title: GM12878, 800U, Cell 24

description:
800U MNase
GM-800U_024.allValidPairs.gz
GM-800U_024.hic
GM-800U_024.mcool
GM-800U_024.clean.smooth.bw
GM-800U_024_20kb_1.3dg.gz
GM-800U_024_20kb_2.3dg.gz
GM-800U_024_20kb_3.3dg.gz
GM-800U_024_20kb_4.3dg.gz
GM-800U_024_20kb_5.3dg.gz
GM-800U_024_10kb_1.3dg.gz
GM-800U_024_10kb_2.3dg.gz
GM-800U_024_10kb_3.3dg.gz
GM-800U_024_10kb_4.3dg.gz
GM-800U_024_10kb_5.3dg.gz
GM-800U_024_5kb_1.3dg.gz
GM-800U_024_5kb_2.3dg.gz
GM-800U_024_5kb_3.3dg.gz
GM-800U_024_5kb_4.3dg.gz
GM-800U_024_5kb_5.3dg.gz
GM-800U_024_20kb_1.clean.3dg.gz
GM-800U_024_20kb_2.clean.3dg.gz
GM-800U_024_20kb_3.clean.3dg.gz
GM-800U_024_20kb_4.clean.3dg.gz
GM-800U_024_20kb_5.clean.3dg.gz
GM-800U_024_10kb_1.clean.3dg.gz
GM-800U_024_10kb_2.clean.3dg.gz
GM-800U_024_10kb_3.clean.3dg.gz
GM-800U_024_10kb_4.clean.3dg.gz
GM-800U_024_10kb_5.clean.3dg.gz
GM-800U_024_5kb_1.clean.3dg.gz
GM-800U_024_5kb_2.clean.3dg.gz
GM-800U_024_5kb_3.clean.3dg.gz
GM-800U_024_5kb_4.clean.3dg.gz
GM-800U_024_5kb_5.clean.3dg.gz

value: WT


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon5 [5H]

status: Public on Feb 28 2025

type: SRA

city: Bundoora

first: Anya

last: Shindler

state: VIC

address: 1 Kingsbury Drive

country: Australia

institute: La Trobe University

library_source: genomic

data_processing:
Library strategy: 16S Metagenomic
Fastq files obtained from the Miseq machine were processed using QIIME2 2021.11
Excel files were the end product from the QIIME2 processing
Assembly: N/A
Supplementary files format and content: Processed files are in excel .csv format.  The MOTU contains the OTUs obtained, the Mtax.csv files contains the Taxonomy identified during the QIIME2 processing, and MSamples.csv contains the metadata for the other two .csv files.

molecule: genomic DNA

organism: Bacteria

source_name: soil sample

extract_protocol:
Qiagen DNeasy® PowerSoil® Kits
Illumina 16S Metagenomic Sequencing Library Preparation

tag: tissue

value: soil sample

tag: season

value: Monsoon

tag: location

tag: building

value: Hospital


title: cell_187

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz

data_processing:
Raw sequencing reads were mapped to the reference genome with BWA mem (0.7.17-r1188) with parameters -5SP. Single-cell contacts were generated with the dip-c and hickit (v0.1.1) packages with default parameters.
PCR duplicates were removed from raw SAM files with samblaster (0.1.26) package with parameters --ignoreUnmated -r. Subsequently, nucleosome occupancy signals were calculated with the DANPOS2 package with paramter -a 5 -count 1000000.
Chromatin loop calling was performed with SnapHiC and Chromosight package with default parameters.
Single-cell 3D genome structures were generated with the hickit v0.1.1 package with parameters  -M and -Sr1m -c1 -r10m -c2 -b4m -b1m -b200k -D5 -b50k -D5 -b20k -D5 -b10k -D5 -b5k.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include contacts for each sample. bigWig files include nucleosome occupancy and ligation junction signals for each sample. hic and mcool files included contact matrices for each sample.

organism: Homo sapiens

source_name: blood

growth_protocol: GM12878 lymphoblastoid cells were grown in RPMI1640 medium (Gibco, Thermo Fisher Scientific, Cat. # 11875093) media supplemented with 15% FBS and 1% Pen/Strep. GM12878 were cultured at 37° C with 5% CO2 at recommended density.

extract_protocol:
1 million cells were permeabilized with 100 μL Micro-C buffer1 (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.2% IGEPAL CA630, 1 x PIC), incubate on ice for 20 min.
Single cells were amplified with the state-of-art transposase-based WGA (Multiplexed End Tagging Amplification), barcoded in 96-well plate, then pooled for library preparation.

value: blood

tag: cell line

tag: cell type

value: lymphoblastoid


title: WT,pDC,d2,Spleen,6,12080

city: New York

first: Endi

middle: K

last: Santosa

state: New York

address: 417 E 68th St

department: Immunology

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.20.0.422).
paired-end reads were trimmed for adaptors and subjected to removal of low-quality reads using Trimmomatic (v0.36)
Transcript quantification was based on the mm10 UCSC Known Gene models and performed using the quasi-mapping-based mode of Salmon (v0.13.1) correcting for potential GC bias
Transcripts were summarized to gene level using tximport (v1.10.1) and differential analyses were executed with DESeq2 (v1.34.0) using the UCSC Known Gene models as reference annotations.
Assembly: mm10
Supplementary files format and content: Raw counts in txt format

molecule: total RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
cDC1s (Lineage- XCR1+ CD11c+), red-pulp macrophages (Lineage- F4/80+ CD64+), and pDCs (Lineage- F4/80- B220+ BST2+ Ly6C+) were sorted from the spleens of uninfected wildtype mice, or those that were d1 or d2 p.i with MCMV. where Lineage refers to CD3, TCRb, CD19, NK1.1, Ly6G. In each independent experiment, RNA was isolated from sorted cells using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher) in accordance with the manufacturer instructions.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.7-2 ng total RNA with RNA integrity numbers ranging from 9.2 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 9-10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a PE100 run, using the NovaSeq 6000 S1 or S4 Reagent Kit (100 or 200 cycles) (Illumina).

treatment_protocol: In vivo MCMV infection

value: Spleen

tag: strain

tag: genotype

value: pDC

tag: replicate

tag: time point

value: d2 post MCMV infection

tag: projectnumber


title: GM12878, 800U, Cell 23

description:
800U MNase
GM-800U_023.allValidPairs.gz
GM-800U_023.hic
GM-800U_023.mcool
GM-800U_023.clean.smooth.bw
GM-800U_023_20kb_1.3dg.gz
GM-800U_023_20kb_2.3dg.gz
GM-800U_023_20kb_3.3dg.gz
GM-800U_023_20kb_4.3dg.gz
GM-800U_023_20kb_5.3dg.gz
GM-800U_023_10kb_1.3dg.gz
GM-800U_023_10kb_2.3dg.gz
GM-800U_023_10kb_3.3dg.gz
GM-800U_023_10kb_4.3dg.gz
GM-800U_023_10kb_5.3dg.gz
GM-800U_023_5kb_1.3dg.gz
GM-800U_023_5kb_2.3dg.gz
GM-800U_023_5kb_3.3dg.gz
GM-800U_023_5kb_4.3dg.gz
GM-800U_023_5kb_5.3dg.gz
GM-800U_023_20kb_1.clean.3dg.gz
GM-800U_023_20kb_2.clean.3dg.gz
GM-800U_023_20kb_3.clean.3dg.gz
GM-800U_023_20kb_4.clean.3dg.gz
GM-800U_023_20kb_5.clean.3dg.gz
GM-800U_023_10kb_1.clean.3dg.gz
GM-800U_023_10kb_2.clean.3dg.gz
GM-800U_023_10kb_3.clean.3dg.gz
GM-800U_023_10kb_4.clean.3dg.gz
GM-800U_023_10kb_5.clean.3dg.gz
GM-800U_023_5kb_1.clean.3dg.gz
GM-800U_023_5kb_2.clean.3dg.gz
GM-800U_023_5kb_3.clean.3dg.gz
GM-800U_023_5kb_4.clean.3dg.gz
GM-800U_023_5kb_5.clean.3dg.gz

