software with FDR 0%.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Genome_build: mm9 (NCBI 37)
Bedgraph files contain genomic locations and normalized tag density profiles.
RNA-Seq alignment was performed by Tophat2 (v2.0.8) with -r 10 --mate-std-dev 200 options

source_name: Liver

extract_protocol: Total RNA was purified using Tryzol reagent and  RNA-seq library was constructed using ribozero kit.  RNA was sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq and libraries of H3K27ac-enriched DNA and DHS-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: C57BL/6J mice (Jackson Laboratory) were fed either a HFD (D12327, Research Diet, 40% fat by calories) or chow diet (NIH-31, Zeigler Brothers Inc., 8% fat by calories) for seven weeks from 12 weeks of age (groups termed HFD and Chow, respectively). After seven weeks, half of the mice where sacrificed by CO2 narcosis followed by cervical dislocation, livers were dissected and processed for RNA purification, nuclei isolation or frozen in liquid nitrogen for subsequent studies. Blood samples were taken as indicated and processed for metabolic measurements. The other half of the animals continued on a chow diet (termed HFD-chow and Chow-chow) for an additional five weeks

value: liver

value: 19 weeks


title: mock mutant replicate 1


title: HFD, rep2

description:
5 mg of liver tissue were homogenized using UltraThorax and RNA was purified using TRIzol-RNA lysis reagent (ThermoFisher) according to manufacturer’s instructions. Sample was prepared for sequencing using polydT-enriched cDNA synthesis.
GH1215


title: HFD, rep1

description:
5 mg of liver tissue were homogenized using UltraThorax and RNA was purified using TRIzol-RNA lysis reagent (ThermoFisher) according to manufacturer’s instructions. Sample was prepared for sequencing using polydT-enriched cDNA synthesis.
GH1214


title: chow, rep3

description:
5 mg of liver tissue were homogenized using UltraThorax and RNA was purified using TRIzol-RNA lysis reagent (ThermoFisher) according to manufacturer’s instructions. Sample was prepared for sequencing using polydT-enriched cDNA synthesis.
GH1213


title: SV40_3

city: Kunming

first: Jiandong

last: Shi

state: Yunnan

address: 935# Jiaoling Road

department: Department of Vaccine Research

institute: Institute of Medical Biology

data_processing:
For miRNA analysis, all raw reads were firstly subjected to the Illumina pipeline filter, and then processed by ACGT101-miR program (LC Sciences, Houston, Texas, USA) to remove adapter dimers, low complexity, junk and repeats.
Due to the lack of miRNA data for the AGM, rhesus monkey, one of the closest species in evolution with AGM with available miRNA data (http://www.mirbase.org/cgi-bin/mirna_summary.pl?org=mml) was selected as miRNA annotation reference.
Subsequently, clean reads were aligned to AGM reference genome, and the unaligned reads were aligned to Rfam by BLAST search (E-value <0.01) to filter out rRNA, scRNA, snoRNA, snRNA and tRNA. The remaining reads were aligned to RepBase, and known miRNAs of rhesus monkey by RepeatMasker and bowtie [9] to identify known miRNAs.
For the unannotated reads, they were used to predict novel miRNAs by Mirdeep2
Genome_build: African green monkey (AGM) (Chlorocebus aethiops) were download from NCBI GenBank (http://www.ncbi.nlm.nih.gov/assembly/) under assembly accession number GCA_000409795.2 (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/409/795/GCF_000409795.2_Chlorocebus_sabeus_1.1/GCF_000409795.2_Chlorocebus_sabeus_1.1_genomic.fna.gz)
Supplementary_files_format_and_content: Counts and TPM expression value of novel and known miRNAs

organism: Chlorocebus aethiops

source_name: SV40-infected Vero cells

growth_protocol: African green monkey kindey-derived Vero cells, an established monkey kidney epithelial cell line, were obtained from the American Type Culture Collection (ATCC) and maintained in Dulbecco’s modified Eagle’s medium (DMEM; HyClone) supplemented with 10% fetal bovine serum (FBS; Gibico), 2 mM L-glutamine, penicillin (100 U/ml) and streptomycin (100 ug/ml) at 37 °c and 5% CO2 atmosphere.

