title: in vitro cell line

type: protein

city: Al-Qadysia

first: Ahmed

middle: Majeed

last: Al-Shammari

state: Baghdad

department: Experimental Therapy

country: Iraq

institute: Mustansiriyah University, Iraqi Center for Cancer and medical Genetic Research

description: Cell lysate protein profiling during logarithmic phase of cell proliferation (after 24h of plating).

hyb_protocol: 1- Add 50 to 100 μl of sample to each sub-array. Be sure to load each sample on 2 slides (Angiogenesis Array G1 and G2). Cover the incubation chambers with Adhesive film (included in kit). Incubate arrays with sample at RT for 2 hours. Dilute sample using 1X Blocking Buffer if necessary.  2- Remove adhesive film, and carefully aspirate samples from sub-arrays, touching only the corners with your pipette tip.  3- Wash 3 x 2 min with 150 μl 1X Wash Buffer I at RT. Be sure to completely remove liquid each time and use fresh buffer for each wash. Decant final wash solution before proceeding to next step.  4- Obtain a clean container (eg, pipette tip box or slide staining jar) and place glass slide assemblies into the container. Add enough 1X Wash Buffer I to submerge both glass slides with chamber assemblies intact (approx. 30-50 ml) and remove all bubbles in wells. Wash 10 min at RT with gentle rocking or shaking.  5- Remove glass slide assemblies from container and invert to decant liquid. Decant buffer from container and replenish with 1X Wash Buffer I. Submerge both chamber assemblies and wash 10 min at RT with gentle rocking or shaking.  6- Remove glass slide assemblies from container and invert to decant liquid. Decant buffer from container. Repeat Steps 8 & 9 with Wash Buffer II.  7- Remove glass slide assemblies from container and invert to decant liquid, then carefully aspirate wash buffer from wells, touching only the corners with your pipette tip.

scan_protocol: 1- Allow glass chip to dry in a laminar flow hood for 20 minutes or until slide is completely dry. Place chip under an aluminum foil tent to protect it from light. Make sure the slides are absolutely dry before scanning or storage.  2- GenePix 4400A laser scanner were used with compatible GAL file formats supplied by Raybiotech company, which define a grid matching the array map.   • Scan using Cy3-compatible (green; 532 nm).  • Define the area for signal capture for all spots as a circle with 110-120 micron  diameter, ignoring any “comet tails”.  • Use MEDIAN signal values, not the total or the mean. This minimizes the  influence of “comet tails” and outlier data.  • Use local background correction (also using Median value).  • The laser power, photomultiplier tube (PMT) or other signal gain settings of the scanner may be used to increase spot signal intensities and/or to reduce  background signals.   • For given analyte, we compared fluorescence data generated  using the same laser power, PMT and/or signal gain settings for all sub-arrays  for which you wish to compare the results.  (duplicate spots for each array = 4 replicates total). Fluorescence intensity was analyzed using GenePix 4000B microarray scanner (Molecular Devices) and its software, which calculated the mean intensity of each spot minus background.

data_processing: The manufacturer provided background-subtracted, positive-control normalized intensities for both Human Angiogenesis Antibody Array G1 & G2. For each one of the subarrays, all samples were mean-centered to a log2 value of 4.5. Data from both subarrays were combined after normalization.

molecule: protein

source_name: ANGM5 Glioblastoma cell line

label_protocol: 1- Add 70 μl of 1X Biotin-conjugated Anti-Cytokines to each sub-array. Cover incubation chamber with Adhesive film (included in kit). Incubate at RT for 2 hours with gentle rocking or shaking.  2- Carefully aspirate all of the Biotin-conjugated Anti-Cytokine reagent from each well. Wash as described in Step 7 above, first with Wash Buffer I then with Wash Buffer II, making sure to completely remove buffer between washes and after final wash.  3- Add 70 μl of 1X Streptavidin-Fluor to each sub-array. Cover the incubation chambers with Adhesive film (included in kit), then cover entire assemblies with aluminum foil to avoid exposure to light or incubate in dark room. Incubate at RT for 2 hours with gentle rocking or shaking.  4- Remove aluminum foil and adhesive film. Carefully aspirate Streptavidin-Fluor reagent from each well. Wash as described in Step 7 above, first with Wash Buffer I then with Wash Buffer II, making sure to completely remove buffer between washes and after final wash.  5- Remove the glass slides from the frame assemblies. Place both slides in 30 ml centrifuge tube provided, or slide staining jar. Add enough Wash Buffer I to cover both slides (about 20 ml) and gently rock or shake at RT for 10 min.  6- Decant buffer and repeat wash as described in Step 16 (1 x 10 min with Wash Buffer I).  7- Decant buffer and repeat wash as described in Step 16, but this time using Wash Buffer II for only 2-3 minutes.  8- Decant buffer, remove the glass chip from the tube, then gently rinse the slide with de-ionized H2O using a plastic wash bottle.  9- Remove water droplets by applying suction gently with a pipette tip.

growth_protocol: ANGM5 was maintained in RPMI-1640, 10% FCS, with L-glutamine, 100 U/mL penicillin, and 100µg/mL streptomycin and grown at 37°C and 5% CO2.

extract_protocol: ANGM5 cells were freeze and thawed for three times and the cell lysate collected using centrifugation for 3000RPM/min for 10 minutes to form them into pellets. The supernatant was collected for the study and the pellets were removed. Supernatant protein concentration was determined using bio-drop spectrophotometer (Biochrom, UK). The resulting supernatant was stored in a -86℃ deep freeze until used.

treatment_protocol: To determine the angiogenesis factors profile of the ANGM5 glioblastoma cell line in exponential growth phase, a protein microarray assay was conducted. Glioblastoma tumor cells were plated in tissue culture flasks (Nunc, Denmark). Two flasks were seeded with 1×10^6 cells in growth medium and incubated at 37°C. Cells collected after 24h.

tag: age of patient when tumor sample obtained

value: Primary Glioblastoma multiforme tumor


title: INPUT_earlyS_rep2

status: Public on Aug 23 2018

type: SRA

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

library_source: genomic

data_processing:
Illumina RTAv2 software was used for basecalling
Reads were aligned to  human genome assembly (GRCh37/hg19) and D. melanogaster genome assembly (BDGP R5/dm3) by Bowtie v. 1.1.2 using parameters -m1 --best. Mapping and subsequent analysis of the data were done using local Galaxy server and custom R scripts
PCR duplicates were removed using RmDup v.2.0 and unique mapped reads were extended to 250 bp to account for the average library size.
Reads were summed in 25 bp non-overlapping bins.
For ChIP-seq samples, reads were normalized to Reads Per Million (RPM).
For ChOR-seq samples, reads were normalized to Reference-adjusted RPM (RRPM) dividing human  values by total Drosophila unique mapped reads.
Peak calling was performed with MACS v. 2.0.9 under broad domain parameters using INPUT from each experiment as a reference with the exception of H3K4me3 analysis where peak calling was done using MACS standard parameters (narrow peaks).
Genome_build: hg19 and dm3
Supplementary_files_format_and_content: bedgraph files were generated using Galaxy. Scores represent the sum of RPM or RRPM in 250bp windows.

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLa S3 cells

growth_protocol: HeLa S3 were grown in suspension in spinners in DMEM medium (Thermo Fisher Scientific) supplemented with dialyzed FBS (Invitrogen) and penicillin and streptomycin at 37ºC and 5% CO2.  Asynchronous Drosophila S2-DRSC cells were grown in suspension in spinners in M3+BPYE (Sigma-Aldrich) media with 10% HI-FBS and penicillin and streptomycin at 25ºC as described in Drosophila Genomics Resource Center.

extract_protocol:
Fixed cells were lysed during 20 min in ice-cold lysis buffer (100mM NaCl, 66mM Tris HCl pH8, 5mM EDTA, 0.3% SDS, 1.6% Triton X-100) supplemented with proteases inhibitors, passed through a 21G needle and sonicated using a Bioruptor nextGen (Diagenode) to obtain chromatin frgament size of 250-500bp. Sonicated chromatin was centrifuged at 14000rpm at 4ºC for 10 min and the supernatant used for subsequent steps. Chromatin associated to each histone mark was obtained by incubating sonicated chromatin with the corresponding antibody. In parallel, and independently, Drosophila S2 cells were fixed, lysed and sonicated as described for Hela S3 cells. After sonication, HeLa S3 input chromatin required for the analysis of all time-points from the same time course experiment was mixed with Drosophila S2 chromatin (0.025% of total chromatin). Chromatin associated to each histone mark was obtained by incubating sonicated chromatin with the corresponding antibody.
Libraries were costructed using the KAPA Hyperprep kit following manufacturer’s instruction, except that 1.25 µM of Illumina compatible indexed adapters (Pentabase) were ligated to A-tailed DNA. Following adapter ligation biotin-TEG-azide (Berry&Associates) was linked to EdU in Click reaction. Biotinylated products were captured using MyOne Streptavidin T1 beads (Thermo Fisher Scientific) and subjected to PCR amplification following the KAPA Hyperprep kit protocol.

treatment_protocol: For all ChOR-seq and ChIP-seq, HeLa S3 cells were synchronized at the G1/S border by single thymidine block (2 mM, 17 h) and released into fresh media containing deoxycytidine (24 μM) for the indicated amount of time (See Cell cycle information). Parental samples were collected 1 hour before labelling. DNA was labelled during 10 min with medium containing 5-ethynyl-2'-deoxyuridine (EdU, 10 μM) and Nascent chromatin was collected (T0). Harvested cells were immediately fixed in 1% formaldehyde for 5 min. Fixation was stopped by adding Glycine (0.125M) and incubating for 5 min at RT.

tag: description

value: cervical carcinoma

tag: ezh2i treatment

value: Non treated

tag: cell cycle

value: G1/S (Immediately after release)

tag: spike-in

value: NO

tag: labelling

value: Non labelled

tag: antibody


title: 3-METHYLCHOLANTHRENE_300mg/kg_5d_NN_OG_Rep1

status: Public on Aug 24 2018

city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

country: USA

institute: NIEHS

library_source: transcriptomic

data_processing:
library strategy: TempO-Seq (Templated Oligo assay with Sequencing readout)
Sequencing was performed using a 50 cycle single-end read flow cell on a NextSeq 550 Sequencing System (Illumina, San Diego, CA, united States). Processing of sequencing data was conducted using Illumina’s BCL2FASTQ software employing default parameter settings.  Sequencing data were demultiplexed to generate fastq files.
We require that >=75% of the reads have an average quality score >=QC30.  The sequences were then filtered for Illumina p5 and p7 adaptors.
Bowtie2-2.1.0
Aligned to a pseudogenome (indexed probe fasta file reflecting the 50 nt sequences targeted by the detector oligos). Indels not allowed.  Up to 2 base pair mismatches  allowed. Multimapping sequences not allowed.
The counts were summarized using QuasR version 1.8.4.
Genome_build: pseudogenome (indexed probe fasta file reflecting the 50 nt sequences targeted by the detector oligos)
Supplementary_files_format_and_content: tab-delimited text file with read count per gene

molecule: total RNA

organism: Rattus norvegicus

extract_protocol:
Livers were harvested 24 hours after the last dose as 100 mg punches using six millimeter disposable biopsy punches. An appropriately staggered schedule was employed so that the harvest times were accurate to ±30 min of the designed dose-to-harvest interval.  Automated RNA isolation was performed according to the manufacture’s protocol using the RNeasy Kit from Qiagen (Germantown, MD).
The sequencing library for the rat liver RNA samples was prepared by BioSpyder (BioSpyder Technologies, Inc., Carlsbad, CA, United States) according to their protocol  guidelines. One μl of each RNA sample (500-660 ng/uL) was hybridized with the S1500+ beta detector oligo pool mix (2 μl per sample) using the following thermocycler settings: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, and ending with 45°C for 1 min. Hybridization was followed by nuclease digestion (24 μl nuclease mix addition followed by 90 min at 37°C), ligation (24 μl ligation mix addition followed by 60 min at 37°C, then heat denaturation at 80°C for 30 min).. Ten microliters of each ligation product were then transferred to a 96-well PCR amplification microplate that also contained 10 μl of PCR mix per well. Through amplification well-specific, “barcoded” primer pairs were introduced to templates. Five microliters of the PCR amplification products from each well were then pooled into a single sequencing library. The TempO-Seq library was then processed with a PCR clean-up kit (Machery-Nagel, Mountain View, CA, United States) prior to sequencing.

treatment_protocol: Male Sprague-Dawley rats (aged 6–8 weeks and weighing 200–260 g) were dosed once daily in triplicate for 3, 5, or 7 days, depending on the test chemical.

tag: strain

value: Sprague-Dawley

tag: animal id

tag: Sex

value: Male

tag: age

value: 6-8 weeks

tag: tissue

value: Liver

tag: compound

tag: compound abbreviation

tag: moa

value: Ahr

tag: exposure

value: Treated

tag: dose (mg/kg)

tag: duration (days)

tag: vehicle

value: CMC %

tag: nutritive status

value: Non nutritive

tag: route

value: ORAL GAVAGE

tag: sample id


title: Streptavidin_pull-down_earlyS_rep2

tag: description

tag: ezh2i treatment

tag: cell cycle

value: Early S (2 h and 15 min after release)

tag: spike-in

value: YES

tag: labelling

value: EdU


title: Streptavidin_pull-down_earlyS_rep1

value: cervical carcinoma

tag: antibody


title: wt1:N-.2

type: RNA

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

country: Germany

institute: Technische Universität München

hyb_protocol: 1.5 ug of Cy3-labeled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60 °C for 30 minutes in a reaction volume of 250 mL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. Upon completion of the fragmentation reaction, 250 mL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Preprocessing steps including background correction, normalization and summarization of probe intensities were performed by employing the oligo R package (Carvalho 2010).

organism: Fusarium fujikuroi

source_name: Strain wt1, 6mM Gln, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Strains were grown for 3 days in Darken medium and subsequently, an aliquot of 500 µL was transferred to liquid ICI medium with either 6 mM or 60 mM glutamine and grown for additional 3 days on a rotary shaker (180 rpm) at 28 °C.

extract_protocol: Total RNA was extracted using the TRI Reagent (Sigma-Aldrich, Steinheim, Germany) and DNA was removed using DNAse I (Roche Diagnostics, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).

treatment_protocol: The mycelium was harvested, shock frozen with liquid nitrogen and lyophilized.