data_processing:
Raw sequencing reads were mapped to the reference genome with BWA mem (0.7.17-r1188) with parameters -5SP. Single-cell contacts were generated with the dip-c and hickit (v0.1.1) packages with default parameters.
PCR duplicates were removed from raw SAM files with samblaster (0.1.26) package with parameters --ignoreUnmated -r. Subsequently, nucleosome occupancy signals were calculated with the DANPOS2 package with paramter -a 5 -count 1000000.
Single-cell 3D genome structures were generated with the hickit v0.1.1 package with parameters  -M and -Sr1m -c1 -r10m -c2 -b4m -b1m -b200k -D5 -b50k -D5 -b20k -D5 -b10k -D5 -b5k.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include contacts for each sample. bigWig files include nucleosome occupancy for each sample. hic and mcool files included contact matrices for each sample.
Supplementary files format and content: .3dg files of single-cell 3D genome structures


title: WT,cDC1,d2,Spleen,2,12080


title: WT,pDC,d2,Spleen,5,12080


title: cell_192


title: GM12878, 800U, Cell 22

description:
800U MNase
GM-800U_022.allValidPairs.gz
GM-800U_022.hic
GM-800U_022.mcool
GM-800U_022.clean.smooth.bw
GM-800U_022_20kb_1.3dg.gz
GM-800U_022_20kb_2.3dg.gz
GM-800U_022_20kb_3.3dg.gz
GM-800U_022_20kb_5.3dg.gz
GM-800U_022_10kb_1.3dg.gz
GM-800U_022_10kb_2.3dg.gz
GM-800U_022_10kb_3.3dg.gz
GM-800U_022_10kb_5.3dg.gz
GM-800U_022_5kb_1.3dg.gz
GM-800U_022_5kb_2.3dg.gz
GM-800U_022_5kb_3.3dg.gz
GM-800U_022_5kb_5.3dg.gz
GM-800U_022_20kb_1.clean.3dg.gz
GM-800U_022_20kb_2.clean.3dg.gz
GM-800U_022_20kb_3.clean.3dg.gz
GM-800U_022_20kb_5.clean.3dg.gz
GM-800U_022_10kb_1.clean.3dg.gz
GM-800U_022_10kb_2.clean.3dg.gz
GM-800U_022_10kb_3.clean.3dg.gz
GM-800U_022_10kb_5.clean.3dg.gz
GM-800U_022_5kb_1.clean.3dg.gz
GM-800U_022_5kb_2.clean.3dg.gz
GM-800U_022_5kb_3.clean.3dg.gz
GM-800U_022_5kb_5.clean.3dg.gz


title: cell_186


title: cell_188


title: GM12878, 800U, Cell 21

description:
800U MNase
GM-800U_021.allValidPairs.gz
GM-800U_021.hic
GM-800U_021.mcool
GM-800U_021.clean.smooth.bw
GM-800U_021_20kb_1.3dg.gz
GM-800U_021_20kb_2.3dg.gz
GM-800U_021_20kb_3.3dg.gz
GM-800U_021_20kb_4.3dg.gz
GM-800U_021_20kb_5.3dg.gz
GM-800U_021_10kb_1.3dg.gz
GM-800U_021_10kb_2.3dg.gz
GM-800U_021_10kb_3.3dg.gz
GM-800U_021_10kb_4.3dg.gz
GM-800U_021_10kb_5.3dg.gz
GM-800U_021_5kb_1.3dg.gz
GM-800U_021_5kb_2.3dg.gz
GM-800U_021_5kb_3.3dg.gz
GM-800U_021_5kb_4.3dg.gz
GM-800U_021_5kb_5.3dg.gz
GM-800U_021_20kb_1.clean.3dg.gz
GM-800U_021_20kb_2.clean.3dg.gz
GM-800U_021_20kb_3.clean.3dg.gz
GM-800U_021_20kb_4.clean.3dg.gz
GM-800U_021_20kb_5.clean.3dg.gz
GM-800U_021_10kb_1.clean.3dg.gz
GM-800U_021_10kb_2.clean.3dg.gz
GM-800U_021_10kb_3.clean.3dg.gz
GM-800U_021_10kb_4.clean.3dg.gz
GM-800U_021_10kb_5.clean.3dg.gz
GM-800U_021_5kb_1.clean.3dg.gz
GM-800U_021_5kb_2.clean.3dg.gz
GM-800U_021_5kb_3.clean.3dg.gz
GM-800U_021_5kb_4.clean.3dg.gz
GM-800U_021_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon4 [4H]


title: WT,cDC1,d2,Spleen,1,12080


title: GM12878, 800U, Cell 20

description:
800U MNase
GM-800U_020.allValidPairs.gz
GM-800U_020.hic
GM-800U_020.mcool
GM-800U_020.clean.smooth.bw
GM-800U_020_20kb_1.3dg.gz
GM-800U_020_20kb_2.3dg.gz
GM-800U_020_20kb_3.3dg.gz
GM-800U_020_20kb_4.3dg.gz
GM-800U_020_20kb_5.3dg.gz
GM-800U_020_10kb_1.3dg.gz
GM-800U_020_10kb_2.3dg.gz
GM-800U_020_10kb_3.3dg.gz
GM-800U_020_10kb_4.3dg.gz
GM-800U_020_10kb_5.3dg.gz
GM-800U_020_5kb_1.3dg.gz
GM-800U_020_5kb_2.3dg.gz
GM-800U_020_5kb_3.3dg.gz
GM-800U_020_5kb_4.3dg.gz
GM-800U_020_5kb_5.3dg.gz
GM-800U_020_20kb_1.clean.3dg.gz
GM-800U_020_20kb_2.clean.3dg.gz
GM-800U_020_20kb_3.clean.3dg.gz
GM-800U_020_20kb_4.clean.3dg.gz
GM-800U_020_20kb_5.clean.3dg.gz
GM-800U_020_10kb_1.clean.3dg.gz
GM-800U_020_10kb_2.clean.3dg.gz
GM-800U_020_10kb_3.clean.3dg.gz
GM-800U_020_10kb_4.clean.3dg.gz
GM-800U_020_10kb_5.clean.3dg.gz
GM-800U_020_5kb_1.clean.3dg.gz
GM-800U_020_5kb_2.clean.3dg.gz
GM-800U_020_5kb_3.clean.3dg.gz
GM-800U_020_5kb_4.clean.3dg.gz
GM-800U_020_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon2 [2H]


title: cell_185


title: cell_184


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon3 [3H]


title: cell_190


title: WT,RPMac,d2,Spleen,8,12080

value: RPMac


title: WT,RPMac,d2,Spleen,5,12080


title: WT,RPMac,d2,Spleen,7,12080


title: GM12878, 800U, Cell 17

description:
800U MNase
GM-800U_017.allValidPairs.gz
GM-800U_017.hic
GM-800U_017.mcool
GM-800U_017.clean.smooth.bw
GM-800U_017_20kb_1.3dg.gz
GM-800U_017_20kb_2.3dg.gz
GM-800U_017_20kb_3.3dg.gz
GM-800U_017_20kb_4.3dg.gz
GM-800U_017_20kb_5.3dg.gz
GM-800U_017_10kb_1.3dg.gz
GM-800U_017_10kb_2.3dg.gz
GM-800U_017_10kb_3.3dg.gz
GM-800U_017_10kb_4.3dg.gz
GM-800U_017_10kb_5.3dg.gz
GM-800U_017_5kb_1.3dg.gz
GM-800U_017_5kb_2.3dg.gz
GM-800U_017_5kb_3.3dg.gz
GM-800U_017_5kb_4.3dg.gz
GM-800U_017_5kb_5.3dg.gz
GM-800U_017_20kb_1.clean.3dg.gz
GM-800U_017_20kb_2.clean.3dg.gz
GM-800U_017_20kb_3.clean.3dg.gz
GM-800U_017_20kb_4.clean.3dg.gz
GM-800U_017_20kb_5.clean.3dg.gz
GM-800U_017_10kb_1.clean.3dg.gz
GM-800U_017_10kb_2.clean.3dg.gz
GM-800U_017_10kb_3.clean.3dg.gz
GM-800U_017_10kb_4.clean.3dg.gz
GM-800U_017_10kb_5.clean.3dg.gz
GM-800U_017_5kb_1.clean.3dg.gz
GM-800U_017_5kb_2.clean.3dg.gz
GM-800U_017_5kb_3.clean.3dg.gz
GM-800U_017_5kb_4.clean.3dg.gz
GM-800U_017_5kb_5.clean.3dg.gz