extract_protocol:
After 72 h post-infection, the cells were harvested and total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) with DNase I digestion (Epicentre, Illumina, San Diego, CA, USA) for 15 minutes at 37℃. The integrity and quality of the total RNA was evaluated using an Agilent 2100 BioAnalyzer (Agilent Technologies) and RNA 6000 Nano Lab Chip Kit (Agilent, CA, USA) with RIN number >7.0. RNA quantity was measured using the NanoDrop 2000 (Thermo Scientific, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Vero cells were mock-infected or virus-infected with the SV40 strain 776 (GenBank: AF316139.1) at a multiplicity of infection of 5 PFU per cell (MOI = 5) in serum-free medium. After 1 h adsorption at 37 C, the medium was replaced with complete DMEM containing 10% FBS and incubated at 37 C.

tag: cell line

value: Vero

tag: cell type

value: African green monkey kindey-derived epithelial cells

tag: passages

tag: infection

value: SV40 strain 776 (GenBank:AF316139.1)


title: Uninfected spleen Rep 1

description:
RNA isolated immediately from spleen harvested 28 days after mock infection
Sample_5


title: SV40_2


title: TCV infected wildtype replicate 2


title: chow, rep1

description:
5 mg of liver tissue were homogenized using UltraThorax and RNA was purified using TRIzol-RNA lysis reagent (ThermoFisher) according to manufacturer’s instructions. Sample was prepared for sequencing using polydT-enriched cDNA synthesis.
GH1211


title: SV40_1


title: Infected spleen Rep 4

description:
RNA isolated immediately from spleen harvested 28 days post-infection
Sample_4


title: TCV infected wildtype replicate 1


title: mock mutant replicate 3


title: Uninfected spleen Rep 4

description:
RNA isolated immediately from spleen harvested 28 days after mock infection
Sample_8


title: HFD, 60U, rep2

description:
Livers were isolated from mice and nuclei were immediately purified. DNase digestions were performed by adding digestion buffer containing 40U of DNase I (Sigma). DNase I digestion efficiency was evaluated by quantitative PCR53 and samples with optimal digestion efficiency were incubated RNase A (Sigma) before 50–500 bp DNA fragments were purified using ultracentrifugation. DNase-seq libraries were constructed according to manufacturer´s (Illumina) instructions as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
GH1189


title: Ctrl_3

source_name: Vero cells


title: Infected spleen Rep 2

description:
RNA isolated immediately from spleen harvested 28 days post-infection
Sample_2


title: chow, rep2

description:
5 mg of liver tissue were homogenized using UltraThorax and RNA was purified using TRIzol-RNA lysis reagent (ThermoFisher) according to manufacturer’s instructions. Sample was prepared for sequencing using polydT-enriched cDNA synthesis.
GH1212


title: Infected spleen Rep 3

description:
RNA isolated immediately from spleen harvested 28 days post-infection
Sample_3


title: Uninfected spleen Rep 2

description:
RNA isolated immediately from spleen harvested 28 days after mock infection
Sample_6


title: mock wildtype replicate 3


title: Infected spleen Rep 1

description:
RNA isolated immediately from spleen harvested 28 days post-infection
Sample_1


title: Ctrl_1


title: mock wildtype replicate 1


title: chow, 60U, rep2

description:
Livers were isolated from mice and nuclei were immediately purified. DNase digestions were performed by adding digestion buffer containing 40U of DNase I (Sigma). DNase I digestion efficiency was evaluated by quantitative PCR53 and samples with optimal digestion efficiency were incubated RNase A (Sigma) before 50–500 bp DNA fragments were purified using ultracentrifugation. DNase-seq libraries were constructed according to manufacturer´s (Illumina) instructions as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
GH1187