tag: treatment

value: 6mM Gln


title: H3K79me3_ChOR-seq_T0_rep1

data_processing:
Library strategy: ChOP-seq
Illumina RTAv2 software was used for basecalling
Reads were aligned to  human genome assembly (GRCh37/hg19) and D. melanogaster genome assembly (BDGP R5/dm3) by Bowtie v. 1.1.2 using parameters -m1 --best. Mapping and subsequent analysis of the data were done using local Galaxy server and custom R scripts
PCR duplicates were removed using RmDup v.2.0 and unique mapped reads were extended to 250 bp to account for the average library size.
Reads were summed in 25 bp non-overlapping bins.
For ChIP-seq samples, reads were normalized to Reads Per Million (RPM).
For ChOR-seq samples, reads were normalized to Reference-adjusted RPM (RRPM) dividing human  values by total Drosophila unique mapped reads.
Peak calling was performed with MACS v. 2.0.9 under broad domain parameters using INPUT from each experiment as a reference with the exception of H3K4me3 analysis where peak calling was done using MACS standard parameters (narrow peaks).
Genome_build: hg19 and dm3
Supplementary_files_format_and_content: bedgraph files were generated using Galaxy. Scores represent the sum of RPM or RRPM in 250bp windows.

value: Non treated

value: Anti-Histone H3 (tri methyl K79) antibody - ChIP Grade, purified (ab195500)


title: H3K79me3_ChIP-seq_Parental_rep1

value: G1/S (Immediately after release)

value: NO

value: Non labelled


title: H3K36me3_ChOR-seq_T0_rep2

value: Histone H3 (tri methyl K36) antibody - ChIP Grade (Abcam Cat# ab9050, RRID:AB_306966)


title: H3K36me3_ChOR-seq_T0_rep1


title: H3K79me3_ChOR-seq_T0_rep2


title: H3K79me3_ChIP-seq_Parental_rep2


title: INPUT_earlyS_rep1


title: wt1:N-.1

source_name: Strain wt1, 6mM Gln, replicate 1


title: H3K4me3_ChOR-seq_T1_rep2

value: Early S (1h after T0)

value: H3K4me3 C42D8 (Cell Signaling Technology, Cat No. 9751S, RRID:AB_2616028)


title: H3K4me3_ChOR-seq_T1_rep1


title: H3K4me3_ChOR-seq_T0_rep1


title: H3K4me3_ChOR-seq_T0_rep2


title: SAMPLE 2: NPB CD141high

city: Lund

first: Kristina

last: Lundberg

address: Medicon Village building 406, Scheelevägen 8

department: Immunotechnology

country: Sweden

institute: Lund University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 2 minutes, then 45° for 5 minutes. Centrifuge at max speed for 1 minute and then transfer 200μl on to the array. Hybridize 18 hours at 45° at 60rpm. Fluidics washing using the program FS450_0001.

scan_protocol: Signals were scanned by Affymetrix GeneChip Scanner 3000 7G

data_processing: Microarray signals were normalized using the RMA algorithm in the Affymetrix® Expression Console software (Affymetrix®).

label: biotin

source_name: Peripheral blood

label_protocol: Labeled with the Encore Biotin Module Kit (NuGEN) according to manufacturer’s protocols

extract_protocol: Total RNA isolated from FACS-sorted cells was amplified using the Ovation Pico WTA System V2 (NuGen, San Carlos, CA)

tag: cell type


title: H3K36me3_ChIP-seq_Parental_rep2


title: H3K4me3_ChOR-seq_T12_rep2

value: G1 (12h after T0)


title: H3K4me3_ChIP-seq_Parental_rep2


title: H3K36me3_ChIP-seq_Parental_rep1


title: H3K4me3_ChOR-seq_T6_rep1

value: G2 (6h after T0)


title: H3K4me3_ChOR-seq_T6_rep2


title: H3K4me3_ChOR-seq_T12_rep1


title: H3K4me3_ChIP-seq_Parental_rep1


title: aGBM086

city: Stanford

first: Michelle

last: Monje

state: CA

address: 265 Campus Drive G3035

department: Neurology

institute: Stanford University

description: SPIA-amplified RNA-seq

data_processing:
Mapping: RNA-seq with tophat2. Default parameters were used against hg19 reference genome
Bed files generated using bedtools bamtobed
bedGraph files were generated using bedtools genomecov, then converted to bigWig using UCSC bedGraphToBigWig
Gene expression: For RNA-seq, gene expression was counted using featureCounts against an RefSeq hg19 GTF without miRNA or snoRNA
Genome_build: hg19
Supplementary_files_format_and_content: raw counts of gene expression abundance

source_name: primary tissue donation

growth_protocol: CD11b+/CD45+ tumor-associated macrophages or cortical microglia were sorted from dissociated primary tissue on a FACSAria II or FACSFusion (BD)

extract_protocol:
RNA-seq samples were pelleted and lysed in Trizol reagent then subsequently precipitated.
After extraction from Trizol, RNA-seq samples were linearly amplified using the Ovation RNAseq v2 kit (NuGEN) and fragmented with a Covaris sonicator. Libraries were end-repaired using T4 DNA Polymerase, E. coli Klenow fragment, and T4 polynucleotide kinase. DNA was then A-tailed using exo(-) Klenow fragment and ligated to adaptors from NEBNext MultiPlex Oligos using New England BioLabs Quick Ligase.
Libraries were sequenced at 1x75 on an Illumina NextSeq 500

tag: tissue

value: adult GBM


title: aGBM092

description: SPIA-amplified RNA-seq


title: DIPG35-normal_cortex

description: SPIA-amplified RNA-seq

tag: Sex

value: female

value: pediatric normal cortex


title: DIPG35-Pons

description: SPIA-amplified RNA-seq

value: early post-mortem DIPG


title: DIPG29-normal_cortex

description: SPIA-amplified RNA-seq


title: DIPG32-Pons

description: SPIA-amplified RNA-seq

value: male


title: DIPG32-normal_cortex

description: SPIA-amplified RNA-seq


title: aGBM085

description: SPIA-amplified RNA-seq


title: SAMPLE 1: NPB CD1c


title: DIPG21-Pons

description: SPIA-amplified RNA-seq


title: aGBM081

description: SPIA-amplified RNA-seq


title: THP1-RNAseq-NS1-IFNb-6h-nuclear-large

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description:
total strand-specific RNA-seq
THP1-RNAseq-NS1-IFNb-6h-nuclear-large
fpkm.txt.gz

data_processing:
Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.17.1.14)
Hi-C reads were trimmed at Mbo I/Dpn II recognition sites (GATC) and aligned to the human genome (GRCh37/hg19) using bowtie2 (Langmead and Salzberg, 2012), keeping only read pairs that both map to unique genomic locations for further analysis (MAPQ > 10). Subsequent Hi-C analysis was performed using HOMER (Lin et al., 2012), and improvements made to HOMER (v4.10) for this study are available at http://homer.ucsd.edu/homer/interactions2/. Hi-C data was also processed using Juicer (v1.7.5) to generate hic files for visualization with Juicebox.
ChIP-seq reads were aligned to the human genome (GRCh37/hg19) using bowtie2 (Langmead and Salzberg, 2012), keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). ChIP-seq peaks were called on pooled replicates using HOMER’s findPeaks program in either “histone” (histone marks, Pol II) or “factor” (CTCF, RAD21, PU.1) mode using default parameters to identify spreading or focal peaks, respectively.
RNA-seq reads were mapped to the human genome (hg19/GRCh37) using STAR (v2.2.0c). Only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis. Gene FPKM values were defined for primary Gencode transcripts using HOMER (v4.10) using only strand-specific exonic reads for each transcript.
Start-seq reads were trimmed to remove 3' illumina adapters and then mapped to the human genome (hg19/GRCh37) using STAR (v2.2.0c). Only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis. TSS (i.e. Start-seq peaks) were called using HOMER’s findPeaks program in "tss" mode using parameters "-style tss -F 2 -P 0.05" to identify sites of nascent transcription initiation
methylC-seq reads were mapped to the human genome (hg19/GRCh37) using Bismark/Bowtie2 (Krueger and Andrews, 2011) and reported as the number of observed methylated and unmethylated cytosines in the CpG context. HOMER (v4.10) was used process the methylation and create bedGraph genome browser tracks reporting the average %mCpG rates in 1 kb bins across the genome.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: ChIP-Seq/Start-seq: Tab-delimited BED files containing peak positions for each ChIP-seq or Start-seq experiment (one peak file per set of replicates, hg19) Columns: 1:chromosome,2:start,3:end,4:peakName,5:set to 1,6:strand.  RNA-seq: Tab-delimited table of FPKM values for all RNA-seq experiments Columns: 1:transcript ID, 2:chr, 3:start, 4:end, 5:strand, 6:mRNA length, 7:gene ID, 8: gene type, 9: gene symbol, 10-29: FPKM for each experiment. Hi-C: binary hic files generated by Juicer (visualize using Juicebox or Juicebox.js)

source_name: THP-1 monocyte AML cell line

growth_protocol: Monocyte derived macrophages (MDM) were prepared from buffy coats of healthy donor blood obtained from the New York Blood Center.  Peripheral blood mononuclear cells (PBMC) were isolated by centrifugation on a Ficoll density gradient (Histopaque; Sigma Aldrich), and CD14+ cells were isolated using Miltenyi liquid separation mini columns and magnetic beads labeled with anti-human CD14 antibody (Miltenyi Biotech).  For differentiation into macrophages, approximately 3 million CD14+ monocytes were cultured for 10 days in RPMI 1640 medium (CellGro, Corning) containing 10% fetal bovine serum (FBS) (HyClone; Thermo Scientific), 2 mM L-glutamine, 1 mM sodium pyruvate, and 100 U/ml penicillin–100 μg/ml streptomycin (Gibco, Invitrogen), and supplemented with 1000 U/ml human granulocyte-macrophage colony-stimulating factor (hGM-CSF) (Peprotech). THP-1 cells (“THP-1 monocytes”) were propagated in THP-1 medium (RPMI-1640 containing 10% low-endotoxin FBS (Peak Serum Inc.), 1x (100 µM) non-essential amino acids (Life Technologies), 1x MEM Sodium Pyruvate Solution (1 mM) (Life Technologies), 1x GlutaMax I (Life Technologies), 50 µM β-mercaptoethanol (Life Technologies)) at 37°C, 5% CO2, 100% humidity. Dexamethasone and, where indicated, IFNβ treatments were performed on differentiated THP-1 cells (“THP-1 macrophages”) that had been treated with 60 ng/ml phorbol myristate acetate (PMA) for 48 h followed overnight culture without PMA. For IAV infections, THP-1 cells were differentiated in the same manner, except 10 ng/ml PMA were used.