title: MSC,PC,CONTUntreated

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

data_processing:
sequences were trimmed for min Pred value of 20, adapters were trimmed with CUTADAPT v1.12
Trimmed reads were aligned with STAR - 2.7.3a (Dobin) with reference genome Equab3.0
Aligned reads were counted with HTSeq v0.11.0 (Givanna) with Ensembl gene annotation 108
Features were filtered for “protein coding” and lowest total coverage of 10 counts, DESeq2 was used for differential analysis
Median ratio normalized counts were used for pathway analysis using GSEA v4.3.2
Assembly: EquCab3.0
Supplementary files format and content: txt file with raw counts for MSC and MSC treated cells (chondrocyte, synoviocytes and Macrophages)

molecule: polyA RNA

organism: Equus caballus

source_name: MSC

growth_protocol: Treatment and collection of treated cell RNA, supernatant – Macrophages were isolated from whole blood of one horse, peripheral blood mononuclear cells were isolated by density gradient centrifugation (Ficoll-Paque TM plus, GE Healthcare BioSciences) and cultured in macrophage media (Dulbecco’s Modified Eagle Medium with 1g/L glucose, 10% fetal bovine serum, penicillin (100 U/ml), streptomycin (100ug/ml), 1M HEPES) supplemented with human M-CSF (PeproTech) at 30 ng/ml for 5 days.  Monocyte-derived macrophages were stimulated with IL-1β (10ng/ml) and TNF-α (10 ng/ml), and treated with activated MSC conditioned culture media at a ratio of 1:3 MSC CM:Macrophage media. Controls included non-stimulated macrophages, and macrophages stimulated with IL-1β/TNF-α with no MSC treatment. The stimulated and treated macrophages were cultured for 24 hours, then washed with PBS, and cultured for an additional 24 hours in macrophage media. At that time, macrophage supernatant was collected and frozen at -20c for cytokine analysis (multiplex bead assay and ELISA immunoassay), and macrophages were collected in RLT lysis buffer and frozen at –20 °C until RNA isolation was performed.  Synoviocytes were obtained from synovium of one horse, synovium was excised from the femoropatellar joint, minced and digested for 4 hours in complete media (Dulbecco’s Modified Eagle Medium, 10% FBS, penicillin (100units/ml), streptomycin (100 ug/ml), 1M HEPES) with type II collagenase (0.75 mg/ml). Digested synovium was filtered through 70uM and 40uM cell strainers, where cells were counted, plated and expanded to second passage, then cryopreserved in Freeze Media (95% FBS, 5% DMSO). For treatment, synoviocytes were thawed in 37 °C water bath and recovered overnight in complete media. Cells were plated at 100,000 per well in a 24 well plate. Synoviocytes were stimulated with IL-1β (20  ng/ml) and TNF-α (20 ng/ml) and treated with activated MSC conditioned culture media at a ratio of 1:3 MSC CM:Complete media. The stimulated and treated synoviocytes were cultured for 24 hours, then washed with PBS, and cultured for an additional 24 hours in complete media. At that time, synoviocyte supernatant was collected and frozen at –20 °C for cytokine analysis (multiplex bead assay and ELISA immunoassay), and synoviocytes were collected in RLT lysis buffer and frozen at –20 °C until RNA isolation was performed. Chondrocytes were isolated from cartilage from the femur and caudal surface of the patella of the femoropatellar joint, Cartilage tissue samples were digested as for synoviocytes overnight, passed through cell strainers, and expanded in culture to second passage where they were cryopreserved. Chondrocytes were stimulated and treated as for synoviocytes above, and supernatant and chondrocytes in RLT lysis buffer were collected as above.

extract_protocol:
RNA was extracted from frozen samples in RLT lysis buffer using the RNeasy kit (Qiagen) according to manufacturer’s instruction
Library was constructed with Abclonal Fast RNA-seq Lib Prep Kit V2 (ABclonal Technology, Woburn, Massachusetts).

treatment_protocol: To generate MSC conditioned supernatant, cells were thawed in a 37 °C water bath, plated and cultured 24 hours in complete growth media, activated with poly I:C (10 ng/ml) or 2’3’cGAMP (10 ng/ml) for 2 hours, washed with PBS, then replated on 24 well-plates at 100,000 cells/well.

value: MSC

value: PC

tag: treatment

value: CTRL


title: WT,pDC,d0,Spleen,6,12080

value: d0 post MCMV infection


title: WT,pDC,d0,Spleen,7,12080


title: cell_182


title: cell_183


title: WT,pDC,d0,Spleen,5,12080


title: cell_180


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon1 [1H]


title: GM12878, 800U, Cell 19

description:
800U MNase
GM-800U_019.allValidPairs.gz
GM-800U_019.hic
GM-800U_019.mcool
GM-800U_019.clean.smooth.bw
GM-800U_019_20kb_1.3dg.gz
GM-800U_019_20kb_2.3dg.gz
GM-800U_019_20kb_3.3dg.gz
GM-800U_019_20kb_4.3dg.gz
GM-800U_019_20kb_5.3dg.gz
GM-800U_019_10kb_1.3dg.gz
GM-800U_019_10kb_2.3dg.gz
GM-800U_019_10kb_3.3dg.gz
GM-800U_019_10kb_4.3dg.gz
GM-800U_019_10kb_5.3dg.gz
GM-800U_019_5kb_1.3dg.gz
GM-800U_019_5kb_2.3dg.gz
GM-800U_019_5kb_3.3dg.gz
GM-800U_019_5kb_4.3dg.gz
GM-800U_019_5kb_5.3dg.gz
GM-800U_019_20kb_1.clean.3dg.gz
GM-800U_019_20kb_2.clean.3dg.gz
GM-800U_019_20kb_3.clean.3dg.gz
GM-800U_019_20kb_4.clean.3dg.gz
GM-800U_019_20kb_5.clean.3dg.gz
GM-800U_019_10kb_1.clean.3dg.gz
GM-800U_019_10kb_2.clean.3dg.gz
GM-800U_019_10kb_3.clean.3dg.gz
GM-800U_019_10kb_4.clean.3dg.gz
GM-800U_019_10kb_5.clean.3dg.gz
GM-800U_019_5kb_1.clean.3dg.gz
GM-800U_019_5kb_2.clean.3dg.gz
GM-800U_019_5kb_3.clean.3dg.gz
GM-800U_019_5kb_4.clean.3dg.gz
GM-800U_019_5kb_5.clean.3dg.gz