title: chow, 60U, rep1

description:
Livers were isolated from mice and nuclei were immediately purified. DNase digestions were performed by adding digestion buffer containing 40U of DNase I (Sigma). DNase I digestion efficiency was evaluated by quantitative PCR53 and samples with optimal digestion efficiency were incubated RNase A (Sigma) before 50–500 bp DNA fragments were purified using ultracentrifugation. DNase-seq libraries were constructed according to manufacturer´s (Illumina) instructions as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
GH1186


title: mock wildtype replicate 2


title: GATA1_ChIP-seq

status: Public on Jan 10 2017

city: Boston

first: Daniel

middle: E

last: Bauer

state: MA

address: 1 Blackfan Circle

department: Medicine, Hematology-Oncology

institute: Boston Children's Hospital

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using MACS1.4 with default parameter

source_name: Erythroid precursor cells

growth_protocol: Human CD34+ G-CSF mobilized peripheral blood hematopoietic stem and progenitor cells were cultured in 2-phase erythroid differentiation conditions with 6 days of expansion and 6 days of differentiation (per Bauer et al Science 2013 342:253-257).

extract_protocol:
Transcription factor-DNA and histone-DNA complexes were isolated from sonicated crosslinked chromatin by antibody precipitation.
Libraries were generated using the ChIP-seq Sample Preparation Kit (Illumina) following manufacturer instructions.

value: peripheral blood

value: CD34+ HSPC derived erythroid precursors

tag: culture days

value: 6 days expansion followed by 6 days differentiation

value: GATA1 (Abcam, ab11852)


title: H3K27ac_ChIP-seq

value: H3K27ac (Abcam, ab4729)


title: ChIP-seq from A549 (ENCLB741BXW)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR979IOT/
***************
biological replicate number: 1
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR979IOT
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR600LQZ
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB741BXW
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens A549 immortalized cell line

tag: antibody

tag: line

value: immortalized cell line

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: male

value: 58 year

tag: lab

value: Tim Reddy, Duke

tag: link

value: ENCBS267YAE at ENCODE; https://www.encodeproject.org/ENCBS267YAE/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB103NIQ)

description:
https://www.encodeproject.org/experiments/ENCSR964KSS/
***************
biological replicate number: 2
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 hours.
experiment encode accession: ENCSR964KSS
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR730UDX
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB103NIQ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 5 hours

tag: age

tag: treatments

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:hour;

value: ENCBS638OUQ at ENCODE; https://www.encodeproject.org/ENCBS638OUQ/


title: ChIP-seq from A549 (ENCLB570FED)

description:
https://www.encodeproject.org/experiments/ENCSR979IOT/
***************
biological replicate number: 2
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR979IOT
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR600LQZ
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB570FED
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS656MMP at ENCODE; https://www.encodeproject.org/ENCBS656MMP/


title: ChIP-seq from A549 (ENCLB605CCZ)

description:
https://www.encodeproject.org/experiments/ENCSR964KSS/
***************
biological replicate number: 1
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 hours.
experiment encode accession: ENCSR964KSS
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR730UDX
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB605CCZ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS089RUP at ENCODE; https://www.encodeproject.org/ENCBS089RUP/


title: Ctrl_2

value: Vero

value: African green monkey kindey-derived epithelial cells


title: ChIP-seq from A549 (ENCLB194ZDW)

description:
https://www.encodeproject.org/experiments/ENCSR964KSS/
***************
biological replicate number: 3
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 hours.
experiment encode accession: ENCSR964KSS
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR730UDX
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB194ZDW
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS737MBE at ENCODE; https://www.encodeproject.org/ENCBS737MBE/


title: ChIP-seq from A549 (ENCLB145SMP)

description:
https://www.encodeproject.org/experiments/ENCSR951SNW/
***************
biological replicate number: 1
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR951SNW
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR005CRY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB145SMP
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 12 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS063ZVJ at ENCODE; https://www.encodeproject.org/ENCBS063ZVJ/