extract_protocol:
RNAseq: Cells were lysed in Trizol (Thermo) and RNA was extracted either by adding chloroform, phase separation and isolating RNA from the upper phase using RNeasy columns with on-column DNase treatment or by using DirectZol kits (Zymo) with on-column DNase treatment, following the manufacturer’s instructions. For cytoplasmic, nuclear, and large nuclear fraction RNA-seq (North-seq), RNA from 15 million live cells was isolated according to (Bhatt et al., 2012). Briefly, cells were washed with ice-cold PBS, resuspended at 75 million cells/ml final in cytoplasmic lysis buffer (0.15% NP-40, 10 mM Tris pH 7.5, 150 mM NaCl) and incubated on ice for 5 minutes. The lysate was layered onto 500 µl ice-cold sucrose buffer (10 mM Tris pH 7.5, 150 mM NaCl, 24% sucrose w/v) and centrifuged in microfuge tubes for 10 minutes at 13,000g, 4°C. The supernatant containing the cytoplasmic RNA (~ 700 µl) was transferred to a new tube, and the nuclear pellet was resuspended in 500 µl glycerol buffer (20 mM Tris pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.85 mM DTT). RNA was extracted from the cytoplasmic and nuclear fraction with Trizol LS according to the manufacturer’s instructions, DNase-treated with RQ1 DNase (Promega), extracted once with phenol:chloroform, once with chloroform, and ethanol-precipitated. For size selection of large nuclear RNAs, two micrograms nuclear RNA were denatured with an equal amount of 2x RNA loading dye (NEB, 47.5% formamide final) for 5 minutes at 70°C and separated on a 1.5% agarose/1x TBE gel for 30 minutes. After staining the RNA with 1x SYBR Gold in 1x TBE for 15 minutes, RNA above the 45S RNA band was excised with a scalpel blade and gel-extracted (Zymoclean Gel RNA Recovery, Zymo Research).
Strand-specific total RNA-seq libraries from ribosomal RNA-depleted were prepared using the TruSeq kit (Illumina) according to the supplied protocol. ChIP-seq was essentially performed as described (Heinz et al., 2013), except that libraries were prepared using NEB Ultra II DNA library prep kit reagents. Start-seq was essentially performed as described (Scruggs et al., 2015) from total RNA with minor modifications, replacing phenol/chloroform extractions with Trizol LS (Thermo), using RppH (NEB) instead of tobacco acid pyrophosphatase, and generating sequencing libraries with a NEBNext Small RNA Library Prep kit (NEB). MethylC-seq libraries were prepared from ChIP input DNA that had been isolated as from formaldehyde-fixed samples as previously described (Heinz et al., 2013). Briefly, chromatin was sheared to an average size of 300 bp in ChIP lysis buffer, crosslinks reversed in 1% SDS/TE/300 mM NaCl ON at 65°C, treated for 30 minutes with 5 µg RNase A, digested for 2 h with 20 µg proteinase K and DNA was isolated with Speedbeads/PEG as described above. DNA libraries were made from 100 ng input DNA by adding methylated DNA sequencing adapters (Bioo) with NEB Ultra II DNA library prep kit reagents and cleaned up using Speedbeads/PEG/NaCl as above. Fifty nanograms of adapter-ligated DNA were bisulfite-treated using a Zymo EZ DNA methylation kit (Zymo Research) according to the manufacturer’s instructions, and PCR-amplified using KAPA HiFi U+ ReadyMix and Solexa 1GA/1GB primers. In situ Hi-C was performed as described (Rao et al., 2014) with modifications. Cells were pelleted by centrifugation and resuspended and cross-linked in 1% formaldehyde/PBS for 10 minutes at room temperature (RT). After quenching the reaction by adding 1/20th volume of 2.625 M glycine, cells were pelleted by centrifugation and washed twice with ice-cold 0.5% BSA/PBS. Aliquots of 2 M cells each were snap-frozen and stored at -80°C. After thawing cells on ice, nuclei were isolated by resuspending the cell pellet in 200 µl wash buffer (50 mM Tris/HCl pH 7.5, 10 mM NaCl, 1 mM EDTA, 0.5% SDS, 1x protease inhibitor cocktail (Sigma P8340)). Nuclei were spun down at 2500g for 5 minutes at room temperature. Most of the supernatant was discarded, leaving the nuclei in 10 µl liquid. Samples were resuspended in Dpn II buffer, 195 µl water and rotated at 37°C for 15 minutes. Chromatin was digested overnight (ON) with 2 µl (100 U) Dpn II (NEB) at 37°C, rotating overhead with 8 RPM. The next day, Mbo I digests (not Dpn II digests) were inactivated by incubating for 20 minutes at 62°C, and nuclei were collected centrifugation (5 minutes, 500 g, RT). Two-hundred µl of the supernatant were discarded, leaving the nuclei in 50 µl liquid, and overhangs were filled in with Biotin-14-dATP by adding 50 µl Klenow Master Mix (31.95 µl water, 5 µl NEBuffer 2, 0.35 µl 10 mM dATP (or dCTP), 0.35 µl 10 mM dTTP, 0.35 µl 10 mM dGTP, 7.5 µl 0.4 mM Biotin-14-dCTP (or Biotin-14-dATP)(Thermo), 2 µl 10% Triton X-100, 2.5 µl (12.5 U) Klenow fragment (Enzymatics) and rotating overhead at RT, 8 RPM for 40 minutes. Reactions were stopped by adding 2.5 µl 0.5 M EDTA and placed on ice. Proximity ligation was performed by transferring the entire reaction into 1.5 ml Eppendorf tubes containing 400 µl ligase mix (320 µl water, 40 µl 10x T4 DNA ligase buffer (Enzymatics), 36 µl 10% Triton X-100, 0.5 µl 10 % BSA, 1 µl (600 U) T4 DNA ligase (HC, Enzymatics) and rotating ON at 16°C, 8 RPM. Reactions were stopped with 20 µl 0.5 M EDTA, treated with 1 µl 10 mg/ml DNase-free RNAse A for 15 minutes at 42°C, 33 µl 5 M NaCl and 55 µl 10 % SDS were added and crosslinks reversed for 4 h to ON at 65°C. Proteins were digested with 10 µl 20 mg/ml DNase-free proteinase K (Thermo) for 2 h at 55°C while shaking at 800 RPM, then 90 minutes at 65°C. After extraction with 600 µl ph 8-buffered phenol/chloroform/isoamyl alcohol (Ambion) followed by 300 µl chloroform, DNA was precipitated with 1.5 µl (22.5 µg) Glycoblue (Ambion) and 1400 µl 100% ethanol ON at -20°C, pelleted for 20’ at 16000g, 4°C, washed twice with 80% ethanol, and the pellet air-dried and dissolved in 131 µl TT (0.05% Tween 20/Tris pH 8). DNA (800 ng) was sheared to 300 bp in 130 µl TT on a Covaris M220 or S220, using the manufacturer’s protocol. DNA was then directly bound to streptavidin-coated Dynabeads. Biotinylated DNA captured on Dynabeads MyOne Streptavidin T1 (Thermo) by combining the sample (50 µl or 130 µl) with 20 µl Dynabeads that had previously been washed once with 1x B&W buffer (2X B&W: 10 mM Tris-HCl pH=7.5, 1 mM EDTA, 2 M NaCl), and had been resuspended in 50 µl or 130 µl 2x B&W containing 0.2% Tween 20. The binding reaction was rotated at RT for 30 minutes, and DNA-bound beads were washed once with 1 ml 1x B&W/0.1% Triton-X 100, once with TET (0.2% Tween 20, 10 mM Tris pH 8, 1 mM EDTA). Beads were resuspended in 100 µl Blunting Mix (74.5 µl water, 0.5 µl 10% Tween 20, 10 µl 10x T4 DNA ligase buffer (Enzymatics), 4 µl 10 mM dNTP, 2 µl (6 U) T4 DNA polymerase (Enzymatics), 0.4 µl (2 U) Klenow fragment (Enzymatics), 2 µl (20 U) T4 polynucleotide kinase (Enzymatics)) and incubated for 30 minutes at 20°C. Reactions were stopped by adding 2.5 µl 0.5 M EDTA, beads collected on a magnet and washed twice with 150 µl 1x B&W/0.1% Triton-X 100, once with 180 µl TET. Beads were resuspended in 50 µl A-tail Mix (44.25 µl water, 0.5 µl 10% Tween 20, 5 µl NEBuffer 2, 0.2 µl 100 mM dATP, 0.3 µl (15 U) Exo--Klenow (Enzymatics) and incubated for 30 minutes at 37°C. Reactions were stopped by adding 1.5 µl 0.5 M EDTA, beads collected on a magnet and the SN was discarded. Beads were resuspended on ice in 48 µl ice-cold Ligation mix (25 µl 2x T4 DNA ligation buffer (Enzymatics), 0.5 µl 10% Tween 20, 22.5 µl water), 2 µl 0.6 µM Bioo Nextflex DNA sequencing adapters were added, and the reaction incubated for 20 minutes at RT. Reactions were stopped by adding 5 µl 0.5 M EDTA, and beads were washed twice with 1x B&W/0.1% Triton-X 100, once with TET and resuspended in 30 µl 0.05% Tween 20/LoTE (TE dilute 1:4 with water). Libraries were amplified by PCR for 10 or 12 cycles (98°C, 30s; 10

treatment_protocol: Influenza A/Vietnam/1203/2004 (H5N1) HAlo virus is a recombinant virus that has been engineered to remove the multibasic cleavage site in the HA protein (Steel et al., 2009).  The H5N1-dNS1  (dNS1) virus expresses a truncated NS1 protein (residues 1-73) in the H5N1 HAlo background (Steel et al., 2009).  Viruses were propagated in ten-day-old embryonated chicken eggs (Charles River Laboratories) and titers were determined by plaque assay in MDCK cells. For infections, MDMs were washed with serum-free RPMI 1640 medium, and infected at a multiplicity of two with H5N1 HAlo virus or H5N1 NS1trunc virus. After 1 hour, virus inoculum was removed, cells were washed twice with serum-free RPMI 1640 medium, and then incubated in RPMI 1640 medium containing 10% serum and antibiotics. THP-1 mRNA electroporation: IVT mRNA was generated from PCR-synthesized, T7 promoter-containing templates with an mMESSAGE mMACHINE T7 Ultra Kit (Ambion) according to the manufacturer’s instructions, using either normal NTP or incorporating methyl-cytosine and pseudo-uridine. IVT RNA preparations that were used without concomitant interferon treatment were dephosphorylated with calf intestinal phosphatase to eliminate the RIG-I response and subsequent IFNβ production that 5’-triphosphorylated RNA can trigger. For electroporations, 3 M THP-1 cells were pelleted by centrifugation, serum RNases were removed by washing cells twice at room temperature with phenol red-free OptiMEM (Life Technologies). Cells were electroporated in 200 µl phenol red-free OptiMEM in a 4 mm cuvette with a rectangular pulse of 400 V and 5 ms duration, delivering 5 µg IVT mRNA using Gene Pulser Xcell (Bio-Rad). Immediately after electroporation, the cell suspension was transferred into a well of a six-well plate filled with 2 ml pre-warmed THP-1 medium (RPMI-1640 containing 10% low-endotoxin FBS (Peak Serum Inc.), 1x (100 µM) non-essential amino acids (Life Technologies), 1x MEM Sodium Pyruvate Solution (1 mM) (Life Technologies), 1x GlutaMax I (Life Technologies), 50 µM β-mercaptoethanol) and cultured at 37°C, 5% CO2, 100% humidity for 6 h. THP-1 cells were electroporated with siRNA against WAPL and NIBPL (or control) using the same protocol as described for mRNA electroporation. Agonists were used at the following concentrations: IFNβ - 1000 U/ml , Pam3CSK4 - 1 µg/ml, Dexamethasone - 1 µM, flavopiridol - 2 µM.

value: THP-1 monocyte AML cell line

value: IFNb treated (6h)

tag: treatment time

tag: donor or replicate

tag: electroporated mrna

value: IAV NS1

tag: sirna

tag: chip antibody


title: DIPG20-Pons

description: SPIA-amplified RNA-seq


title: DIPG14-Pons

description: SPIA-amplified RNA-seq


title: DIPG19-Pons

description: SPIA-amplified RNA-seq


title: THP1-RNAseq-NS1-IFNb-6h-nuclear

description:
total strand-specific RNA-seq
THP1-RNAseq-NS1-IFNb-6h-nuclear
fpkm.txt.gz


title: THP1-RNAseq-NS1-IFNb-6h-cytoplasmic

description:
total strand-specific RNA-seq
THP1-RNAseq-NS1-IFNb-6h-cytoplasmic
fpkm.txt.gz


title: THP1-RNAseq-eGFP-IFNb-6h-nuclear-large

description:
total strand-specific RNA-seq
THP1-RNAseq-eGFP-IFNb-6h-nuclear-large
fpkm.txt.gz

value: eGFP


title: THP1-RNAseq-eGFP-IFNb-6h-cytoplasmic

description:
total strand-specific RNA-seq
THP1-RNAseq-eGFP-IFNb-6h-cytoplasmic
fpkm.txt.gz


title: THP1mac-RNAseq-Mock-r2

description:
total strand-specific RNA-seq
THP1mac-RNAseq-Mock-r2
fpkm.txt.gz

source_name: THP-1 monocyte AML cell line (+PMA)

value: THP-1 monocyte AML cell line (+PMA)

value: Mock infected (06h)


title: THP1mac-RNAseq-H5N1-r1

description:
total strand-specific RNA-seq
THP1mac-RNAseq-H5N1-r1
fpkm.txt.gz

value: H5N1 IAV infected (06h)


title: THP1mac-StartseqInput-Mock

description:
Start-seq (no cap removal)
total RNA (short < 70bp, uncapped)
THP1mac-StartseqInput-Mock
none

data_processing:
Library strategy: Start-seq (no cap removal)
Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.17.1.14)
Hi-C reads were trimmed at Mbo I/Dpn II recognition sites (GATC) and aligned to the human genome (GRCh37/hg19) using bowtie2 (Langmead and Salzberg, 2012), keeping only read pairs that both map to unique genomic locations for further analysis (MAPQ > 10). Subsequent Hi-C analysis was performed using HOMER (Lin et al., 2012), and improvements made to HOMER (v4.10) for this study are available at http://homer.ucsd.edu/homer/interactions2/. Hi-C data was also processed using Juicer (v1.7.5) to generate hic files for visualization with Juicebox.
ChIP-seq reads were aligned to the human genome (GRCh37/hg19) using bowtie2 (Langmead and Salzberg, 2012), keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). ChIP-seq peaks were called on pooled replicates using HOMER’s findPeaks program in either “histone” (histone marks, Pol II) or “factor” (CTCF, RAD21, PU.1) mode using default parameters to identify spreading or focal peaks, respectively.
RNA-seq reads were mapped to the human genome (hg19/GRCh37) using STAR (v2.2.0c). Only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis. Gene FPKM values were defined for primary Gencode transcripts using HOMER (v4.10) using only strand-specific exonic reads for each transcript.
Start-seq reads were trimmed to remove 3' illumina adapters and then mapped to the human genome (hg19/GRCh37) using STAR (v2.2.0c). Only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis. TSS (i.e. Start-seq peaks) were called using HOMER’s findPeaks program in "tss" mode using parameters "-style tss -F 2 -P 0.05" to identify sites of nascent transcription initiation
methylC-seq reads were mapped to the human genome (hg19/GRCh37) using Bismark/Bowtie2 (Krueger and Andrews, 2011) and reported as the number of observed methylated and unmethylated cytosines in the CpG context. HOMER (v4.10) was used process the methylation and create bedGraph genome browser tracks reporting the average %mCpG rates in 1 kb bins across the genome.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: ChIP-Seq/Start-seq: Tab-delimited BED files containing peak positions for each ChIP-seq or Start-seq experiment (one peak file per set of replicates, hg19) Columns: 1:chromosome,2:start,3:end,4:peakName,5:set to 1,6:strand.  RNA-seq: Tab-delimited table of FPKM values for all RNA-seq experiments Columns: 1:transcript ID, 2:chr, 3:start, 4:end, 5:strand, 6:mRNA length, 7:gene ID, 8: gene type, 9: gene symbol, 10-29: FPKM for each experiment. Hi-C: binary hic files generated by Juicer (visualize using Juicebox or Juicebox.js)


title: THP1-Fos-eGFP-Pam3csk-4h

description:
Fos ChIP-seq
THP1-Fos-eGFP-Pam3csk-4h
Sample251.THP1-Fos-eGFP-Pam3csk-4h.peaks.bed.gz

value: Pam3csk4 treated (4h)

value: FOS, Santa Cruz:sc-7202


title: THP1mac-Startseq-H5N1

description:
Start-seq
total RNA (short < 70bp, capped)
THP1mac-Startseq-H5N1
Sample253.THP1mac-Startseq-H5N1.peaks.bed.gz