title: GM12878, 800U, Cell 15

description:
800U MNase
GM-800U_015.allValidPairs.gz
GM-800U_015.hic
GM-800U_015.mcool
GM-800U_015.clean.smooth.bw
GM-800U_015_20kb_1.3dg.gz
GM-800U_015_20kb_2.3dg.gz
GM-800U_015_20kb_3.3dg.gz
GM-800U_015_20kb_4.3dg.gz
GM-800U_015_20kb_5.3dg.gz
GM-800U_015_10kb_1.3dg.gz
GM-800U_015_10kb_2.3dg.gz
GM-800U_015_10kb_3.3dg.gz
GM-800U_015_10kb_4.3dg.gz
GM-800U_015_10kb_5.3dg.gz
GM-800U_015_5kb_1.3dg.gz
GM-800U_015_5kb_2.3dg.gz
GM-800U_015_5kb_3.3dg.gz
GM-800U_015_5kb_4.3dg.gz
GM-800U_015_5kb_5.3dg.gz
GM-800U_015_20kb_1.clean.3dg.gz
GM-800U_015_20kb_2.clean.3dg.gz
GM-800U_015_20kb_3.clean.3dg.gz
GM-800U_015_20kb_4.clean.3dg.gz
GM-800U_015_20kb_5.clean.3dg.gz
GM-800U_015_10kb_1.clean.3dg.gz
GM-800U_015_10kb_2.clean.3dg.gz
GM-800U_015_10kb_3.clean.3dg.gz
GM-800U_015_10kb_4.clean.3dg.gz
GM-800U_015_10kb_5.clean.3dg.gz
GM-800U_015_5kb_1.clean.3dg.gz
GM-800U_015_5kb_2.clean.3dg.gz
GM-800U_015_5kb_3.clean.3dg.gz
GM-800U_015_5kb_4.clean.3dg.gz
GM-800U_015_5kb_5.clean.3dg.gz


title: Macrophage,ORC,Untreated

source_name: Macrophage

value: Macrophage

value: ORC


title: MSC,PC,STNGTreated

value: STNG


title: MSC,99,CPGTreated

value: CPG


title: cell_179


title: WT,cDC1,d0,Spleen,3,12080

value: WT


title: GM12878, 800U, Cell 14

description:
800U MNase
GM-800U_014.allValidPairs.gz
GM-800U_014.hic
GM-800U_014.mcool
GM-800U_014.clean.smooth.bw
GM-800U_014_20kb_1.3dg.gz
GM-800U_014_20kb_2.3dg.gz
GM-800U_014_20kb_3.3dg.gz
GM-800U_014_20kb_4.3dg.gz
GM-800U_014_20kb_5.3dg.gz
GM-800U_014_10kb_1.3dg.gz
GM-800U_014_10kb_2.3dg.gz
GM-800U_014_10kb_3.3dg.gz
GM-800U_014_10kb_4.3dg.gz
GM-800U_014_10kb_5.3dg.gz
GM-800U_014_5kb_1.3dg.gz
GM-800U_014_5kb_2.3dg.gz
GM-800U_014_5kb_3.3dg.gz
GM-800U_014_5kb_4.3dg.gz
GM-800U_014_5kb_5.3dg.gz
GM-800U_014_20kb_1.clean.3dg.gz
GM-800U_014_20kb_2.clean.3dg.gz
GM-800U_014_20kb_3.clean.3dg.gz
GM-800U_014_20kb_4.clean.3dg.gz
GM-800U_014_20kb_5.clean.3dg.gz
GM-800U_014_10kb_1.clean.3dg.gz
GM-800U_014_10kb_2.clean.3dg.gz
GM-800U_014_10kb_3.clean.3dg.gz
GM-800U_014_10kb_4.clean.3dg.gz
GM-800U_014_10kb_5.clean.3dg.gz
GM-800U_014_5kb_1.clean.3dg.gz
GM-800U_014_5kb_2.clean.3dg.gz
GM-800U_014_5kb_3.clean.3dg.gz
GM-800U_014_5kb_4.clean.3dg.gz
GM-800U_014_5kb_5.clean.3dg.gz


title: MSC,92,CONTUntreated


title: cell_178


title: GM12878, 800U, Cell 18

description:
800U MNase
GM-800U_018.allValidPairs.gz
GM-800U_018.hic
GM-800U_018.mcool
GM-800U_018.clean.smooth.bw
GM-800U_018_20kb_1.3dg.gz
GM-800U_018_20kb_2.3dg.gz
GM-800U_018_20kb_3.3dg.gz
GM-800U_018_20kb_4.3dg.gz
GM-800U_018_20kb_5.3dg.gz
GM-800U_018_10kb_1.3dg.gz
GM-800U_018_10kb_2.3dg.gz
GM-800U_018_10kb_3.3dg.gz
GM-800U_018_10kb_4.3dg.gz
GM-800U_018_10kb_5.3dg.gz
GM-800U_018_5kb_1.3dg.gz
GM-800U_018_5kb_2.3dg.gz
GM-800U_018_5kb_3.3dg.gz
GM-800U_018_5kb_4.3dg.gz
GM-800U_018_5kb_5.3dg.gz
GM-800U_018_20kb_1.clean.3dg.gz
GM-800U_018_20kb_2.clean.3dg.gz
GM-800U_018_20kb_3.clean.3dg.gz
GM-800U_018_20kb_4.clean.3dg.gz
GM-800U_018_20kb_5.clean.3dg.gz
GM-800U_018_10kb_1.clean.3dg.gz
GM-800U_018_10kb_2.clean.3dg.gz
GM-800U_018_10kb_3.clean.3dg.gz
GM-800U_018_10kb_4.clean.3dg.gz
GM-800U_018_10kb_5.clean.3dg.gz
GM-800U_018_5kb_1.clean.3dg.gz
GM-800U_018_5kb_2.clean.3dg.gz
GM-800U_018_5kb_3.clean.3dg.gz
GM-800U_018_5kb_4.clean.3dg.gz
GM-800U_018_5kb_5.clean.3dg.gz


title: GM12878, 800U, Cell 13

description:
800U MNase
GM-800U_013.allValidPairs.gz
GM-800U_013.hic
GM-800U_013.mcool
GM-800U_013.clean.smooth.bw
GM-800U_013_20kb_1.3dg.gz
GM-800U_013_20kb_2.3dg.gz
GM-800U_013_20kb_3.3dg.gz
GM-800U_013_20kb_5.3dg.gz
GM-800U_013_10kb_1.3dg.gz
GM-800U_013_10kb_2.3dg.gz
GM-800U_013_10kb_3.3dg.gz
GM-800U_013_10kb_5.3dg.gz
GM-800U_013_5kb_1.3dg.gz
GM-800U_013_5kb_2.3dg.gz
GM-800U_013_5kb_3.3dg.gz
GM-800U_013_5kb_5.3dg.gz
GM-800U_013_20kb_1.clean.3dg.gz
GM-800U_013_20kb_2.clean.3dg.gz
GM-800U_013_20kb_3.clean.3dg.gz
GM-800U_013_20kb_5.clean.3dg.gz
GM-800U_013_10kb_1.clean.3dg.gz
GM-800U_013_10kb_2.clean.3dg.gz
GM-800U_013_10kb_3.clean.3dg.gz
GM-800U_013_10kb_5.clean.3dg.gz
GM-800U_013_5kb_1.clean.3dg.gz
GM-800U_013_5kb_2.clean.3dg.gz
GM-800U_013_5kb_3.clean.3dg.gz
GM-800U_013_5kb_5.clean.3dg.gz