title: ChIP-seq from A549 (ENCLB736OCC)

description:
https://www.encodeproject.org/experiments/ENCSR951SNW/
***************
biological replicate number: 2
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR951SNW
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR005CRY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB736OCC
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS161JYI at ENCODE; https://www.encodeproject.org/ENCBS161JYI/


title: TAL1_ChIP-seq

tag: tissue

value: peripheral blood

value: CD34+ HSPC derived erythroid precursors

value: 6 days expansion followed by 6 days differentiation

tag: chip antibody

value: TAL1 (Santa Cruz, sc-12984)


title: ChIP-seq from A549 (ENCLB102UET)

description:
https://www.encodeproject.org/experiments/ENCSR951SNW/
***************
biological replicate number: 3
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR951SNW
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR005CRY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB102UET
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: adult

value: 58 year

value: male

value: Tim Reddy, Duke

value: ENCBS952TPH at ENCODE; https://www.encodeproject.org/ENCBS952TPH/


title: ChIP-seq from A549 (ENCLB414ZCM)

description:
https://www.encodeproject.org/experiments/ENCSR952GOL/
***************
biological replicate number: 3
technical replicate number: 1
description: NR3C1 (GR) ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR952GOL
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR317VER
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB414ZCM
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 7 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:7; duration_units:hour;

value: ENCBS380JKY at ENCODE; https://www.encodeproject.org/ENCBS380JKY/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB122QDG)

description:
https://www.encodeproject.org/experiments/ENCSR948JXU/
***************
biological replicate number: 2
technical replicate number: 1
description: BCL3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 hours.
experiment encode accession: ENCSR948JXU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR730UDX
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB122QDG
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:hour;

value: ENCBS966VII at ENCODE; https://www.encodeproject.org/ENCBS966VII/


title: input DNA

value: none (input)


title: ChIP-seq from A549 (ENCLB533PLM)

description:
https://www.encodeproject.org/experiments/ENCSR949IDI/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me1 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR949IDI
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR872BBM
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB533PLM
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 4 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS478XMC at ENCODE; https://www.encodeproject.org/ENCBS478XMC/


title: ChIP-seq from A549 (ENCLB984XKB)

description:
https://www.encodeproject.org/experiments/ENCSR954HUB/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me1 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR954HUB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR310TYO
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB984XKB
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 10 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:hour;

value: ENCBS261PDK at ENCODE; https://www.encodeproject.org/ENCBS261PDK/


title: ChIP-seq from A549 (ENCLB112MHU)

description:
https://www.encodeproject.org/experiments/ENCSR948JXU/
***************
biological replicate number: 1
technical replicate number: 1
description: BCL3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 hours.
experiment encode accession: ENCSR948JXU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR730UDX
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB112MHU
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: ENCBS133IJF at ENCODE; https://www.encodeproject.org/ENCBS133IJF/


title: ChIP-seq from A549 (ENCLB827QLU)

description:
https://www.encodeproject.org/experiments/ENCSR944WVU/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR944WVU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR549SVK
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB827QLU
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: 58 year

value: ENCBS336FCB at ENCODE; https://www.encodeproject.org/ENCBS336FCB/


title: HFD, 60U, rep1

description:
Livers were isolated from mice and nuclei were immediately purified. DNase digestions were performed by adding digestion buffer containing 40U of DNase I (Sigma). DNase I digestion efficiency was evaluated by quantitative PCR53 and samples with optimal digestion efficiency were incubated RNase A (Sigma) before 50–500 bp DNA fragments were purified using ultracentrifugation. DNase-seq libraries were constructed according to manufacturer´s (Illumina) instructions as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
GH1188

tag: strain

value: liver

value: 19 weeks


title: ChIP-seq from A549 (ENCLB098HFU)

description:
https://www.encodeproject.org/experiments/ENCSR936UEX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR936UEX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR344ERJ
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB098HFU
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 2 hours

value: male

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS685QBT at ENCODE; https://www.encodeproject.org/ENCBS685QBT/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB679JJQ)

description:
https://www.encodeproject.org/experiments/ENCSR919OXR/
***************
biological replicate number: 3
technical replicate number: 1
description: NR3C1 (GR) ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR919OXR
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR548SPY
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB679JJQ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 1 hour