data_processing:
Library strategy: Start-seq
Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.17.1.14)
Hi-C reads were trimmed at Mbo I/Dpn II recognition sites (GATC) and aligned to the human genome (GRCh37/hg19) using bowtie2 (Langmead and Salzberg, 2012), keeping only read pairs that both map to unique genomic locations for further analysis (MAPQ > 10). Subsequent Hi-C analysis was performed using HOMER (Lin et al., 2012), and improvements made to HOMER (v4.10) for this study are available at http://homer.ucsd.edu/homer/interactions2/. Hi-C data was also processed using Juicer (v1.7.5) to generate hic files for visualization with Juicebox.
ChIP-seq reads were aligned to the human genome (GRCh37/hg19) using bowtie2 (Langmead and Salzberg, 2012), keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). ChIP-seq peaks were called on pooled replicates using HOMER’s findPeaks program in either “histone” (histone marks, Pol II) or “factor” (CTCF, RAD21, PU.1) mode using default parameters to identify spreading or focal peaks, respectively.
RNA-seq reads were mapped to the human genome (hg19/GRCh37) using STAR (v2.2.0c). Only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis. Gene FPKM values were defined for primary Gencode transcripts using HOMER (v4.10) using only strand-specific exonic reads for each transcript.
Start-seq reads were trimmed to remove 3' illumina adapters and then mapped to the human genome (hg19/GRCh37) using STAR (v2.2.0c). Only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis. TSS (i.e. Start-seq peaks) were called using HOMER’s findPeaks program in "tss" mode using parameters "-style tss -F 2 -P 0.05" to identify sites of nascent transcription initiation
methylC-seq reads were mapped to the human genome (hg19/GRCh37) using Bismark/Bowtie2 (Krueger and Andrews, 2011) and reported as the number of observed methylated and unmethylated cytosines in the CpG context. HOMER (v4.10) was used process the methylation and create bedGraph genome browser tracks reporting the average %mCpG rates in 1 kb bins across the genome.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: ChIP-Seq/Start-seq: Tab-delimited BED files containing peak positions for each ChIP-seq or Start-seq experiment (one peak file per set of replicates, hg19) Columns: 1:chromosome,2:start,3:end,4:peakName,5:set to 1,6:strand.  RNA-seq: Tab-delimited table of FPKM values for all RNA-seq experiments Columns: 1:transcript ID, 2:chr, 3:start, 4:end, 5:strand, 6:mRNA length, 7:gene ID, 8: gene type, 9: gene symbol, 10-29: FPKM for each experiment. Hi-C: binary hic files generated by Juicer (visualize using Juicebox or Juicebox.js)


title: THP1mac-RNAseq-Mock-r1

description:
total strand-specific RNA-seq
THP1mac-RNAseq-Mock-r1
fpkm.txt.gz


title: THP1mac-StartseqInput-H5N1

description:
Start-seq (no cap removal)
total RNA (short < 70bp, uncapped)
THP1mac-StartseqInput-H5N1
none


title: THP1-input-NS1-Pam3csk-4h

description:
Input ChIP-seq
THP1-input-NS1-Pam3csk-4h
none


title: THP1-input-eGFP-Pam3csk-4h

description:
Input ChIP-seq
THP1-input-eGFP-Pam3csk-4h
none


title: THP1-input-NS1-Pam3csk-0h

description:
Input ChIP-seq
THP1-input-NS1-Pam3csk-0h
none

value: untreated


title: THP1-Fos-eGFP-Pam3csk-0h

description:
Fos ChIP-seq
THP1-Fos-eGFP-Pam3csk-0h
Sample250.THP1-Fos-eGFP-Pam3csk-0h.peaks.bed.gz


title: THP1-input-eGFP-Pam3csk-0h

description:
Input ChIP-seq
THP1-input-eGFP-Pam3csk-0h
none


title: THP1-p65-eGFP-Pam3csk-0h

description:
NFKB p65 ChIP-seq
THP1-p65-eGFP-Pam3csk-0h
Sample248.THP1-p65-eGFP-Pam3csk-0h.peaks.bed.gz

value: p65, Santa Cruz:sc-372


title: THP1-PU1-NS1-Pam3csk-0h

description:
PU.1 ChIP-seq
THP1-PU1-NS1-Pam3csk-0h
Sample242.THP1-PU1-NS1-Pam3csk-0h.peaks.bed.gz

value: PU.1, Santa Cruz:sc-352


title: THP1-PU1-NS1-Pam3csk-4h

description:
PU.1 ChIP-seq
THP1-PU1-NS1-Pam3csk-4h
Sample243.THP1-PU1-NS1-Pam3csk-4h.peaks.bed.gz


title: THP1-PU1-eGFP-Pam3csk-0h

description:
PU.1 ChIP-seq
THP1-PU1-eGFP-Pam3csk-0h
Sample240.THP1-PU1-eGFP-Pam3csk-0h.peaks.bed.gz


title: THP1-PU1-eGFP-Pam3csk-4h

description:
PU.1 ChIP-seq
THP1-PU1-eGFP-Pam3csk-4h
Sample241.THP1-PU1-eGFP-Pam3csk-4h.peaks.bed.gz


title: THP1-CEBPb-NS1-Pam3csk-4h

description:
CEBPb ChIP-seq
THP1-CEBPb-NS1-Pam3csk-4h
Sample239.THP1-CEBPb-NS1-Pam3csk-4h.peaks.bed.gz

value: CEBPb, Santa Cruz:sc-150


title: THP1mac-Startseq-Mock

description:
Start-seq
total RNA (short < 70bp, capped)
THP1mac-Startseq-Mock
Sample252.THP1mac-Startseq-Mock.peaks.bed.gz


title: THP1-CEBPb-NS1-Pam3csk-0h

description:
CEBPb ChIP-seq
THP1-CEBPb-NS1-Pam3csk-0h
Sample238.THP1-CEBPb-NS1-Pam3csk-0h.peaks.bed.gz


title: THP1mac-RNAseq-H5N1-r2

description:
total strand-specific RNA-seq
THP1mac-RNAseq-H5N1-r2
fpkm.txt.gz


title: THP1-CEBPb-eGFP-Pam3csk-4h

description:
CEBPb ChIP-seq
THP1-CEBPb-eGFP-Pam3csk-4h
Sample237.THP1-CEBPb-eGFP-Pam3csk-4h.peaks.bed.gz


title: THP1-RNAseq-eGFP-IFNb-6h-nuclear

description:
total strand-specific RNA-seq
THP1-RNAseq-eGFP-IFNb-6h-nuclear
fpkm.txt.gz


title: THP1-CEBPb-eGFP-Pam3csk-0h

description:
CEBPb ChIP-seq
THP1-CEBPb-eGFP-Pam3csk-0h
Sample236.THP1-CEBPb-eGFP-Pam3csk-0h.peaks.bed.gz


title: THP1-PolII-NS1-Pam3csk-0h

description:
RNAPII ChIP-seq
THP1-PolII-NS1-Pam3csk-0h
Sample234.THP1-PolII-NS1-Pam3csk-0h.peaks.bed.gz

value: PolII, Genetex:GTX102535 (RBP2)


title: THP1-PolII-NS1-Pam3csk-4h

description:
RNAPII ChIP-seq
THP1-PolII-NS1-Pam3csk-4h
Sample235.THP1-PolII-NS1-Pam3csk-4h.peaks.bed.gz


title: THP1-PolII-eGFP-Pam3csk-0h

description:
RNAPII ChIP-seq
THP1-PolII-eGFP-Pam3csk-0h
Sample232.THP1-PolII-eGFP-Pam3csk-0h.peaks.bed.gz


title: THP1mac-input-Dex-0h

description:
Input ChIP-seq
THP1mac-input-Dex-0h
none


title: THP1mac-CTCF-Dex-0h

description:
CTCF ChIP-seq
THP1mac-CTCF-Dex-0h
Sample228.THP1mac-CTCF-Dex-0h.peaks.bed.gz

value: CTCF, Active Motif:#61311


title: THP1mac-CTCF-Dex-6h

description:
CTCF ChIP-seq
THP1mac-CTCF-Dex-6h
Sample229.THP1mac-CTCF-Dex-6h.peaks.bed.gz

value: dexamethasone (6h)


title: THP1mac-Rad21-IFNb-6h

description:
RAD21 (Cohesin) ChIP-seq
THP1mac-Rad21-IFNb-6h
Sample227.THP1mac-Rad21-IFNb-6h.peaks.bed.gz

value: RAD21, Genetex:GTX106012


title: THP1-p65-eGFP-Pam3csk-4h

description:
NFKB p65 ChIP-seq
THP1-p65-eGFP-Pam3csk-4h
Sample249.THP1-p65-eGFP-Pam3csk-4h.peaks.bed.gz

value: THP-1 monocyte AML cell line


title: THP1-PolII-eGFP-Pam3csk-4h

description:
RNAPII ChIP-seq
THP1-PolII-eGFP-Pam3csk-4h
Sample233.THP1-PolII-eGFP-Pam3csk-4h.peaks.bed.gz


title: THP1mac-input-IFNb-0h

description:
Input ChIP-seq
THP1mac-input-IFNb-0h
none


title: THP1mac-Rad21-IFNb-0h

description:
RAD21 (Cohesin) ChIP-seq
THP1mac-Rad21-IFNb-0h
Sample226.THP1mac-Rad21-IFNb-0h.peaks.bed.gz


title: THP1mac-Rad21-Dex-0h

description:
RAD21 (Cohesin) ChIP-seq
THP1mac-Rad21-Dex-0h
Sample224.THP1mac-Rad21-Dex-0h.peaks.bed.gz


title: THP1mac-PolII-Dex-6h

description:
RNAPII ChIP-seq
THP1mac-PolII-Dex-6h
Sample221.THP1mac-PolII-Dex-6h.peaks.bed.gz


title: THP1-H3K27ac

description:
H3K27ac ChIP-seq
THP1-H3K27ac
Sample219.THP1-H3K27ac.peaks.bed.gz

value: H3K27ac, Active Motif:#39133


title: THP1mac-PolII-IFNb-6h

description:
RNAPII ChIP-seq
THP1mac-PolII-IFNb-6h
Sample223.THP1mac-PolII-IFNb-6h.peaks.bed.gz

value: IFNb treated (6h)


title: THP1mac-Rad21-Dex-6h

description:
RAD21 (Cohesin) ChIP-seq
THP1mac-Rad21-Dex-6h
Sample225.THP1mac-Rad21-Dex-6h.peaks.bed.gz


title: THP1mac-PolII-IFNb-0h

description:
RNAPII ChIP-seq
THP1mac-PolII-IFNb-0h
Sample222.THP1mac-PolII-IFNb-0h.peaks.bed.gz


title: THP1mac-PolII-Dex-0h

description:
RNAPII ChIP-seq
THP1mac-PolII-Dex-0h
Sample220.THP1mac-PolII-Dex-0h.peaks.bed.gz


title: THP1-input-Pam3csk-030m-Flavo-000m

description:
Input ChIP-seq
THP1-input-Pam3csk-030m-Flavo-000m
none

value: Pam3csk4 treated (030m)


title: THP1-input-Pam3csk-020m-Flavo-000m

description:
Input ChIP-seq
THP1-input-Pam3csk-020m-Flavo-000m
none

value: Pam3csk4 treated (020m)


title: THP1-input-Pam3csk-025m-Flavo-000m

description:
Input ChIP-seq
THP1-input-Pam3csk-025m-Flavo-000m
none

value: Pam3csk4 treated (025m)


title: THP1-input-Pam3csk-180m-Flavo-060m

description:
Input ChIP-seq
THP1-input-Pam3csk-180m-Flavo-060m
none

value: Pam3csk4 treated (180m) + Flavopiridol (60m)


title: THP1-input-Pam3csk-150m-Flavo-030m

description:
Input ChIP-seq
THP1-input-Pam3csk-150m-Flavo-030m
none

value: Pam3csk4 treated (150m) + Flavopiridol (30m)


title: THP1-input-Pam3csk-060m-Flavo-000m

description:
Input ChIP-seq
THP1-input-Pam3csk-060m-Flavo-000m
none

value: Pam3csk4 treated (060m)


title: THP1-input-Pam3csk-000m-Flavo-240m

description:
Input ChIP-seq
THP1-input-Pam3csk-000m-Flavo-240m
none

value: Flavopiridol (240m)


title: THP1-input-Pam3csk-045m-Flavo-000m

description:
Input ChIP-seq
THP1-input-Pam3csk-045m-Flavo-000m
none

value: Pam3csk4 treated (045m)


title: THP1-input-Pam3csk-000m-Flavo-000m

description:
Input ChIP-seq
THP1-input-Pam3csk-000m-Flavo-000m
none

value: untreated


title: THP1-CTCF-Pam3csk-000m-Flavo-240m

description:
CTCF ChIP-seq
THP1-CTCF-Pam3csk-000m-Flavo-240m
Sample207.THP1-CTCF-Pam3csk-000m-Flavo-240m.peaks.bed.gz


title: THP1-CTCF-Pam3csk-360m-Flavo-240m

description:
CTCF ChIP-seq
THP1-CTCF-Pam3csk-360m-Flavo-240m
Sample206.THP1-CTCF-Pam3csk-360m-Flavo-240m.peaks.bed.gz

value: Pam3csk4 treated (360m) + Flavopiridol (240m)


title: THP1-CTCF-Pam3csk-180m-Flavo-060m

description:
CTCF ChIP-seq
THP1-CTCF-Pam3csk-180m-Flavo-060m
Sample205.THP1-CTCF-Pam3csk-180m-Flavo-060m.peaks.bed.gz


title: THP1-CTCF-Pam3csk-060m-Flavo-000m

description:
CTCF ChIP-seq
THP1-CTCF-Pam3csk-060m-Flavo-000m
Sample202.THP1-CTCF-Pam3csk-060m-Flavo-000m.peaks.bed.gz


title: THP1-CTCF-Pam3csk-120m-Flavo-000m

description:
CTCF ChIP-seq
THP1-CTCF-Pam3csk-120m-Flavo-000m
Sample203.THP1-CTCF-Pam3csk-120m-Flavo-000m.peaks.bed.gz

value: Pam3csk4 treated (120m)


title: THP1-CTCF-Pam3csk-025m-Flavo-000m

description:
CTCF ChIP-seq
THP1-CTCF-Pam3csk-025m-Flavo-000m
Sample199.THP1-CTCF-Pam3csk-025m-Flavo-000m.peaks.bed.gz

value: CTCF, Active Motif:#61311


title: THP1-CTCF-Pam3csk-150m-Flavo-030m

description:
CTCF ChIP-seq
THP1-CTCF-Pam3csk-150m-Flavo-030m
Sample204.THP1-CTCF-Pam3csk-150m-Flavo-030m.peaks.bed.gz


title: THP1-CTCF-Pam3csk-030m-Flavo-000m

description:
CTCF ChIP-seq
THP1-CTCF-Pam3csk-030m-Flavo-000m
Sample200.THP1-CTCF-Pam3csk-030m-Flavo-000m.peaks.bed.gz


title: THP1-CTCF-Pam3csk-020m-Flavo-000m

description:
CTCF ChIP-seq
THP1-CTCF-Pam3csk-020m-Flavo-000m
Sample198.THP1-CTCF-Pam3csk-020m-Flavo-000m.peaks.bed.gz


title: THP1-CTCF-Pam3csk-045m-Flavo-000m

description:
CTCF ChIP-seq
THP1-CTCF-Pam3csk-045m-Flavo-000m
Sample201.THP1-CTCF-Pam3csk-045m-Flavo-000m.peaks.bed.gz