title: MSC,92,CPGTreated


title: WT,cDC1,d0,Spleen,2,12080


title: cell_177


title: GM12878, 800U, Cell 16

description:
800U MNase
GM-800U_016.allValidPairs.gz
GM-800U_016.hic
GM-800U_016.mcool
GM-800U_016.clean.smooth.bw
GM-800U_016_20kb_1.3dg.gz
GM-800U_016_20kb_2.3dg.gz
GM-800U_016_20kb_3.3dg.gz
GM-800U_016_20kb_4.3dg.gz
GM-800U_016_20kb_5.3dg.gz
GM-800U_016_10kb_1.3dg.gz
GM-800U_016_10kb_2.3dg.gz
GM-800U_016_10kb_3.3dg.gz
GM-800U_016_10kb_4.3dg.gz
GM-800U_016_10kb_5.3dg.gz
GM-800U_016_5kb_1.3dg.gz
GM-800U_016_5kb_2.3dg.gz
GM-800U_016_5kb_3.3dg.gz
GM-800U_016_5kb_4.3dg.gz
GM-800U_016_5kb_5.3dg.gz
GM-800U_016_20kb_1.clean.3dg.gz
GM-800U_016_20kb_2.clean.3dg.gz
GM-800U_016_20kb_3.clean.3dg.gz
GM-800U_016_20kb_4.clean.3dg.gz
GM-800U_016_20kb_5.clean.3dg.gz
GM-800U_016_10kb_1.clean.3dg.gz
GM-800U_016_10kb_2.clean.3dg.gz
GM-800U_016_10kb_3.clean.3dg.gz
GM-800U_016_10kb_4.clean.3dg.gz
GM-800U_016_10kb_5.clean.3dg.gz
GM-800U_016_5kb_1.clean.3dg.gz
GM-800U_016_5kb_2.clean.3dg.gz
GM-800U_016_5kb_3.clean.3dg.gz
GM-800U_016_5kb_4.clean.3dg.gz
GM-800U_016_5kb_5.clean.3dg.gz


title: MSC,PC,PICTreated

value: PIC


title: GM12878, 800U, Cell 12

description:
800U MNase
GM-800U_012.allValidPairs.gz
GM-800U_012.hic
GM-800U_012.mcool
GM-800U_012.clean.smooth.bw
GM-800U_012_20kb_1.3dg.gz
GM-800U_012_20kb_2.3dg.gz
GM-800U_012_20kb_3.3dg.gz
GM-800U_012_20kb_4.3dg.gz
GM-800U_012_20kb_5.3dg.gz
GM-800U_012_10kb_1.3dg.gz
GM-800U_012_10kb_2.3dg.gz
GM-800U_012_10kb_3.3dg.gz
GM-800U_012_10kb_4.3dg.gz
GM-800U_012_10kb_5.3dg.gz
GM-800U_012_5kb_1.3dg.gz
GM-800U_012_5kb_2.3dg.gz
GM-800U_012_5kb_3.3dg.gz
GM-800U_012_5kb_4.3dg.gz
GM-800U_012_5kb_5.3dg.gz
GM-800U_012_20kb_1.clean.3dg.gz
GM-800U_012_20kb_2.clean.3dg.gz
GM-800U_012_20kb_3.clean.3dg.gz
GM-800U_012_20kb_4.clean.3dg.gz
GM-800U_012_20kb_5.clean.3dg.gz
GM-800U_012_10kb_1.clean.3dg.gz
GM-800U_012_10kb_2.clean.3dg.gz
GM-800U_012_10kb_3.clean.3dg.gz
GM-800U_012_10kb_4.clean.3dg.gz
GM-800U_012_10kb_5.clean.3dg.gz
GM-800U_012_5kb_1.clean.3dg.gz
GM-800U_012_5kb_2.clean.3dg.gz
GM-800U_012_5kb_3.clean.3dg.gz
GM-800U_012_5kb_4.clean.3dg.gz
GM-800U_012_5kb_5.clean.3dg.gz


title: cell_176


title: MSC,99,STNGTreated


title: MSC,92,STNGTreated


title: GM12878, 800U, Cell 10

description:
800U MNase
GM-800U_010.allValidPairs.gz
GM-800U_010.hic
GM-800U_010.mcool
GM-800U_010.clean.smooth.bw
GM-800U_010_20kb_2.3dg.gz
GM-800U_010_20kb_3.3dg.gz
GM-800U_010_20kb_4.3dg.gz
GM-800U_010_20kb_5.3dg.gz
GM-800U_010_10kb_2.3dg.gz
GM-800U_010_10kb_3.3dg.gz
GM-800U_010_10kb_4.3dg.gz
GM-800U_010_10kb_5.3dg.gz
GM-800U_010_5kb_2.3dg.gz
GM-800U_010_5kb_3.3dg.gz
GM-800U_010_5kb_4.3dg.gz
GM-800U_010_5kb_5.3dg.gz
GM-800U_010_20kb_2.clean.3dg.gz
GM-800U_010_20kb_3.clean.3dg.gz
GM-800U_010_20kb_4.clean.3dg.gz
GM-800U_010_20kb_5.clean.3dg.gz
GM-800U_010_10kb_2.clean.3dg.gz
GM-800U_010_10kb_3.clean.3dg.gz
GM-800U_010_10kb_4.clean.3dg.gz
GM-800U_010_10kb_5.clean.3dg.gz
GM-800U_010_5kb_2.clean.3dg.gz
GM-800U_010_5kb_3.clean.3dg.gz
GM-800U_010_5kb_4.clean.3dg.gz
GM-800U_010_5kb_5.clean.3dg.gz


title: WT,cDC1,d0,Spleen,1,12080


title: WT,RPMac,d0,Spleen,7,12080


title: GM12878, 800U, Cell 11

description:
800U MNase
GM-800U_011.allValidPairs.gz
GM-800U_011.hic
GM-800U_011.mcool
GM-800U_011.clean.smooth.bw
GM-800U_011_20kb_1.3dg.gz
GM-800U_011_20kb_2.3dg.gz
GM-800U_011_20kb_3.3dg.gz
GM-800U_011_20kb_4.3dg.gz
GM-800U_011_20kb_5.3dg.gz
GM-800U_011_10kb_1.3dg.gz
GM-800U_011_10kb_2.3dg.gz
GM-800U_011_10kb_3.3dg.gz
GM-800U_011_10kb_4.3dg.gz
GM-800U_011_10kb_5.3dg.gz
GM-800U_011_5kb_1.3dg.gz
GM-800U_011_5kb_2.3dg.gz
GM-800U_011_5kb_3.3dg.gz
GM-800U_011_5kb_4.3dg.gz
GM-800U_011_5kb_5.3dg.gz
GM-800U_011_20kb_1.clean.3dg.gz
GM-800U_011_20kb_2.clean.3dg.gz
GM-800U_011_20kb_3.clean.3dg.gz
GM-800U_011_20kb_4.clean.3dg.gz
GM-800U_011_20kb_5.clean.3dg.gz
GM-800U_011_10kb_1.clean.3dg.gz
GM-800U_011_10kb_2.clean.3dg.gz
GM-800U_011_10kb_3.clean.3dg.gz
GM-800U_011_10kb_4.clean.3dg.gz
GM-800U_011_10kb_5.clean.3dg.gz
GM-800U_011_5kb_1.clean.3dg.gz
GM-800U_011_5kb_2.clean.3dg.gz
GM-800U_011_5kb_3.clean.3dg.gz
GM-800U_011_5kb_4.clean.3dg.gz
GM-800U_011_5kb_5.clean.3dg.gz


title: MSC,99,PICTreated


title: WT,RPMac,d0,Spleen,5,12080


title: MSC,99,CONTUntreated


title: cell_173


title: GM12878, 800U, Cell 9

description:
800U MNase
GM-800U_009.allValidPairs.gz
GM-800U_009.hic
GM-800U_009.mcool
GM-800U_009.clean.smooth.bw
GM-800U_009_20kb_1.3dg.gz
GM-800U_009_20kb_2.3dg.gz
GM-800U_009_20kb_3.3dg.gz
GM-800U_009_20kb_4.3dg.gz
GM-800U_009_20kb_5.3dg.gz
GM-800U_009_10kb_1.3dg.gz
GM-800U_009_10kb_2.3dg.gz
GM-800U_009_10kb_3.3dg.gz
GM-800U_009_10kb_4.3dg.gz
GM-800U_009_10kb_5.3dg.gz
GM-800U_009_5kb_1.3dg.gz
GM-800U_009_5kb_2.3dg.gz
GM-800U_009_5kb_3.3dg.gz
GM-800U_009_5kb_4.3dg.gz
GM-800U_009_5kb_5.3dg.gz
GM-800U_009_20kb_1.clean.3dg.gz
GM-800U_009_20kb_2.clean.3dg.gz
GM-800U_009_20kb_3.clean.3dg.gz
GM-800U_009_20kb_4.clean.3dg.gz
GM-800U_009_20kb_5.clean.3dg.gz
GM-800U_009_10kb_1.clean.3dg.gz
GM-800U_009_10kb_2.clean.3dg.gz
GM-800U_009_10kb_3.clean.3dg.gz
GM-800U_009_10kb_4.clean.3dg.gz
GM-800U_009_10kb_5.clean.3dg.gz
GM-800U_009_5kb_1.clean.3dg.gz
GM-800U_009_5kb_2.clean.3dg.gz
GM-800U_009_5kb_3.clean.3dg.gz
GM-800U_009_5kb_4.clean.3dg.gz
GM-800U_009_5kb_5.clean.3dg.gz