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS108VDW at ENCODE; https://www.encodeproject.org/ENCBS108VDW/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: polyA mRNA RNA-seq from A549 (ENCLB119DMF)

description:
https://www.encodeproject.org/experiments/ENCSR924BHF/
***************
biological replicate number: 4
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR924BHF
assay title: polyA mRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR632DQP
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB119DMF
size range: >200
spikeins used: /references/ENCSR866KGS/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

extract_protocol:
general protocol: https://www.encodeproject.org/documents/5533fb32-41f1-4c7a-b62d-0095a33cab20/@@download/attachment/01_RNA_HARVEST_and_ISOLATION_Reddy_GGR.pdf
extraction protocol: https://www.encodeproject.org/documents/53726435-7acc-4248-a5df-3eef6ea3b422/@@download/attachment/02_Rev%20D%20Quick%20Reference%20Card%2C%20PrepX%20PolyA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/5f9d4f74-4e39-4818-9ee9-d8e9b8004ceb/@@download/attachment/03_RevC%20Quick%20Reference%20Card%2C%20PrepX%20mRNA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/c72e898e-82c7-478d-b043-8945133a7724/@@download/attachment/04_Rev%20C%20Quick%20Reference%20Card%2C%20PrepX%20PCR%20Cleanup%2048%20Protocol.pdf
general protocol: https://www.encodeproject.org/documents/7a683e77-85ac-45f9-b1fa-b6ceb50ca1bc/@@download/attachment/05_POST_RNA_LIB_PREP_Reddy_GGR.pdf
extraction method: RNeasy Plus Mini Kit Qiagen cat#74134 plus additional on column Dnase treatment

value: ENCBS061GHE at ENCODE; https://www.encodeproject.org/ENCBS061GHE/


title: ChIP-seq from A549 (ENCLB082WTS)

description:
https://www.encodeproject.org/experiments/ENCSR928FDN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR928FDN
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR548SPY
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB082WTS
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: ENCBS706OMV at ENCODE; https://www.encodeproject.org/ENCBS706OMV/


title: ChIP-seq from A549 (ENCLB949UJZ)

description:
https://www.encodeproject.org/experiments/ENCSR952GOL/
***************
biological replicate number: 1
technical replicate number: 1
description: NR3C1 (GR) ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR952GOL
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR317VER
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB949UJZ
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:7; duration_units:hour;

value: ENCBS349YRA at ENCODE; https://www.encodeproject.org/ENCBS349YRA/


title: ChIP-seq from A549 (ENCLB448CLI)

description:
https://www.encodeproject.org/experiments/ENCSR949IDI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR949IDI
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR872BBM
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB448CLI
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: 58 year

value: ENCBS059RHT at ENCODE; https://www.encodeproject.org/ENCBS059RHT/


title: ChIP-seq from A549 (ENCLB463ZRK)

description:
https://www.encodeproject.org/experiments/ENCSR918VQU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR918VQU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR325PXS
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB463ZRK
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 3 hours

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:3; duration_units:hour;

value: ENCBS929VTV at ENCODE; https://www.encodeproject.org/ENCBS929VTV/


title: ChIP-seq from A549 (ENCLB458LFA)

description:
https://www.encodeproject.org/experiments/ENCSR928FDN/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR928FDN
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR548SPY
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB458LFA
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: ENCBS837CSI at ENCODE; https://www.encodeproject.org/ENCBS837CSI/


title: ChIP-seq from A549 (ENCLB498IJZ)

description:
https://www.encodeproject.org/experiments/ENCSR919OXR/
***************
biological replicate number: 1
technical replicate number: 1
description: NR3C1 (GR) ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR919OXR
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR548SPY
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB498IJZ
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS756YTM at ENCODE; https://www.encodeproject.org/ENCBS756YTM/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB572ZVF)