title: THP1-input-Pam3csk-360m-Flavo-240m

description:
Input ChIP-seq
THP1-input-Pam3csk-360m-Flavo-240m
none


title: THP1-input-Pam3csk-120m-Flavo-000m

description:
Input ChIP-seq
THP1-input-Pam3csk-120m-Flavo-000m
none


title: THP1-Rad21-Pam3csk-120m-Flavo-000m

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-Pam3csk-120m-Flavo-000m
Sample192.THP1-Rad21-Pam3csk-120m-Flavo-000m.peaks.bed.gz


title: THP1-Rad21-Pam3csk-060m-Flavo-000m

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-Pam3csk-060m-Flavo-000m
Sample191.THP1-Rad21-Pam3csk-060m-Flavo-000m.peaks.bed.gz


title: THP1-Rad21-Pam3csk-000m-Flavo-240m

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-Pam3csk-000m-Flavo-240m
Sample196.THP1-Rad21-Pam3csk-000m-Flavo-240m.peaks.bed.gz


title: THP1-Rad21-Pam3csk-180m-Flavo-060m

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-Pam3csk-180m-Flavo-060m
Sample194.THP1-Rad21-Pam3csk-180m-Flavo-060m.peaks.bed.gz


title: THP1-Rad21-Pam3csk-025m-Flavo-000m

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-Pam3csk-025m-Flavo-000m
Sample188.THP1-Rad21-Pam3csk-025m-Flavo-000m.peaks.bed.gz


title: THP1-PolII-Pam3csk-000m-Flavo-240m

description:
RNAPII ChIP-seq
THP1-PolII-Pam3csk-000m-Flavo-240m
Sample185.THP1-PolII-Pam3csk-000m-Flavo-240m.peaks.bed.gz

value: PolII, Genetex:GTX102535 (RBP2)


title: THP1-Rad21-Pam3csk-045m-Flavo-000m

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-Pam3csk-045m-Flavo-000m
Sample190.THP1-Rad21-Pam3csk-045m-Flavo-000m.peaks.bed.gz

value: RAD21, Genetex:GTX106012


title: THP1-PolII-Pam3csk-360m-Flavo-240m

description:
RNAPII ChIP-seq
THP1-PolII-Pam3csk-360m-Flavo-240m
Sample184.THP1-PolII-Pam3csk-360m-Flavo-240m.peaks.bed.gz

value: THP-1 monocyte AML cell line


title: THP1-Rad21-Pam3csk-360m-Flavo-240m

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-Pam3csk-360m-Flavo-240m
Sample195.THP1-Rad21-Pam3csk-360m-Flavo-240m.peaks.bed.gz


title: THP1-Rad21-Pam3csk-000m-Flavo-000m

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-Pam3csk-000m-Flavo-000m
Sample186.THP1-Rad21-Pam3csk-000m-Flavo-000m.peaks.bed.gz


title: THP1-Rad21-Pam3csk-020m-Flavo-000m

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-Pam3csk-020m-Flavo-000m
Sample187.THP1-Rad21-Pam3csk-020m-Flavo-000m.peaks.bed.gz


title: THP1-CTCF-Pam3csk-000m-Flavo-000m

description:
CTCF ChIP-seq
THP1-CTCF-Pam3csk-000m-Flavo-000m
Sample197.THP1-CTCF-Pam3csk-000m-Flavo-000m.peaks.bed.gz


title: THP1-PolII-Pam3csk-045m-Flavo-000m

description:
RNAPII ChIP-seq
THP1-PolII-Pam3csk-045m-Flavo-000m
Sample179.THP1-PolII-Pam3csk-045m-Flavo-000m.peaks.bed.gz


title: THP1-PolII-Pam3csk-020m-Flavo-000m

description:
RNAPII ChIP-seq
THP1-PolII-Pam3csk-020m-Flavo-000m
Sample176.THP1-PolII-Pam3csk-020m-Flavo-000m.peaks.bed.gz


title: THP1-PolII-Pam3csk-030m-Flavo-000m

description:
RNAPII ChIP-seq
THP1-PolII-Pam3csk-030m-Flavo-000m
Sample178.THP1-PolII-Pam3csk-030m-Flavo-000m.peaks.bed.gz


title: THP1-PolII-Pam3csk-120m-Flavo-000m

description:
RNAPII ChIP-seq
THP1-PolII-Pam3csk-120m-Flavo-000m
Sample181.THP1-PolII-Pam3csk-120m-Flavo-000m.peaks.bed.gz


title: THP1-PolII-Pam3csk-180m-Flavo-060m

description:
RNAPII ChIP-seq
THP1-PolII-Pam3csk-180m-Flavo-060m
Sample183.THP1-PolII-Pam3csk-180m-Flavo-060m.peaks.bed.gz


title: THP1-PolII-Pam3csk-025m-Flavo-000m

description:
RNAPII ChIP-seq
THP1-PolII-Pam3csk-025m-Flavo-000m
Sample177.THP1-PolII-Pam3csk-025m-Flavo-000m.peaks.bed.gz


title: THP1-PolII-Pam3csk-000m-Flavo-000m

description:
RNAPII ChIP-seq
THP1-PolII-Pam3csk-000m-Flavo-000m
Sample175.THP1-PolII-Pam3csk-000m-Flavo-000m.peaks.bed.gz


title: THP1-PolII-Pam3csk-150m-Flavo-030m

description:
RNAPII ChIP-seq
THP1-PolII-Pam3csk-150m-Flavo-030m
Sample182.THP1-PolII-Pam3csk-150m-Flavo-030m.peaks.bed.gz


title: THP1-Rad21-Pam3csk-150m-Flavo-030m

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-Pam3csk-150m-Flavo-030m
Sample193.THP1-Rad21-Pam3csk-150m-Flavo-030m.peaks.bed.gz


title: THP1-input-siWAPL-NS1-Pam3csk-4h

description:
Input ChIP-seq
THP1-input-siWAPL-NS1-Pam3csk-4h
none

value: Pam3csk4 treated (4h)

value: IAV NS1

value: siWAPL


title: THP1-PolII-Pam3csk-060m-Flavo-000m

description:
RNAPII ChIP-seq
THP1-PolII-Pam3csk-060m-Flavo-000m
Sample180.THP1-PolII-Pam3csk-060m-Flavo-000m.peaks.bed.gz


title: THP1-input-siNIPBL-NS1-Pam3csk-4h

description:
Input ChIP-seq
THP1-input-siNIPBL-NS1-Pam3csk-4h
none

value: siNIPBL


title: THP1-CTCF-siWAPL-NS1-Pam3csk-4h

description:
CTCF ChIP-seq
THP1-CTCF-siWAPL-NS1-Pam3csk-4h
Sample170.THP1-CTCF-siWAPL-NS1-Pam3csk-4h.peaks.bed.gz


title: THP1-CTCF-siWAPL-eGFP-Pam3csk-4h

description:
CTCF ChIP-seq
THP1-CTCF-siWAPL-eGFP-Pam3csk-4h
Sample169.THP1-CTCF-siWAPL-eGFP-Pam3csk-4h.peaks.bed.gz

value: eGFP


title: THP1-CTCF-siNIPBL-eGFP-Pam3csk-4h

description:
CTCF ChIP-seq
THP1-CTCF-siNIPBL-eGFP-Pam3csk-4h
Sample166.THP1-CTCF-siNIPBL-eGFP-Pam3csk-4h.peaks.bed.gz


description:
CTCF ChIP-seq
THP1-CTCF-siNIPBL-NS1-Pam3csk-7h-Flavo-3h
Sample168.THP1-CTCF-siNIPBL-NS1-Pam3csk-7h-Flavo-3h.peaks.bed.gz

value: Pam3csk4 treated (7h) + Flavopiridol (3h)


title: THP1-CTCF-siCtrl-NS1-Pam3csk-4h

description:
CTCF ChIP-seq
THP1-CTCF-siCtrl-NS1-Pam3csk-4h
Sample164.THP1-CTCF-siCtrl-NS1-Pam3csk-4h.peaks.bed.gz

value: siCtrl


title: THP1-CTCF-siNIPBL-NS1-Pam3csk-4h

description:
CTCF ChIP-seq
THP1-CTCF-siNIPBL-NS1-Pam3csk-4h
Sample167.THP1-CTCF-siNIPBL-NS1-Pam3csk-4h.peaks.bed.gz


title: THP1-Rad21-Pam3csk-030m-Flavo-000m

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-Pam3csk-030m-Flavo-000m
Sample189.THP1-Rad21-Pam3csk-030m-Flavo-000m.peaks.bed.gz

value: Pam3csk4 treated (030m)


title: THP1-CTCF-siCtrl-eGFP-Pam3csk-0h

description:
CTCF ChIP-seq
THP1-CTCF-siCtrl-eGFP-Pam3csk-0h
Sample161.THP1-CTCF-siCtrl-eGFP-Pam3csk-0h.peaks.bed.gz


title: THP1-CTCF-siCtrl-NS1-Pam3csk-0h

description:
CTCF ChIP-seq
THP1-CTCF-siCtrl-NS1-Pam3csk-0h
Sample163.THP1-CTCF-siCtrl-NS1-Pam3csk-0h.peaks.bed.gz


title: THP1-Rad21-siWAPL-NS1-Pam3csk-4h

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-siWAPL-NS1-Pam3csk-4h
Sample159.THP1-Rad21-siWAPL-NS1-Pam3csk-4h.peaks.bed.gz


title: THP1-Rad21-siWAPL-eGFP-Pam3csk-4h

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-siWAPL-eGFP-Pam3csk-4h
Sample158.THP1-Rad21-siWAPL-eGFP-Pam3csk-4h.peaks.bed.gz


description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-siWAPL-NS1-Pam3csk-7h-Flavo-3h
Sample160.THP1-Rad21-siWAPL-NS1-Pam3csk-7h-Flavo-3h.peaks.bed.gz


title: THP1-Rad21-siNIPBL-NS1-Pam3csk-4h

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-siNIPBL-NS1-Pam3csk-4h
Sample156.THP1-Rad21-siNIPBL-NS1-Pam3csk-4h.peaks.bed.gz


title: THP1-Rad21-siNIPBL-eGFP-Pam3csk-4h

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-siNIPBL-eGFP-Pam3csk-4h
Sample155.THP1-Rad21-siNIPBL-eGFP-Pam3csk-4h.peaks.bed.gz


description:
CTCF ChIP-seq
THP1-CTCF-siWAPL-NS1-Pam3csk-7h-Flavo-3h
Sample171.THP1-CTCF-siWAPL-NS1-Pam3csk-7h-Flavo-3h.peaks.bed.gz


title: THP1-Rad21-siCtrl-eGFP-Pam3csk-4h

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-siCtrl-eGFP-Pam3csk-4h
Sample151.THP1-Rad21-siCtrl-eGFP-Pam3csk-4h.peaks.bed.gz


title: THP1-PolII-siWAPL-eGFP-Pam3csk-4h

description:
RNAPII ChIP-seq
THP1-PolII-siWAPL-eGFP-Pam3csk-4h
Sample147.THP1-PolII-siWAPL-eGFP-Pam3csk-4h.peaks.bed.gz


title: THP1-Rad21-siCtrl-NS1-Pam3csk-4h

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-siCtrl-NS1-Pam3csk-4h
Sample153.THP1-Rad21-siCtrl-NS1-Pam3csk-4h.peaks.bed.gz


description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-siCtrl-NS1-Pam3csk-7h-Flavo-3h
Sample154.THP1-Rad21-siCtrl-NS1-Pam3csk-7h-Flavo-3h.peaks.bed.gz


title: THP1-PolII-siNIPBL-NS1-Pam3csk-4h

description:
RNAPII ChIP-seq
THP1-PolII-siNIPBL-NS1-Pam3csk-4h
Sample145.THP1-PolII-siNIPBL-NS1-Pam3csk-4h.peaks.bed.gz


description:
RNAPII ChIP-seq
THP1-PolII-siNIPBL-NS1-Pam3csk-7h-Flavo-3h
Sample146.THP1-PolII-siNIPBL-NS1-Pam3csk-7h-Flavo-3h.peaks.bed.gz


description:
CTCF ChIP-seq
THP1-CTCF-siCtrl-NS1-Pam3csk-7h-Flavo-3h
Sample165.THP1-CTCF-siCtrl-NS1-Pam3csk-7h-Flavo-3h.peaks.bed.gz


title: THP1-Rad21-siCtrl-eGFP-Pam3csk-0h

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-siCtrl-eGFP-Pam3csk-0h
Sample150.THP1-Rad21-siCtrl-eGFP-Pam3csk-0h.peaks.bed.gz


title: THP1-Rad21-siCtrl-NS1-Pam3csk-0h

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-siCtrl-NS1-Pam3csk-0h
Sample152.THP1-Rad21-siCtrl-NS1-Pam3csk-0h.peaks.bed.gz


title: THP1-PolII-siCtrl-NS1-Pam3csk-4h

description:
RNAPII ChIP-seq
THP1-PolII-siCtrl-NS1-Pam3csk-4h
Sample142.THP1-PolII-siCtrl-NS1-Pam3csk-4h.peaks.bed.gz


title: THP1-PolII-siNIPBL-eGFP-Pam3csk-4h

description:
RNAPII ChIP-seq
THP1-PolII-siNIPBL-eGFP-Pam3csk-4h
Sample144.THP1-PolII-siNIPBL-eGFP-Pam3csk-4h.peaks.bed.gz


title: THP1-PolII-siCtrl-eGFP-Pam3csk-0h

description:
RNAPII ChIP-seq
THP1-PolII-siCtrl-eGFP-Pam3csk-0h
Sample139.THP1-PolII-siCtrl-eGFP-Pam3csk-0h.peaks.bed.gz


title: THP1-CTCF-siCtrl-eGFP-Pam3csk-4h

description:
CTCF ChIP-seq
THP1-CTCF-siCtrl-eGFP-Pam3csk-4h
Sample162.THP1-CTCF-siCtrl-eGFP-Pam3csk-4h.peaks.bed.gz


description:
Input ChIP-seq
THP1-input-siCtrl-NS1-Pam3csk-7h-Flavo-3h
none


title: THP1-PolII-siCtrl-NS1-Pam3csk-0h

description:
RNAPII ChIP-seq
THP1-PolII-siCtrl-NS1-Pam3csk-0h
Sample141.THP1-PolII-siCtrl-NS1-Pam3csk-0h.peaks.bed.gz