title: cell_174


title: GM12878, 800U, Cell 8

description:
800U MNase
GM-800U_008.allValidPairs.gz
GM-800U_008.hic
GM-800U_008.mcool
GM-800U_008.clean.smooth.bw
GM-800U_008_20kb_1.3dg.gz
GM-800U_008_20kb_2.3dg.gz
GM-800U_008_20kb_3.3dg.gz
GM-800U_008_20kb_4.3dg.gz
GM-800U_008_20kb_5.3dg.gz
GM-800U_008_10kb_1.3dg.gz
GM-800U_008_10kb_2.3dg.gz
GM-800U_008_10kb_3.3dg.gz
GM-800U_008_10kb_4.3dg.gz
GM-800U_008_10kb_5.3dg.gz
GM-800U_008_5kb_1.3dg.gz
GM-800U_008_5kb_2.3dg.gz
GM-800U_008_5kb_3.3dg.gz
GM-800U_008_5kb_4.3dg.gz
GM-800U_008_5kb_5.3dg.gz
GM-800U_008_20kb_1.clean.3dg.gz
GM-800U_008_20kb_2.clean.3dg.gz
GM-800U_008_20kb_3.clean.3dg.gz
GM-800U_008_20kb_4.clean.3dg.gz
GM-800U_008_20kb_5.clean.3dg.gz
GM-800U_008_10kb_1.clean.3dg.gz
GM-800U_008_10kb_2.clean.3dg.gz
GM-800U_008_10kb_3.clean.3dg.gz
GM-800U_008_10kb_4.clean.3dg.gz
GM-800U_008_10kb_5.clean.3dg.gz
GM-800U_008_5kb_1.clean.3dg.gz
GM-800U_008_5kb_2.clean.3dg.gz
GM-800U_008_5kb_3.clean.3dg.gz
GM-800U_008_5kb_4.clean.3dg.gz
GM-800U_008_5kb_5.clean.3dg.gz


title: cell_172

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz


title: WT,RPMac,d0,Spleen,6,12080


title: MSC,92,PICTreated


title: MSC,PC,CPGTreated


title: WT,pDC,24h,Spleen,6,12080

value: 24h post MCMV infection


title: GM12878, 800U, Cell 7

description:
800U MNase
GM-800U_007.allValidPairs.gz
GM-800U_007.hic
GM-800U_007.mcool
GM-800U_007.clean.smooth.bw
GM-800U_007_20kb_1.3dg.gz
GM-800U_007_20kb_2.3dg.gz
GM-800U_007_20kb_3.3dg.gz
GM-800U_007_20kb_4.3dg.gz
GM-800U_007_10kb_1.3dg.gz
GM-800U_007_10kb_2.3dg.gz
GM-800U_007_10kb_3.3dg.gz
GM-800U_007_10kb_4.3dg.gz
GM-800U_007_5kb_1.3dg.gz
GM-800U_007_5kb_2.3dg.gz
GM-800U_007_5kb_3.3dg.gz
GM-800U_007_5kb_4.3dg.gz
GM-800U_007_20kb_1.clean.3dg.gz
GM-800U_007_20kb_2.clean.3dg.gz
GM-800U_007_20kb_3.clean.3dg.gz
GM-800U_007_20kb_4.clean.3dg.gz
GM-800U_007_10kb_1.clean.3dg.gz
GM-800U_007_10kb_2.clean.3dg.gz
GM-800U_007_10kb_3.clean.3dg.gz
GM-800U_007_10kb_4.clean.3dg.gz
GM-800U_007_5kb_1.clean.3dg.gz
GM-800U_007_5kb_2.clean.3dg.gz
GM-800U_007_5kb_3.clean.3dg.gz
GM-800U_007_5kb_4.clean.3dg.gz

value: blood


title: GM12878, 800U, Cell 6

description:
800U MNase
GM-800U_006.allValidPairs.gz
GM-800U_006.hic
GM-800U_006.mcool
GM-800U_006.clean.smooth.bw
GM-800U_006_20kb_1.3dg.gz
GM-800U_006_20kb_2.3dg.gz
GM-800U_006_20kb_3.3dg.gz
GM-800U_006_20kb_4.3dg.gz
GM-800U_006_20kb_5.3dg.gz
GM-800U_006_10kb_1.3dg.gz
GM-800U_006_10kb_2.3dg.gz
GM-800U_006_10kb_3.3dg.gz
GM-800U_006_10kb_4.3dg.gz
GM-800U_006_10kb_5.3dg.gz
GM-800U_006_5kb_1.3dg.gz
GM-800U_006_5kb_2.3dg.gz
GM-800U_006_5kb_3.3dg.gz
GM-800U_006_5kb_4.3dg.gz
GM-800U_006_5kb_5.3dg.gz
GM-800U_006_20kb_1.clean.3dg.gz
GM-800U_006_20kb_2.clean.3dg.gz
GM-800U_006_20kb_3.clean.3dg.gz
GM-800U_006_20kb_4.clean.3dg.gz
GM-800U_006_20kb_5.clean.3dg.gz
GM-800U_006_10kb_1.clean.3dg.gz
GM-800U_006_10kb_2.clean.3dg.gz
GM-800U_006_10kb_3.clean.3dg.gz
GM-800U_006_10kb_4.clean.3dg.gz
GM-800U_006_10kb_5.clean.3dg.gz
GM-800U_006_5kb_1.clean.3dg.gz
GM-800U_006_5kb_2.clean.3dg.gz
GM-800U_006_5kb_3.clean.3dg.gz
GM-800U_006_5kb_4.clean.3dg.gz
GM-800U_006_5kb_5.clean.3dg.gz

value: lymphoblastoid


title: WT,pDC,24h,Spleen,7,12080

value: Spleen


title: cell_170


title: Synoviocytes,PC,CTRLUntreated

source_name: Synoviocytes

value: Synoviocytes


title: cell_171


title: GM12878, 800U, Cell 5

description:
800U MNase
GM-800U_005.allValidPairs.gz
GM-800U_005.hic
GM-800U_005.mcool
GM-800U_005.clean.smooth.bw
GM-800U_005_20kb_1.3dg.gz
GM-800U_005_20kb_2.3dg.gz
GM-800U_005_20kb_3.3dg.gz
GM-800U_005_20kb_4.3dg.gz
GM-800U_005_20kb_5.3dg.gz
GM-800U_005_10kb_1.3dg.gz
GM-800U_005_10kb_2.3dg.gz
GM-800U_005_10kb_3.3dg.gz
GM-800U_005_10kb_4.3dg.gz
GM-800U_005_10kb_5.3dg.gz
GM-800U_005_5kb_1.3dg.gz
GM-800U_005_5kb_2.3dg.gz
GM-800U_005_5kb_3.3dg.gz
GM-800U_005_5kb_4.3dg.gz
GM-800U_005_5kb_5.3dg.gz
GM-800U_005_20kb_1.clean.3dg.gz
GM-800U_005_20kb_2.clean.3dg.gz
GM-800U_005_20kb_3.clean.3dg.gz
GM-800U_005_20kb_4.clean.3dg.gz
GM-800U_005_20kb_5.clean.3dg.gz
GM-800U_005_10kb_1.clean.3dg.gz
GM-800U_005_10kb_2.clean.3dg.gz
GM-800U_005_10kb_3.clean.3dg.gz
GM-800U_005_10kb_4.clean.3dg.gz
GM-800U_005_10kb_5.clean.3dg.gz
GM-800U_005_5kb_1.clean.3dg.gz
GM-800U_005_5kb_2.clean.3dg.gz
GM-800U_005_5kb_3.clean.3dg.gz
GM-800U_005_5kb_4.clean.3dg.gz
GM-800U_005_5kb_5.clean.3dg.gz