description:
https://www.encodeproject.org/experiments/ENCSR954SQX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR954SQX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR548SPY
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB572ZVF
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS525GZL at ENCODE; https://www.encodeproject.org/ENCBS525GZL/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB156GQH)

description:
https://www.encodeproject.org/experiments/ENCSR911KBJ/
***************
biological replicate number: 1
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR911KBJ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR909GTY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB156GQH
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: ENCBS904ZPH at ENCODE; https://www.encodeproject.org/ENCBS904ZPH/


title: ChIP-seq from A549 (ENCLB535URM)

description:
https://www.encodeproject.org/experiments/ENCSR909GTY/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR909GTY
assay title: ChIP-seq
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB535URM
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Control

value: adult

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:7; duration_units:hour;

value: ENCBS485DRF at ENCODE; https://www.encodeproject.org/ENCBS485DRF/


title: ChIP-seq from A549 (ENCLB121EBT)

description:
https://www.encodeproject.org/experiments/ENCSR909GTY/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR909GTY
assay title: ChIP-seq
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB121EBT
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: 58 year

value: ENCBS794GVB at ENCODE; https://www.encodeproject.org/ENCBS794GVB/


title: ChIP-seq from A549 (ENCLB364GAV)

description:
https://www.encodeproject.org/experiments/ENCSR911KBJ/
***************
biological replicate number: 2
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR911KBJ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR909GTY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB364GAV
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: ENCBS284JUE at ENCODE; https://www.encodeproject.org/ENCBS284JUE/


title: ChIP-seq from A549 (ENCLB954LTJ)

description:
https://www.encodeproject.org/experiments/ENCSR911KBJ/
***************
biological replicate number: 3
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR911KBJ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR909GTY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB954LTJ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: ENCBS177ULF at ENCODE; https://www.encodeproject.org/ENCBS177ULF/


title: ChIP-seq from A549 (ENCLB643MRN)

description:
https://www.encodeproject.org/experiments/ENCSR948JXU/
***************
biological replicate number: 3
technical replicate number: 1
description: BCL3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 hours.
experiment encode accession: ENCSR948JXU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR730UDX
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB643MRN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:hour;

value: ENCBS672OLU at ENCODE; https://www.encodeproject.org/ENCBS672OLU/


title: ChIP-seq from A549 (ENCLB945INE)

description:
https://www.encodeproject.org/experiments/ENCSR918VQU/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR918VQU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR325PXS
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB945INE
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:3; duration_units:hour;

value: ENCBS972JHA at ENCODE; https://www.encodeproject.org/ENCBS972JHA/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB003YNN)

description:
https://www.encodeproject.org/experiments/ENCSR909GTY/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR909GTY
assay title: ChIP-seq
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB003YNN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: ENCBS293DPI at ENCODE; https://www.encodeproject.org/ENCBS293DPI/


title: ChIP-seq from A549 (ENCLB254TAA)

description:
https://www.encodeproject.org/experiments/ENCSR887SZF/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR887SZF
assay title: ChIP-seq
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB254TAA
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 6 hours

value: Control

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS198BBA at ENCODE; https://www.encodeproject.org/ENCBS198BBA/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB424BWD)

description:
https://www.encodeproject.org/experiments/ENCSR905REY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR905REY
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR887SZF
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB424BWD
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: ENCBS485UNU at ENCODE; https://www.encodeproject.org/ENCBS485UNU/


title: ChIP-seq from A549 (ENCLB257CNY)

description:
https://www.encodeproject.org/experiments/ENCSR900RUE/
***************
biological replicate number: 2
technical replicate number: 1
description: FOSL2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR900RUE
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR909GTY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB257CNY
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:7; duration_units:hour;

value: ENCBS920QFZ at ENCODE; https://www.encodeproject.org/ENCBS920QFZ/


title: ChIP-seq from A549 (ENCLB125ANB)