title: THP1-PolII-siCtrl-eGFP-Pam3csk-4h

description:
RNAPII ChIP-seq
THP1-PolII-siCtrl-eGFP-Pam3csk-4h
Sample140.THP1-PolII-siCtrl-eGFP-Pam3csk-4h.peaks.bed.gz


title: THP1-HiC-siWAPL-NS1-Pam3csk-4h

description:
in situ Hi-C
THP1-HiC-siWAPL-NS1-Pam3csk-4h
Sample129.THP1-HiC-siWAPL-NS1-Pam3csk-4h.hic


title: THP1-HiC-siWAPL-eGFP-Pam3csk-4h

description:
in situ Hi-C
THP1-HiC-siWAPL-eGFP-Pam3csk-4h
Sample128.THP1-HiC-siWAPL-eGFP-Pam3csk-4h.hic


title: THP1-PolII-siWAPL-NS1-Pam3csk-4h

description:
RNAPII ChIP-seq
THP1-PolII-siWAPL-NS1-Pam3csk-4h
Sample148.THP1-PolII-siWAPL-NS1-Pam3csk-4h.peaks.bed.gz


description:
RNAPII ChIP-seq
THP1-PolII-siWAPL-NS1-Pam3csk-7h-Flavo-3h
Sample149.THP1-PolII-siWAPL-NS1-Pam3csk-7h-Flavo-3h.peaks.bed.gz


title: THP1-HiC-siWAPL-NS1-Pam3csk-7h-Flavo-3h

description:
in situ Hi-C
THP1-HiC-siWAPL-NS1-Pam3csk-7h-Flavo-3h
Sample130.THP1-HiC-siWAPL-NS1-Pam3csk-7h-Flavo-3h.hic


title: THP1-HiC-siCtrl-NS1-Pam3csk-7h-Flavo-3h

description:
in situ Hi-C
THP1-HiC-siCtrl-NS1-Pam3csk-7h-Flavo-3h
Sample124.THP1-HiC-siCtrl-NS1-Pam3csk-7h-Flavo-3h.hic


title: THP1-HiC-siNIPBL-NS1-Pam3csk-4h

description:
in situ Hi-C
THP1-HiC-siNIPBL-NS1-Pam3csk-4h
Sample126.THP1-HiC-siNIPBL-NS1-Pam3csk-4h.hic


title: THP1-HiC-siCtrl-NS1-Pam3csk-4h

description:
in situ Hi-C
THP1-HiC-siCtrl-NS1-Pam3csk-4h
Sample123.THP1-HiC-siCtrl-NS1-Pam3csk-4h.hic


description:
in situ Hi-C
THP1-HiC-siNIPBL-NS1-Pam3csk-7h-Flavo-3h
Sample127.THP1-HiC-siNIPBL-NS1-Pam3csk-7h-Flavo-3h.hic


description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-siNIPBL-NS1-Pam3csk-7h-Flavo-3h
Sample157.THP1-Rad21-siNIPBL-NS1-Pam3csk-7h-Flavo-3h.peaks.bed.gz


title: THP1-input

description:
Input ChIP-seq
THP1-input
none

value: IFNb treated (06h)


title: THP1-HiC-siNIPBL-eGFP-Pam3csk-4h

description:
in situ Hi-C
THP1-HiC-siNIPBL-eGFP-Pam3csk-4h
Sample125.THP1-HiC-siNIPBL-eGFP-Pam3csk-4h.hic


title: THP1-HiC-siCtrl-NS1-Pam3csk-0h

description:
in situ Hi-C
THP1-HiC-siCtrl-NS1-Pam3csk-0h
Sample122.THP1-HiC-siCtrl-NS1-Pam3csk-0h.hic


title: THP1-CTCF-NS1-IFNb-r2

description:
CTCF ChIP-seq
THP1-CTCF-NS1-IFNb-r2
Sample116.THP1-CTCF-NS1-IFNb-r1.peaks.bed.gz


title: MDM-mCpG-H5N1

description:
bisulfite/methylC-seq
MDM-mCpG-H5N1
Sample119.MDM-mCpG-H5N1.bedGraph.gz

source_name: monocyte derived macrophages (MDM)

value: monocyte derived macrophages (MDM)

value: H5N1 IAV infected (06h)


title: THP1-HiC-siCtrl-eGFP-Pam3csk-4h

description:
in situ Hi-C
THP1-HiC-siCtrl-eGFP-Pam3csk-4h
Sample121.THP1-HiC-siCtrl-eGFP-Pam3csk-4h.hic


title: THP1-CTCF-eGFP-IFNb-r1

description:
CTCF ChIP-seq
THP1-CTCF-eGFP-IFNb-r1
Sample115.THP1-CTCF-eGFP-IFNb-r1.peaks.bed.gz


title: MDM-mCpG-Mock

description:
bisulfite/methylC-seq
MDM-mCpG-Mock
Sample118.MDM-mCpG-Mock.bedGraph.gz

value: mock infected (06h)


title: THP1-PolII-NS1-IFNb-r1

description:
RNAPII ChIP-seq
THP1-PolII-NS1-IFNb-r1
Sample112.THP1-PolII-NS1-IFNb-r1.peaks.bed.gz


title: THP1-PolII-NS1-IFNb-Flavopiridol-r1

description:
RNAPII ChIP-seq
THP1-PolII-NS1-IFNb-Flavopiridol-r1
Sample114.THP1-PolII-NS1-IFNb-Flavopiridol-r1.peaks.bed.gz

value: IFNb treated (06h) + Flavopiridol (03h)


description:
RNAPII ChIP-seq
THP1-PolII-siCtrl-NS1-Pam3csk-7h-Flavo-3h
Sample143.THP1-PolII-siCtrl-NS1-Pam3csk-7h-Flavo-3h.peaks.bed.gz


title: THP1-HiC-siCtrl-eGFP-Pam3csk-0h

description:
in situ Hi-C
THP1-HiC-siCtrl-eGFP-Pam3csk-0h
Sample120.THP1-HiC-siCtrl-eGFP-Pam3csk-0h.hic

value: untreated


title: THP1-PolII-eGFP-IFNb-r2

description:
RNAPII ChIP-seq
THP1-PolII-eGFP-IFNb-r2
Sample111.THP1-PolII-eGFP-IFNb-r2.peaks.bed.gz

value: PolII, Genetex:GTX102535 (RBP2)


title: THP1-PolII-NS1-IFNb-r2

description:
RNAPII ChIP-seq
THP1-PolII-NS1-IFNb-r2
Sample113.THP1-PolII-NS1-IFNb-r2.peaks.bed.gz


title: THP1-Rad21-NS1-IFNb-Flavopiridol-r1

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-NS1-IFNb-Flavopiridol-r1
Sample109.THP1-Rad21-NS1-IFNb-Flavopiridol-r1.peaks.bed.gz

value: RAD21, Genetex:GTX106012


title: THP1-PolII-eGFP-IFNb-r1

description:
RNAPII ChIP-seq
THP1-PolII-eGFP-IFNb-r1
Sample110.THP1-PolII-eGFP-IFNb-r1.peaks.bed.gz

value: THP-1 monocyte AML cell line


title: THP1-Rad21-NS1-IFNb-r2

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-NS1-IFNb-r2
Sample108.THP1-Rad21-NS1-IFNb-r2.peaks.bed.gz


title: THP1-Rad21-eGFP-IFNb-r2

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-eGFP-IFNb-r2
Sample106.THP1-Rad21-eGFP-IFNb-r2.peaks.bed.gz


title: THP1-Rad21-eGFP-IFNb-r1

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-eGFP-IFNb-r1
Sample105.THP1-Rad21-eGFP-IFNb-r1.peaks.bed.gz


title: MDM-PU1-dNS1-r1

description:
PU.1 ChIP-seq
MDM-PU1-dNS1-r1
Sample102.MDM-PU1-dNS1.peaks.bed.gz

value: H5N1-dNS1 IAV infected (06h)

value: PU.1, Santa Cruz:sc-352


title: MDM-Input-Mock-r1

description:
Input ChIP-seq
MDM-Input-Mock-r1
none


title: MDM-PU1-Mock-r1

description:
PU.1 ChIP-seq
MDM-PU1-Mock-r1
Sample100.MDM-PU1-Mock.peaks.bed.gz


title: MDM-PU1-IFNb-r1

description:
PU.1 ChIP-seq
MDM-PU1-IFNb-r1
Sample103.MDM-PU1-IFNb.peaks.bed.gz


title: MDM-PU1-H5N1-r1

description:
PU.1 ChIP-seq
MDM-PU1-H5N1-r1
Sample101.MDM-PU1-H5N1.peaks.bed.gz


title: MDM-PolIIs7p-dNS1-r1

description:
PolIIs7p ChIP-seq
MDM-PolIIs7p-dNS1-r1
Sample98.MDM-PolIIs7p-dNS1.peaks.bed.gz

value: PolIIs7p, EMD Millipore:04-1570


title: MDM-PolIIs7p-Mock-r1

description:
PolIIs7p ChIP-seq
MDM-PolIIs7p-Mock-r1
Sample96.MDM-PolIIs7p-Mock.peaks.bed.gz


title: MDM-PolIIs5p-IFNb-r1

description:
PolIIs5p ChIP-seq
MDM-PolIIs5p-IFNb-r1
Sample95.MDM-PolIIs5p-IFNb.peaks.bed.gz

value: PolIIs5p, Diagenode:C15200007


title: MDM-PolIIs5p-dNS1-r1

description:
PolIIs5p ChIP-seq
MDM-PolIIs5p-dNS1-r1
Sample94.MDM-PolIIs5p-dNS1.peaks.bed.gz


title: MDM-PolIIs2p-dNS1-r1

description:
PolIIs2p ChIP-seq
MDM-PolIIs2p-dNS1-r1
Sample90.MDM-PolIIs2p-dNS1.peaks.bed.gz

value: PolIIs2p, Diagenode:C15200005


title: MDM-PolIIs5p-H5N1-r1

description:
PolIIs5p ChIP-seq
MDM-PolIIs5p-H5N1-r1
Sample93.MDM-PolIIs5p-H5N1.peaks.bed.gz


title: MDM-PolIIs2p-H5N1-r1

description:
PolIIs2p ChIP-seq
MDM-PolIIs2p-H5N1-r1
Sample89.MDM-PolIIs2p-H5N1.peaks.bed.gz


title: MDM-PolIIs5p-Mock-r1

description:
PolIIs5p ChIP-seq
MDM-PolIIs5p-Mock-r1
Sample92.MDM-PolIIs5p-Mock.peaks.bed.gz


title: MDM-PolIIs2p-IFNb-r1

description:
PolIIs2p ChIP-seq
MDM-PolIIs2p-IFNb-r1
Sample91.MDM-PolIIs2p-IFNb.peaks.bed.gz


title: MDM-PolIIs7p-H5N1-r1

description:
PolIIs7p ChIP-seq
MDM-PolIIs7p-H5N1-r1
Sample97.MDM-PolIIs7p-H5N1.peaks.bed.gz


title: MDM-PolII-IFNb-r1

description:
RNAPII ChIP-seq
MDM-PolII-IFNb-r1
Sample86.MDM-PolII-IFNb.peaks.bed.gz


title: MDM-PolIIs2p-Mock-r1

description:
PolIIs2p ChIP-seq
MDM-PolIIs2p-Mock-r1
Sample88.MDM-PolIIs2p-Mock.peaks.bed.gz


title: MDM-PolIIs7p-IFNb-r1

description:
PolIIs7p ChIP-seq
MDM-PolIIs7p-IFNb-r1
Sample99.MDM-PolIIs7p-IFNb.peaks.bed.gz


title: MDM-PolII-dNS1-r1

description:
RNAPII ChIP-seq
MDM-PolII-dNS1-r1
Sample84.MDM-PolII-dNS1.peaks.bed.gz


title: MDM-PolII-dNS1-r2

description:
RNAPII ChIP-seq
MDM-PolII-dNS1-r2
Sample84.MDM-PolII-dNS1.peaks.bed.gz


title: MDM-H3K9me3-IFNb-r1

description:
H3K9me3 ChIP-seq
MDM-H3K9me3-IFNb-r1
Sample78.MDM-H3K9me3-IFNb.peaks.bed.gz

value: H3K9me3, Abcam:ab8898


title: MDM-PolII-H5N1-r2

description:
RNAPII ChIP-seq
MDM-PolII-H5N1-r2
Sample82.MDM-PolII-H5N1.peaks.bed.gz


title: MDM-PolII-Mock-r1

description:
RNAPII ChIP-seq
MDM-PolII-Mock-r1
Sample80.MDM-PolII-Mock.peaks.bed.gz


title: MDM-PolII-Mock-r2

description:
RNAPII ChIP-seq
MDM-PolII-Mock-r2
Sample80.MDM-PolII-Mock.peaks.bed.gz


title: MDM-PolII-H5N1-r1

description:
RNAPII ChIP-seq
MDM-PolII-H5N1-r1
Sample82.MDM-PolII-H5N1.peaks.bed.gz


title: MDM-PolII-IFNb-r2

description:
RNAPII ChIP-seq
MDM-PolII-IFNb-r2
Sample86.MDM-PolII-IFNb.peaks.bed.gz


title: THP1-Rad21-NS1-IFNb-r1

description:
RAD21 (Cohesin) ChIP-seq
THP1-Rad21-NS1-IFNb-r1
Sample107.THP1-Rad21-NS1-IFNb-r1.peaks.bed.gz

value: IAV NS1


title: MDM-H3K9me3-dNS1-r2

description:
H3K9me3 ChIP-seq
MDM-H3K9me3-dNS1-r2
Sample76.MDM-H3K9me3-dNS1.peaks.bed.gz


title: MDM-H3K9me3-H5N1-r2

description:
H3K9me3 ChIP-seq
MDM-H3K9me3-H5N1-r2
Sample74.MDM-H3K9me3-H5N1.peaks.bed.gz


title: MDM-H3K9me3-Mock-r2

description:
H3K9me3 ChIP-seq
MDM-H3K9me3-Mock-r2
Sample72.MDM-H3K9me3-Mock.peaks.bed.gz


title: MDM-H3K9me3-Mock-r1

description:
H3K9me3 ChIP-seq
MDM-H3K9me3-Mock-r1
Sample72.MDM-H3K9me3-Mock.peaks.bed.gz


title: MDM-H3K4me3-IFNb-r1

description:
H3K4me3 ChIP-seq
MDM-H3K4me3-IFNb-r1
Sample71.MDM-H3K4me3-IFNb.peaks.bed.gz