title: cell_175


title: WT,cDC1,24h,Spleen,3,12080


title: GM12878, 800U, Cell 4

description:
800U MNase
GM-800U_004.allValidPairs.gz
GM-800U_004.hic
GM-800U_004.mcool
GM-800U_004.clean.smooth.bw
GM-800U_004_20kb_1.3dg.gz
GM-800U_004_20kb_2.3dg.gz
GM-800U_004_20kb_3.3dg.gz
GM-800U_004_20kb_4.3dg.gz
GM-800U_004_20kb_5.3dg.gz
GM-800U_004_10kb_1.3dg.gz
GM-800U_004_10kb_2.3dg.gz
GM-800U_004_10kb_3.3dg.gz
GM-800U_004_10kb_4.3dg.gz
GM-800U_004_10kb_5.3dg.gz
GM-800U_004_5kb_1.3dg.gz
GM-800U_004_5kb_2.3dg.gz
GM-800U_004_5kb_3.3dg.gz
GM-800U_004_5kb_4.3dg.gz
GM-800U_004_5kb_5.3dg.gz
GM-800U_004_20kb_1.clean.3dg.gz
GM-800U_004_20kb_2.clean.3dg.gz
GM-800U_004_20kb_3.clean.3dg.gz
GM-800U_004_20kb_4.clean.3dg.gz
GM-800U_004_20kb_5.clean.3dg.gz
GM-800U_004_10kb_1.clean.3dg.gz
GM-800U_004_10kb_2.clean.3dg.gz
GM-800U_004_10kb_3.clean.3dg.gz
GM-800U_004_10kb_4.clean.3dg.gz
GM-800U_004_10kb_5.clean.3dg.gz
GM-800U_004_5kb_1.clean.3dg.gz
GM-800U_004_5kb_2.clean.3dg.gz
GM-800U_004_5kb_3.clean.3dg.gz
GM-800U_004_5kb_4.clean.3dg.gz
GM-800U_004_5kb_5.clean.3dg.gz


title: GM12878, 800U, Cell 3

description:
800U MNase
GM-800U_003.allValidPairs.gz
GM-800U_003.hic
GM-800U_003.mcool
GM-800U_003.clean.smooth.bw
GM-800U_003_20kb_1.3dg.gz
GM-800U_003_20kb_3.3dg.gz
GM-800U_003_20kb_5.3dg.gz
GM-800U_003_10kb_1.3dg.gz
GM-800U_003_10kb_3.3dg.gz
GM-800U_003_10kb_5.3dg.gz
GM-800U_003_5kb_1.3dg.gz
GM-800U_003_5kb_3.3dg.gz
GM-800U_003_5kb_5.3dg.gz
GM-800U_003_20kb_1.clean.3dg.gz
GM-800U_003_20kb_3.clean.3dg.gz
GM-800U_003_20kb_5.clean.3dg.gz
GM-800U_003_10kb_1.clean.3dg.gz
GM-800U_003_10kb_3.clean.3dg.gz
GM-800U_003_10kb_5.clean.3dg.gz
GM-800U_003_5kb_1.clean.3dg.gz
GM-800U_003_5kb_3.clean.3dg.gz
GM-800U_003_5kb_5.clean.3dg.gz


title: Synoviocytes,AG1,CTRLUntreated


title: Macrophage,AG1,CTRLUntreated


title: WT,cDC1,24h,Spleen,1,12080


title: WT,cDC1,24h,Spleen,2,12080


title: cell_169


title: GM12878, 800U, Cell 2

description:
800U MNase
GM-800U_002.allValidPairs.gz
GM-800U_002.hic
GM-800U_002.mcool
GM-800U_002.clean.smooth.bw
GM-800U_002_20kb_1.3dg.gz
GM-800U_002_20kb_2.3dg.gz
GM-800U_002_20kb_3.3dg.gz
GM-800U_002_20kb_4.3dg.gz
GM-800U_002_20kb_5.3dg.gz
GM-800U_002_10kb_1.3dg.gz
GM-800U_002_10kb_2.3dg.gz
GM-800U_002_10kb_3.3dg.gz
GM-800U_002_10kb_4.3dg.gz
GM-800U_002_10kb_5.3dg.gz
GM-800U_002_5kb_1.3dg.gz
GM-800U_002_5kb_2.3dg.gz
GM-800U_002_5kb_3.3dg.gz
GM-800U_002_5kb_4.3dg.gz
GM-800U_002_5kb_5.3dg.gz
GM-800U_002_20kb_1.clean.3dg.gz
GM-800U_002_20kb_2.clean.3dg.gz
GM-800U_002_20kb_3.clean.3dg.gz
GM-800U_002_20kb_4.clean.3dg.gz
GM-800U_002_20kb_5.clean.3dg.gz
GM-800U_002_10kb_1.clean.3dg.gz
GM-800U_002_10kb_2.clean.3dg.gz
GM-800U_002_10kb_3.clean.3dg.gz
GM-800U_002_10kb_4.clean.3dg.gz
GM-800U_002_10kb_5.clean.3dg.gz
GM-800U_002_5kb_1.clean.3dg.gz
GM-800U_002_5kb_2.clean.3dg.gz
GM-800U_002_5kb_3.clean.3dg.gz
GM-800U_002_5kb_4.clean.3dg.gz
GM-800U_002_5kb_5.clean.3dg.gz


title: cell_167


title: Synoviocytes,PC,TNFTreated

value: TNF


title: cell_166


title: WT,pDC,24h,Spleen,5,12080

value: pDC


title: WT,RPMac,24h,Spleen,6,12080

value: RPMac


title: GM12878, 800U, Cell 1

description:
800U MNase
GM-800U_001.allValidPairs.gz
GM-800U_001.hic
GM-800U_001.mcool
GM-800U_001.clean.smooth.bw
GM-800U_001_20kb_1.3dg.gz
GM-800U_001_20kb_2.3dg.gz
GM-800U_001_20kb_3.3dg.gz
GM-800U_001_20kb_5.3dg.gz
GM-800U_001_10kb_1.3dg.gz
GM-800U_001_10kb_2.3dg.gz
GM-800U_001_10kb_3.3dg.gz
GM-800U_001_10kb_5.3dg.gz
GM-800U_001_5kb_1.3dg.gz
GM-800U_001_5kb_2.3dg.gz
GM-800U_001_5kb_3.3dg.gz
GM-800U_001_5kb_5.3dg.gz
GM-800U_001_20kb_2.clean.3dg.gz
GM-800U_001_20kb_3.clean.3dg.gz
GM-800U_001_20kb_5.clean.3dg.gz
GM-800U_001_10kb_2.clean.3dg.gz
GM-800U_001_10kb_3.clean.3dg.gz
GM-800U_001_10kb_5.clean.3dg.gz
GM-800U_001_5kb_2.clean.3dg.gz
GM-800U_001_5kb_3.clean.3dg.gz
GM-800U_001_5kb_5.clean.3dg.gz