description:
https://www.encodeproject.org/experiments/ENCSR904OTM/
***************
biological replicate number: 1
technical replicate number: 1
description: BCL3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR904OTM
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR147APP
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB125ANB
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: Tim Reddy, Duke

value: ENCBS141HBH at ENCODE; https://www.encodeproject.org/ENCBS141HBH/


title: ChIP-seq from A549 (ENCLB620RGF)

description:
https://www.encodeproject.org/experiments/ENCSR901AAW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR901AAW
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR872BBM
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB620RGF
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS025UWS at ENCODE; https://www.encodeproject.org/ENCBS025UWS/


title: ChIP-seq from A549 (ENCLB563VVY)

description:
https://www.encodeproject.org/experiments/ENCSR872BBM/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR872BBM
assay title: ChIP-seq
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB563VVY
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: ENCBS435PZT at ENCODE; https://www.encodeproject.org/ENCBS435PZT/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB684MNN)

description:
https://www.encodeproject.org/experiments/ENCSR900RUE/
***************
biological replicate number: 1
technical replicate number: 1
description: FOSL2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR900RUE
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR909GTY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB684MNN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS637FHG at ENCODE; https://www.encodeproject.org/ENCBS637FHG/


title: ChIP-seq from A549 (ENCLB364NIU)

description:
https://www.encodeproject.org/experiments/ENCSR904OTM/
***************
biological replicate number: 3
technical replicate number: 1
description: BCL3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR904OTM
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR147APP
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB364NIU
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS465DXD at ENCODE; https://www.encodeproject.org/ENCBS465DXD/


title: ChIP-seq from A549 (ENCLB668HLP)

description:
https://www.encodeproject.org/experiments/ENCSR900RUE/
***************
biological replicate number: 3
technical replicate number: 1
description: FOSL2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR900RUE
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR909GTY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB668HLP
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS079SJM at ENCODE; https://www.encodeproject.org/ENCBS079SJM/


title: ChIP-seq from A549 (ENCLB690TKB)

description:
https://www.encodeproject.org/experiments/ENCSR873VJA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR873VJA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR317VER
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB690TKB
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: ENCBS888YJZ at ENCODE; https://www.encodeproject.org/ENCBS888YJZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB059MTL)

description:
https://www.encodeproject.org/experiments/ENCSR905REY/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR905REY
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR887SZF
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB059MTL
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: male

value: 58 year

value: ENCBS229QHJ at ENCODE; https://www.encodeproject.org/ENCBS229QHJ/


title: ChIP-seq from A549 (ENCLB808WKG)

description:
https://www.encodeproject.org/experiments/ENCSR872BBM/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR872BBM
assay title: ChIP-seq
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB808WKG
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Control

value: Tim Reddy, Duke

value: ENCBS777ZVL at ENCODE; https://www.encodeproject.org/ENCBS777ZVL/


title: ChIP-seq from A549 (ENCLB302JEH)

description:
https://www.encodeproject.org/experiments/ENCSR904OTM/
***************
biological replicate number: 2
technical replicate number: 1
description: BCL3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR904OTM
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR147APP
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB302JEH
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS442FTF at ENCODE; https://www.encodeproject.org/ENCBS442FTF/


title: ChIP-seq from A549 (ENCLB838SXO)

description:
https://www.encodeproject.org/experiments/ENCSR853DWE/
***************
biological replicate number: 3
technical replicate number: 1
description: CEBPB ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR853DWE
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR909GTY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB838SXO
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: CEBPB

value: immortalized cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:7; duration_units:hour;

value: ENCBS016ESU at ENCODE; https://www.encodeproject.org/ENCBS016ESU/


title: ChIP-seq from A549 (ENCLB372ZYK)

description:
https://www.encodeproject.org/experiments/ENCSR868MLT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR868MLT
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR887SZF
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB372ZYK
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS807RCH at ENCODE; https://www.encodeproject.org/ENCBS807RCH/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB444RBI)