value: H3K4me3, Abcam:ab8580


title: MDM-H3K9me3-IFNb-r2

description:
H3K9me3 ChIP-seq
MDM-H3K9me3-IFNb-r2
Sample78.MDM-H3K9me3-IFNb.peaks.bed.gz

value: IFNb treated (06h)


title: MDM-H3K4me3-dNS1-r1

description:
H3K4me3 ChIP-seq
MDM-H3K4me3-dNS1-r1
Sample70.MDM-H3K4me3-dNS1.peaks.bed.gz

value: monocyte derived macrophages (MDM)


title: MDM-H3K9me3-dNS1-r1

description:
H3K9me3 ChIP-seq
MDM-H3K9me3-dNS1-r1
Sample76.MDM-H3K9me3-dNS1.peaks.bed.gz


title: MDM-H3K4me3-H5N1-r1

description:
H3K4me3 ChIP-seq
MDM-H3K4me3-H5N1-r1
Sample69.MDM-H3K4me3-H5N1.peaks.bed.gz

value: H5N1 IAV infected


title: MDM-H3K36me3-IFNb-r1

description:
H3K36me3 ChIP-seq
MDM-H3K36me3-IFNb-r1
Sample66.MDM-H3K36me3-IFNb.peaks.bed.gz

value: H3K36me3, Abcam:ab9050


title: MDM-H3K9me3-H5N1-r1

description:
H3K9me3 ChIP-seq
MDM-H3K9me3-H5N1-r1
Sample74.MDM-H3K9me3-H5N1.peaks.bed.gz

value: H5N1 IAV infected (06h)


title: MDM-H3K36me3-dNS1-r1

description:
H3K36me3 ChIP-seq
MDM-H3K36me3-dNS1-r1
Sample64.MDM-H3K36me3-dNS1.peaks.bed.gz


title: MDM-H3K36me3-Mock-r1

description:
H3K36me3 ChIP-seq
MDM-H3K36me3-Mock-r1
Sample60.MDM-H3K36me3-Mock.peaks.bed.gz

value: mock infected (06h)


title: MDM-H3K36me3-dNS1-r2

description:
H3K36me3 ChIP-seq
MDM-H3K36me3-dNS1-r2
Sample64.MDM-H3K36me3-dNS1.peaks.bed.gz


title: MDM-H3K36me3-H5N1-r1

description:
H3K36me3 ChIP-seq
MDM-H3K36me3-H5N1-r1
Sample62.MDM-H3K36me3-H5N1.peaks.bed.gz


title: MDM-H3K4me3-Mock-r1

description:
H3K4me3 ChIP-seq
MDM-H3K4me3-Mock-r1
Sample68.MDM-H3K4me3-Mock.peaks.bed.gz


title: MDM-H3K27me3-dNS1-r2

description:
H3K27me3 ChIP-seq
MDM-H3K27me3-dNS1-r2
Sample56.MDM-H3K27me3-dNS1.peaks.bed.gz

value: H3K27me3, EMD Millipore:07-0449


title: MDM-H3K27me3-H5N1-r2

description:
H3K27me3 ChIP-seq
MDM-H3K27me3-H5N1-r2
Sample54.MDM-H3K27me3-H5N1.peaks.bed.gz


title: MDM-H3K27ac-dNS1-r1

description:
H3K27ac ChIP-seq
MDM-H3K27ac-dNS1-r1
Sample50.MDM-H3K27ac-dNS1.peaks.bed.gz

value: H3K27ac, Active Motif:#39133


title: MDM-H3K36me3-Mock-r2

description:
H3K36me3 ChIP-seq
MDM-H3K36me3-Mock-r2
Sample60.MDM-H3K36me3-Mock.peaks.bed.gz


title: MDM-H3K27me3-IFNb-r2

description:
H3K27me3 ChIP-seq
MDM-H3K27me3-IFNb-r2
Sample58.MDM-H3K27me3-IFNb.peaks.bed.gz


title: MDM-H3K27me3-IFNb-r1

description:
H3K27me3 ChIP-seq
MDM-H3K27me3-IFNb-r1
Sample58.MDM-H3K27me3-IFNb.peaks.bed.gz


title: MDM-H3K27me3-dNS1-r1

description:
H3K27me3 ChIP-seq
MDM-H3K27me3-dNS1-r1
Sample56.MDM-H3K27me3-dNS1.peaks.bed.gz


title: MDM-H3K27ac-IFNb-r1

description:
H3K27ac ChIP-seq
MDM-H3K27ac-IFNb-r1
Sample51.MDM-H3K27ac-IFNb.peaks.bed.gz


title: MDM-H3K27me3-Mock-r2

description:
H3K27me3 ChIP-seq
MDM-H3K27me3-Mock-r2
Sample52.MDM-H3K27me3-Mock.peaks.bed.gz


title: MDM-H3K27ac-H5N1-r1

description:
H3K27ac ChIP-seq
MDM-H3K27ac-H5N1-r1
Sample49.MDM-H3K27ac-H5N1.peaks.bed.gz


title: MDM-H3K27me3-H5N1-r1

description:
H3K27me3 ChIP-seq
MDM-H3K27me3-H5N1-r1
Sample54.MDM-H3K27me3-H5N1.peaks.bed.gz


title: MDM-H3K36me3-H5N1-r2

description:
H3K36me3 ChIP-seq
MDM-H3K36me3-H5N1-r2
Sample62.MDM-H3K36me3-H5N1.peaks.bed.gz


title: MDM-Rad21-IFNb-r1

description:
RAD21 (Cohesin) ChIP-seq
MDM-Rad21-IFNb-r1
Sample47.MDM-Rad21-IFNb.peaks.bed.gz

value: RAD21, Genetex:GTX106012


title: MDM-CTCF-H5N1-r2

description:
CTCF ChIP-seq
MDM-CTCF-H5N1-r2
Sample38.MDM-CTCF-H5N1.peaks.bed.gz

value: CTCF, Active Motif:#61311


title: MDM-Rad21-Mock-r1

description:
RAD21 (Cohesin) ChIP-seq
MDM-Rad21-Mock-r1
Sample44.MDM-Rad21-Mock.peaks.bed.gz


title: THP1-RNAseq-NS1-IFNb-r1

description:
total strand-specific RNA-seq
THP1-RNAseq-NS1-IFNb-r1
fpkm.txt.gz

value: THP-1 monocyte AML cell line


title: MDM-H3K27me3-Mock-r1

description:
H3K27me3 ChIP-seq
MDM-H3K27me3-Mock-r1
Sample52.MDM-H3K27me3-Mock.peaks.bed.gz


title: MDM-CTCF-Mock-r1

description:
CTCF ChIP-seq
MDM-CTCF-Mock-r1
Sample36.MDM-CTCF-Mock.peaks.bed.gz


title: THP1-RNAseq-eGFP-IFNb-r1

description:
total strand-specific RNA-seq
THP1-RNAseq-eGFP-IFNb-r1
fpkm.txt.gz

value: eGFP


title: MDM-H3K27ac-Mock-r1

description:
H3K27ac ChIP-seq
MDM-H3K27ac-Mock-r1
Sample48.MDM-H3K27ac-Mock.peaks.bed.gz


title: MDM-CTCF-IFNb-r1

description:
CTCF ChIP-seq
MDM-CTCF-IFNb-r1
Sample42.MDM-CTCF-IFNb.peaks.bed.gz


title: MDM-H3K36me3-IFNb-r2

description:
H3K36me3 ChIP-seq
MDM-H3K36me3-IFNb-r2
Sample66.MDM-H3K36me3-IFNb.peaks.bed.gz


title: MDM-CTCF-dNS1-r1

description:
CTCF ChIP-seq
MDM-CTCF-dNS1-r1
Sample40.MDM-CTCF-dNS1.peaks.bed.gz

value: H5N1-dNS1 IAV infected (06h)


title: MDM-Rad21-H5N1-r1

description:
RAD21 (Cohesin) ChIP-seq
MDM-Rad21-H5N1-r1
Sample45.MDM-Rad21-H5N1.peaks.bed.gz


title: THP1-HiC-NS1-IFNb-r1

description:
in situ Hi-C
THP1-HiC-NS1-IFNb-r1
Sample23.THP1-HiC-NS1-IFNb.hic


title: THP1-HiC-NS1-IFNb-Flavopiridol-r1

description:
in situ Hi-C
THP1-HiC-NS1-IFNb-Flavopiridol-r1
Sample25.THP1-HiC-NS1-IFNb-Flavopiridol.hic

value: IFNb treated (06h) + Flavopiridol (03h)


title: MDM-CTCF-dNS1-r2

description:
CTCF ChIP-seq
MDM-CTCF-dNS1-r2
Sample40.MDM-CTCF-dNS1.peaks.bed.gz


title: MDM-Rad21-dNS1-r1

description:
RAD21 (Cohesin) ChIP-seq
MDM-Rad21-dNS1-r1
Sample46.MDM-Rad21-dNS1.peaks.bed.gz


title: THP1-HiC-eGFP-IFNb-r2

description:
in situ Hi-C
THP1-HiC-eGFP-IFNb-r2
Sample21.THP1-HiC-eGFP-IFNb.hic


title: MDM-CTCF-Mock-r2

description:
CTCF ChIP-seq
MDM-CTCF-Mock-r2
Sample36.MDM-CTCF-Mock.peaks.bed.gz


title: THP1-HiC-NS1-IFNb-r2

description:
in situ Hi-C
THP1-HiC-NS1-IFNb-r2
Sample23.THP1-HiC-NS1-IFNb.hic


title: MDM-CTCF-H5N1-r1

description:
CTCF ChIP-seq
MDM-CTCF-H5N1-r1
Sample38.MDM-CTCF-H5N1.peaks.bed.gz


title: THP1-HiC-eGFP-IFNb-r1

description:
in situ Hi-C
THP1-HiC-eGFP-IFNb-r1
Sample21.THP1-HiC-eGFP-IFNb.hic


title: MDM-CTCF-IFNb-r2

description:
CTCF ChIP-seq
MDM-CTCF-IFNb-r2
Sample42.MDM-CTCF-IFNb.peaks.bed.gz


title: MDM-HiC-06h-IFNb-r2

description:
in situ Hi-C
MDM-HiC-06h-IFNb-r2
Sample19.MDM-HiC-06h-IFNb.hic


title: MDM-HiC-06h-IFNb-r1

description:
in situ Hi-C
MDM-HiC-06h-IFNb-r1
Sample19.MDM-HiC-06h-IFNb.hic


title: MDM-HiC-06h-dNS1-r2

description:
in situ Hi-C
MDM-HiC-06h-dNS1-r2
Sample17.MDM-HiC-06h-dNS1.hic


title: MDM-HiC-06h-Mock-r4

description:
in situ Hi-C
MDM-HiC-06h-Mock-r4
Sample13.MDM-HiC-06h-Mock.hic


title: MDM-HiC-06h-dNS1-r1

description:
in situ Hi-C
MDM-HiC-06h-dNS1-r1
Sample17.MDM-HiC-06h-dNS1.hic


title: MDM-HiC-06h-H5N1-r3

description:
in situ Hi-C
MDM-HiC-06h-H5N1-r3
Sample15.MDM-HiC-06h-H5N1.hic


title: MDM-HiC-06h-Mock-r3

description:
in situ Hi-C
MDM-HiC-06h-Mock-r3
Sample13.MDM-HiC-06h-Mock.hic


title: H3K27me3_ChOR-seq_T10+EZH2i_rep2

data_processing:
Library strategy: ChOR-seq
Illumina RTAv2 software was used for basecalling
Reads were aligned to  human genome assembly (GRCh37/hg19) and D. melanogaster genome assembly (BDGP R5/dm3) by Bowtie v. 1.1.2 using parameters -m1 --best. Mapping and subsequent analysis of the data were done using local Galaxy server and custom R scripts
PCR duplicates were removed using RmDup v.2.0 and unique mapped reads were extended to 250 bp (H3K4me3) or 500bp (H3K27me3) to account for the average library size.
Reads were summed in 500 bp non-overlapping bins.
For ChIP-seq samples, reads were normalized to Reads Per Million (RPM).
For ChOR-seq samples, reads were normalized to Reference-adjusted RPM (RRPM) dividing human  values by total Drosophila unique mapped reads.
Peak calling was performed with MACS v. 2.0.9 under broad domain parameters using Parental ChIP-seq of Total H3 from each experiment as a reference.
Genome_build: hg19 and dm3
Supplementary_files_format_and_content: bedgraph files were generated using Galaxy. Scores represent the sum of RPM or RRPM in 500bp windows

growth_protocol: HeLa S3 were grown in suspension in spinners in DMEM medium (Thermo Fisher Scientific) supplemented with dialyzed FBS (Invitrogen) and penicillin and streptomycin at 37ºC and 5% CO2. Asynchronous Drosophila S2-DRSC cells were grown in suspension in spinners in M3+BPYE (Sigma-Aldrich) media with 10% HI-FBS and penicillin and streptomycin at 25ºC as described in Drosophila Genomics Resource Center.

extract_protocol:
Fixed cells were lysed during 20 min in ice-cold lysis buffer (100mM NaCl, 66mM Tris HCl pH8, 5mM EDTA, 0.3% SDS, 1.6% Triton X-100) supplemented with proteases inhibitors, passed through a 21G needle and sonicated using a Bioruptor nextGen (Diagenode) to obtain chromatin frgament size of 250-500bp. Sonicated chromatin was centrifuged at 14000rpm at 4ºC for 10 min and the supernatant used for subsequent steps. In parallel, and independently, Drosophila S2 cells were fixed, lysed and sonicated as described for Hela S3 cells. After sonication, HeLa S3 input chromatin required for the analysis of all time-points from the same time course experiment was mixed with Drosophila S2 chromatin (2.5% of total chromatin). Chromatin associated to each histone mark was obtained by incubating sonicated chromatin with the corresponding antibody.
Libraries were costructed using the KAPA Hyperprep kit following manufacturer’s instruction, except that 1.25 µM of Illumina compatible indexed adapters (Pentabase) were ligated to A-tailed DNA. Following adapter ligation biotin-TEG-azide (Berry&Associates) was linked to EdU in Click reaction. Biotinylated products were captured using MyOne Streptavidin T1 beads (Thermo Fisher Scientific) and subjected to PCR amplification following the KAPA Hyperprep kit protocol.

treatment_protocol: For all ChOR-seq and ChIP-seq, HeLa S3 cells were synchronized at the G1/S border by single thymidine block (2 mM, 17 h) and released into fresh media containing deoxycytidine (24 μM) for the indicated amount of time (See Cell cycle information). Parental samples were collected 1 hour before labelling. DNA was labelled during 20 min with medium containing 5-ethynyl-2'-deoxyuridine (EdU, 10 μM) and Nascent chromatin was collected (T0). Then, the remaining cells were washed with PBS, resuspended into new medium containing deoxycytidine and incubated at 37ºC for the indicated amount of time. To avoid entering into a second round of replication, thymidine (2mM) was added to the medium after 10 h of release and cells were incubated until reaching 24 h post-thymidine release. For experiments using EZH2 inhibitor (EPZ-6438, 1 μM), inhibitor was added to the medium 30 min before collecting Nascent chromatin and kept in culture medium until the end of the experiment. For each time-course experiment, replicated DNA was isolated by single Streptavidin pull-down on Nascent chromatin. In ChOR-seq analysis, asynchronous Drosophila S2 chromatin was labelled with EdU (10 μM) for 39 h and was used as internal control. Harvested cells were immediately fixed in 1% formaldehyde for 15 min. Fixation was stopped by adding Glycine (0.125M) and incubating for 5 min at RT.

tag: cell line

value: HeLa S3

value: cervical carcinoma

value: EZH2 inhibitor (EPZ-6438)

value: G1 (10h after T0)

value: YES

value: EdU

value: H3K27me3 C36B11(Cell Signaling Technology, Cat No. 9733S_RRID:AB_2616029)


title: H3K27me3_ChOR-seq_T24+EZH2i_rep2

value: G1/S (24h after T0)


title: H3_ChIP-seq_Parental_rep2

data_processing:
Illumina RTAv2 software was used for basecalling
Reads were aligned to  human genome assembly (GRCh37/hg19) and D. melanogaster genome assembly (BDGP R5/dm3) by Bowtie v. 1.1.2 using parameters -m1 --best. Mapping and subsequent analysis of the data were done using local Galaxy server and custom R scripts
PCR duplicates were removed using RmDup v.2.0 and unique mapped reads were extended to 250 bp (H3K4me3) or 500bp (H3K27me3) to account for the average library size.
Reads were summed in 500 bp non-overlapping bins.
For ChIP-seq samples, reads were normalized to Reads Per Million (RPM).
For ChOR-seq samples, reads were normalized to Reference-adjusted RPM (RRPM) dividing human  values by total Drosophila unique mapped reads.
Peak calling was performed with MACS v. 2.0.9 under broad domain parameters using Parental ChIP-seq of Total H3 from each experiment as a reference.
Genome_build: hg19 and dm3
Supplementary_files_format_and_content: bedgraph files were generated using Galaxy. Scores represent the sum of RPM or RRPM in 500bp windows

value: Non treated

value: Early S (2 h and 15 min after release)

value: NO

value: Non labelled

value: Total H3 (Abcam, Cat No. Ab179, RRID:AB_302613)


title: H3_ChOR-seq_T0_rep1

value: Mid S (3 h and 15 min after release)


title: H3K27me3_ChOR-seq_T4_rep2

value: G2 (4h after T0)


title: Streptavidin_pull-down_midS_rep1


title: Streptavidin_pull-down_midS_rep2


title: H3K27me3_ChOR-seq_T24_rep2


title: H3K27me3_ChOR-seq_T0+EZH2i_rep2


title: MDM-HiC-06h-H5N1-r4

description:
in situ Hi-C
MDM-HiC-06h-H5N1-r4
Sample15.MDM-HiC-06h-H5N1.hic

value: monocyte derived macrophages (MDM)

value: H5N1 IAV infected (06h)


title: H3_ChOR-seq_T0_rep2

value: HeLa S3


title: H3K27me3_ChOR-seq_T0+EZH2i_rep1

value: cervical carcinoma


title: H3K27me3_ChOR-seq_T10_rep1


title: H3K27me3_ChIP-seq_Parental_rep2


title: H3K27me3_ChOR-seq_T10_rep2


title: H3K27me3_ChOR-seq_T24+EZH2i_rep1

value: EZH2 inhibitor (EPZ-6438)


title: H3_ChIP-seq_Parental_rep1


title: H3K27me3_ChOR-seq_T10+EZH2i_rep1

value: G1 (10h after T0)


title: 7m m3 S12

city: Madison

first: Youngsook

last: Lee

state: WI

address: 1111 Highland Ave

department: CRB

institute: University of Wisconsin-Madison

data_processing:
Single end 100bp sequencing was performed, using standard SBS chemistry (v4) on an Illumina HiSeq2500 sequencer.  Images were analyzed using the standard Illumina Pipeline, version 1.8.2.
Following quality assessment using FASQC, the sequencing reads were aligned to reference sequences of transcriptome obtained from NCBI (GRCm38.p6) using Bowtie v 1.1.2 allowing 2 mismatches. Based on the aligned reads, countable values, expected counts (EC) and transcript per million (TPM) for each transcript were estimated by RSEM v 1.3.0.
Genome_build: GRCm38.p6

molecule: polyA RNA

organism: Mus musculus

source_name: Jarid2-aMHC heart 3 at 7M

growth_protocol: Jarid2 f/f mice were crossed with aMHC C/+;Jaid2 f/+ mice to generate control (aMHC +/+;Jarid2 f/f) and mutant (aMHC C/+;Jarid2 f/f) mice.

extract_protocol:
Hearts were isolated, flash frozen on dry ice, and RNA was harvested using TRIZOL reagent. Illumina® TruSeq® Stranded mRNA Sample Preparation kit was used and mRNA was   purified from 200ng total RNA using poly-T oligo-attached magnetic beads.
Quality and quantity of the finished libraries were assessed using an Agilent HS DNA or DNA1000 chip and Qubit® dsDNA HS Assay Kit, respectively. Libraries were standardized to 2nM. Cluster generation was performed using standard Cluster Kits (v4) and the Illumina cBot.

tag: strain

value: Mixed 129/Svj and C57BL/6

value: Postnatal heart

tag: developmental stage

value: 7 months

tag: genotype

value: aMHC-C/+;Jarid2 f/f


title: H3K27me3_ChOR-seq_T0_rep2

tag: ezh2i treatment

value: Non treated

tag: cell cycle

value: YES

value: EdU

value: H3K27me3 C36B11(Cell Signaling Technology, Cat No. 9733S_RRID:AB_2616029)


title: H3K27me3_ChOR-seq_T4+EZH2i_rep2

tag: spike-in

tag: labelling


title: H3K27me3_ChOR-seq_T4+EZH2i_rep1

tag: antibody


title: 7m c2 S8

source_name: Control heart 2 at 7M

value: aMHC-+/+;Jarid2 f/f


title: H3K27me3_ChOR-seq_T24_rep1

tag: cell type

value: G1/S (24h after T0)


title: H3K27me3_ChOR-seq_T4_rep1

value: G2 (4h after T0)


title: p10 m2 S5

source_name: Jarid2-aMHC heart 2 at P10

tag: tissue

value: Day 10


title: p10 m1 S4

source_name: Jarid2-aMHC heart 1 at P10


title: H3K27me3_ChOR-seq_T0_rep1

value: Mid S (3 h and 15 min after release)


title: 7m m2 S11

source_name: Jarid2-aMHC heart 2 at 7M


title: OL_Morphine1

city: St. Louis

first: Robi

last: Mitra

state: MO

address: 4515 McKinley Ave

institute: Washington University School of Medicine

description:
FACS-RNAseq_counts.txt
FACS-RNAseq_DESeq_result.txt

data_processing:
Drop-seq: Sequences were filtered and aligned using standard Drop-seq tools (McCarroll Lab). Briefly, raw sequence data was first filtered to remove all read pairs with a barcode base quality of less than 10. The second read (75 bp) was then trimmed at the 5′ end to remove any TSO adaptor sequence and at the 3′ end to remove poly(A) tails of length 6 or greater, then aligned to the mouse (mm10) genome using STAR v2.4.2a with default settings. Uniquely mapped reads were grouped by cell barcode. A list of UMIs (unique molecular identifiers) in each gene, within each cell, was assembled, and UMIs within ED = 1 were merged together. The total number of unique UMI sequences was counted, and this number was reported as the number of transcripts of that gene for a given cell (see summary files).
FACS-RNAseq trimming: java -jar $TRIMMOMATIC_HOME/trimmomatic-0.36.jar SE -phred33 path/to/filtered/OL_mock_1.fq path/to/trimmed/OL_mock_1.fq LEADING:3 TRAILING:3 MINLEN:36
FACS-RNAseq alignment: STAR --genomeDir path/to/mm10/genome_reference --readFilesIn path/to/trimmed/OL_mock_1.fastq  --runThreadN 16 --outFileNamePrefix OL_mock_1 --outSAMtype BAM SortedByCoordinate
FACS-RNAseq counts: htseq-count -f bam -m union -r pos -i gene_name -a 10 --stranded=no OL_mock_1Aligned.sortedByCoord.out.bam path/to/mm10.gtf  > OL_mock_1_counts.txt           The above 3 steps were repeated for all 6 samples, and outputs were combined into "FACS-RNAseq_counts.txt"
FACS-RNAseq differential expression: DESeq2 was employed (standard parameters) to assess differential expression between mock (9-11) and morphine (12-14) samples. The output is included in "FACS-RNAseq_DESeq_result.txt"
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text

source_name: Mouse whole brain (FACS'd oligodendrocytes)

extract_protocol:
Brain tissue was dissected, then the nucleus accumbens (or whole brain) was dissociated in papain solution to obtain a single-cell suspension. Samples 1-8 were then processed by Drop-seq. Samples 9-14 were immunostained and oligodendrocytes were purified by FACS, then RNA was isolated using Trizol.
For samples 1-8, standard Drop-seq (Nextera) library prep; Read 1 was 25 bp and Read 2 was 75 bp. For samples 9-14, RNA was amplified using the Seqplex RNA Amplification Kit (Sigma), then prepared for sequencing using standard Illumina protocols and sequenced 1x50.
single-cell RNAseq; total RNAseq

treatment_protocol: Intraperitoneal injection with saline (mock) or morphine sulfate

tag: Sex

value: Male

tag: age


title: OL_Morphine3


title: OL_Mock3


title: OL_Morphine2


title: H3K27me3_ChIP-seq_Parental_rep1

value: HeLa S3

value: cervical carcinoma

value: Early S (2 h and 15 min after release)

value: NO

value: Non labelled


title: OL_Mock2


title: Morphine4

source_name: Mouse nucleus accumbens

value: P78 (2 mice pooled)


title: 7m m1 S10

source_name: Jarid2-aMHC heart 1 at 7M

value: Mixed 129/Svj and C57BL/6

value: Postnatal heart

value: 7 months

value: aMHC-C/+;Jarid2 f/f


title: 7m c3 S9

source_name: Control heart 3 at 7M


title: Morphine2

value: P37, P42 (2 mice pooled)


title: 7m c1 S7

source_name: Control heart 1 at 7M

value: aMHC-+/+;Jarid2 f/f


title: Mock2


title: Morphine1

value: P42, P45 (2 mice pooled)


title: Sample_A51_4_pSer2

city: Jerusalem

first: Yinon

last: Ben-Neriah

address: Ein Kerem

department: The Lautenberg Center for Immunology

country: Israel

institute: Hebrew University-Hadassah Medical School

description: Primary AML cells treated with A51

data_processing:
Following read duplication removal (picard-tools), all datasets were individually aligned to the mouse genome (GRCm38/mm10) using Bowtie2 (Langmead and Salzberg, 2012) with default parameters.  Next, peaks were called on the aligned BAMs from each IP replicate using MACS2 with the relevant input sample, a q-value threshold of 0.01, and MFOLD of 5 50.
Pileup fragment profiles per million reads were generated by MACS2 using the SPMR parameter and were used for visualization of ChIP-seq data directly on the UCSC genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: Primary MLL-AF9 AML cells

growth_protocol: MLL-AF9-driven leukemic mice were sacrificed and BM was flushed with PBS from the femur and tibia. The cells were cultured ex vivo in StemPro-34 SFM media (Gibco) supplemented with 10 ng/ml of IL3, IL6, thyroid peroxidase (TPO), stem cell factor (SCF) StemPro-34 Nutrient Supplement (25μl/ml), PenSrep (Sigma, 1:100) and L-glutamine (Sigma, 1:100).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to manufacturer’s instructions, quantified by Qubit (Invitrogen) and TapeStation (Agilent) and sequenced on an Illumina HiSeq2500 (50 SR lane V4 reagents).

treatment_protocol: Cell were treated with DMSO or A51 (1 μM) and harvested after 4 hours.

value: Primary MLL-AF9 AML cells

tag: agent

value: anti-RNA polymerase II CTD  (phospho S2) antibody, Abcam Cat #ab5095


title: Sample_A51_3_pSer2

description: Primary AML cells treated with A51


title: p10 m3 S6

source_name: Jarid2-aMHC heart 3 at P10

value: Day 10


title: Sample_A51_pSer2_CTD_1

description: Primary AML cells treated with A51


title: p10 c3 S3

source_name: Control heart 3 at P10


title: p10 C1 S1

source_name: Control heart 1 at P10


title: p10 c2 S2

source_name: Control heart 2 at P10


title: Sample_WT2_Chip

description: Primary WT BM cells

source_name: Bone marrow

value: WT Bone marrow cells

value: anti-H3K27Ac, Abcam:Cat# ab4729


title: A51_4_K27Ac

description: Primary AML cells treated with A51


title: Sample_WT1_Chip

description: Primary WT BM cells


title: Sample_AML_Veh1_input

description: Primary AML cells treated with DMSO

value: control


title: Sample_WT3_Chip

description: Primary WT BM cells


title: Sample_DMSO_pSer2_CTD_1

description: Primary AML cells treated with DMSO


title: A51_3_K27Ac

description: Primary AML cells treated with A51


title: Sample_WT1_input

description: Primary WT BM cells


title: Mock3

value: Male

value: P78, P82 (2 mice pooled)


title: Mock4


title: Mock1


title: OL_Mock1


title: DMSO_4_K27Ac

description: Primary AML cells treated with DMSO


title: Sample_DMSO_4_pSer2

description: Primary AML cells treated with DMSO


title: Sample_DMSO_3_pSer2

description: Primary AML cells treated with DMSO