description:
https://www.encodeproject.org/experiments/ENCSR838ZAU/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR838ZAU
assay title: ChIP-seq
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB444RBI
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: ENCBS890NQU at ENCODE; https://www.encodeproject.org/ENCBS890NQU/


title: ChIP-seq from A549 (ENCLB916AFA)

description:
https://www.encodeproject.org/experiments/ENCSR841ASB/
***************
biological replicate number: 2
technical replicate number: 1
description: EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR841ASB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR608QCS
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB916AFA
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS880AKY at ENCODE; https://www.encodeproject.org/ENCBS880AKY/


title: ChIP-seq from A549 (ENCLB781BDZ)

description:
https://www.encodeproject.org/experiments/ENCSR853DWE/
***************
biological replicate number: 1
technical replicate number: 1
description: CEBPB ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR853DWE
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR909GTY
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB781BDZ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: 58 year

value: ENCBS317OMN at ENCODE; https://www.encodeproject.org/ENCBS317OMN/


title: ChIP-seq from A549 (ENCLB312DIN)

description:
https://www.encodeproject.org/experiments/ENCSR841ASB/
***************
biological replicate number: 3
technical replicate number: 1
description: EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR841ASB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR608QCS
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB312DIN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: ENCBS509USH at ENCODE; https://www.encodeproject.org/ENCBS509USH/


title: ChIP-seq from A549 (ENCLB707OYP)

description:
https://www.encodeproject.org/experiments/ENCSR841ASB/
***************
biological replicate number: 1
technical replicate number: 1
description: EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR841ASB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR608QCS
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB707OYP
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS266TGV at ENCODE; https://www.encodeproject.org/ENCBS266TGV/


title: DNase-seq from A549 (ENCLB033FLH)

description:
https://www.encodeproject.org/experiments/ENCSR837VHE/
***************
biological replicate number: 4
technical replicate number: 1
description: DNase-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR837VHE
assay title: DNase-seq
assembly: GRCh38
possible controls: ENCSR136DNA
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB033FLH

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS157WWD at ENCODE; https://www.encodeproject.org/ENCBS157WWD/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: DNase-seq from A549 (ENCLB546RRH)

description:
https://www.encodeproject.org/experiments/ENCSR837VHE/
***************
biological replicate number: 5
technical replicate number: 1
description: DNase-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR837VHE
assay title: DNase-seq
assembly: GRCh38
possible controls: ENCSR136DNA
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB546RRH

value: immortalized cell line

value: ENCBS570PSF at ENCODE; https://www.encodeproject.org/ENCBS570PSF/


title: ChIP-seq from A549 (ENCLB113JKF)

description:
https://www.encodeproject.org/experiments/ENCSR834LCU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR834LCU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR872BBM
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB113JKF
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS538GZG at ENCODE; https://www.encodeproject.org/ENCBS538GZG/


title: ChIP-seq from A549 (ENCLB133KLY)

description:
https://www.encodeproject.org/experiments/ENCSR796VBR/
***************
biological replicate number: 3
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR796VBR
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR611VYO
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB133KLY
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS339MWA at ENCODE; https://www.encodeproject.org/ENCBS339MWA/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB492TIU)

description:
https://www.encodeproject.org/experiments/ENCSR796VBR/
***************
biological replicate number: 1
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR796VBR
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR611VYO
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB492TIU
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: ENCBS424IHJ at ENCODE; https://www.encodeproject.org/ENCBS424IHJ/


title: ChIP-seq from A549 (ENCLB861ANC)

description:
https://www.encodeproject.org/experiments/ENCSR796VBR/
***************
biological replicate number: 2
technical replicate number: 1
description: HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR796VBR
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR611VYO
encode release date: 2016-10-27
lab: Tim Reddy, Duke
library encode accession: ENCLB861ANC
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: 58 year

value: ENCBS056ESU at ENCODE; https://www.encodeproject.org/ENCBS056ESU/