title: Macrophage,PC,PICTreated

value: PC


title: GM12878, 600U, Cell 96

description:
GM-600U_096.allValidPairs.txt
GM-600U_096.hic
GM-600U_096.mcool
GM-600U_096.clean.smooth.bw
GM-600U_096_20kb_1.3dg.txt
GM-600U_096_20kb_2.3dg.txt
GM-600U_096_20kb_5.3dg.txt
GM-600U_096_10kb_1.3dg.txt
GM-600U_096_10kb_2.3dg.txt
GM-600U_096_10kb_5.3dg.txt
GM-600U_096_5kb_1.3dg.txt
GM-600U_096_5kb_2.3dg.txt
GM-600U_096_5kb_5.3dg.txt
GM-600U_096_20kb_1.clean.3dg.txt
GM-600U_096_20kb_2.clean.3dg.txt
GM-600U_096_20kb_5.clean.3dg.txt
GM-600U_096_10kb_1.clean.3dg.txt
GM-600U_096_10kb_2.clean.3dg.txt
GM-600U_096_10kb_5.clean.3dg.txt
GM-600U_096_5kb_1.clean.3dg.txt
GM-600U_096_5kb_2.clean.3dg.txt
GM-600U_096_5kb_5.clean.3dg.txt

tag: mnase titration

value: 600U MNase


title: WT,RPMac,24h,Spleen,5,12080


title: GM12878, 600U, Cell 95

description:
GM-600U_095.allValidPairs.txt
GM-600U_095.hic
GM-600U_095.mcool
GM-600U_095.clean.smooth.bw
GM-600U_095_20kb_1.3dg.txt
GM-600U_095_20kb_2.3dg.txt
GM-600U_095_20kb_3.3dg.txt
GM-600U_095_20kb_4.3dg.txt
GM-600U_095_20kb_5.3dg.txt
GM-600U_095_10kb_1.3dg.txt
GM-600U_095_10kb_2.3dg.txt
GM-600U_095_10kb_3.3dg.txt
GM-600U_095_10kb_4.3dg.txt
GM-600U_095_10kb_5.3dg.txt
GM-600U_095_5kb_1.3dg.txt
GM-600U_095_5kb_2.3dg.txt
GM-600U_095_5kb_3.3dg.txt
GM-600U_095_5kb_4.3dg.txt
GM-600U_095_5kb_5.3dg.txt
GM-600U_095_20kb_1.clean.3dg.txt
GM-600U_095_20kb_2.clean.3dg.txt
GM-600U_095_20kb_3.clean.3dg.txt
GM-600U_095_20kb_4.clean.3dg.txt
GM-600U_095_20kb_5.clean.3dg.txt
GM-600U_095_10kb_1.clean.3dg.txt
GM-600U_095_10kb_2.clean.3dg.txt
GM-600U_095_10kb_3.clean.3dg.txt
GM-600U_095_10kb_4.clean.3dg.txt
GM-600U_095_10kb_5.clean.3dg.txt
GM-600U_095_5kb_1.clean.3dg.txt
GM-600U_095_5kb_2.clean.3dg.txt
GM-600U_095_5kb_3.clean.3dg.txt
GM-600U_095_5kb_4.clean.3dg.txt
GM-600U_095_5kb_5.clean.3dg.txt


title: Synoviocytes,PC,PICTreated


title: cell_165


title: cell_163


title: WT,Ly49HposNK,d4,Spleen,4,11821

extract_protocol:
Wildtype or TNFR2-/- Ly49H+ NK cells (Ly49H+ CD49b+ TCRb- CD3- CD19- F480-) were sorted from the spleens of mixed bone marrow chimera mice 1, 2, or 4 days p.i with MCMV. In each independent experiment, RNA was isolated from sorted cells using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher) in accordance with the manufacturer instructions.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.7-2 ng total RNA with RNA integrity numbers ranging from 9.2 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 9-10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE50.

value: d4 post MCMV infection


title: Chondrocytes,PC,STNGTreated

source_name: Chondrocytes

value: Chondrocytes


title: Chondrocytes,AG1,CTRLUntreated

value: CTRL


title: GM12878, 600U, Cell 94

description:
GM-600U_094.allValidPairs.txt
GM-600U_094.hic
GM-600U_094.mcool
GM-600U_094.clean.smooth.bw
GM-600U_094_20kb_1.3dg.txt
GM-600U_094_20kb_2.3dg.txt
GM-600U_094_20kb_3.3dg.txt
GM-600U_094_20kb_4.3dg.txt
GM-600U_094_20kb_5.3dg.txt
GM-600U_094_10kb_1.3dg.txt
GM-600U_094_10kb_2.3dg.txt
GM-600U_094_10kb_3.3dg.txt
GM-600U_094_10kb_4.3dg.txt
GM-600U_094_10kb_5.3dg.txt
GM-600U_094_5kb_1.3dg.txt
GM-600U_094_5kb_2.3dg.txt
GM-600U_094_5kb_3.3dg.txt
GM-600U_094_5kb_4.3dg.txt
GM-600U_094_5kb_5.3dg.txt
GM-600U_094_20kb_1.clean.3dg.txt
GM-600U_094_20kb_2.clean.3dg.txt
GM-600U_094_20kb_3.clean.3dg.txt
GM-600U_094_20kb_4.clean.3dg.txt
GM-600U_094_20kb_5.clean.3dg.txt
GM-600U_094_10kb_1.clean.3dg.txt
GM-600U_094_10kb_2.clean.3dg.txt
GM-600U_094_10kb_3.clean.3dg.txt
GM-600U_094_10kb_4.clean.3dg.txt
GM-600U_094_10kb_5.clean.3dg.txt
GM-600U_094_5kb_1.clean.3dg.txt
GM-600U_094_5kb_2.clean.3dg.txt
GM-600U_094_5kb_3.clean.3dg.txt
GM-600U_094_5kb_4.clean.3dg.txt
GM-600U_094_5kb_5.clean.3dg.txt


title: cell_168


title: cell_162


title: WT,Ly49HposNK,d4,Spleen,3,11821


title: WT,RPMac,24h,Spleen,7,12080


title: Macrophage,PC,STNGTreated

value: Macrophage

value: STNG


title: GM12878, 600U, Cell 93

description:
GM-600U_093.allValidPairs.txt
GM-600U_093.hic
GM-600U_093.mcool
GM-600U_093.clean.smooth.bw
GM-600U_093_20kb_1.3dg.txt
GM-600U_093_20kb_2.3dg.txt
GM-600U_093_20kb_3.3dg.txt
GM-600U_093_20kb_4.3dg.txt
GM-600U_093_20kb_5.3dg.txt
GM-600U_093_10kb_1.3dg.txt
GM-600U_093_10kb_2.3dg.txt
GM-600U_093_10kb_3.3dg.txt
GM-600U_093_10kb_4.3dg.txt
GM-600U_093_10kb_5.3dg.txt
GM-600U_093_5kb_1.3dg.txt
GM-600U_093_5kb_2.3dg.txt
GM-600U_093_5kb_3.3dg.txt
GM-600U_093_5kb_4.3dg.txt
GM-600U_093_5kb_5.3dg.txt
GM-600U_093_20kb_1.clean.3dg.txt
GM-600U_093_20kb_2.clean.3dg.txt
GM-600U_093_20kb_3.clean.3dg.txt
GM-600U_093_20kb_4.clean.3dg.txt
GM-600U_093_20kb_5.clean.3dg.txt
GM-600U_093_10kb_1.clean.3dg.txt
GM-600U_093_10kb_2.clean.3dg.txt
GM-600U_093_10kb_3.clean.3dg.txt
GM-600U_093_10kb_4.clean.3dg.txt
GM-600U_093_10kb_5.clean.3dg.txt
GM-600U_093_5kb_1.clean.3dg.txt
GM-600U_093_5kb_2.clean.3dg.txt
GM-600U_093_5kb_3.clean.3dg.txt
GM-600U_093_5kb_4.clean.3dg.txt
GM-600U_093_5kb_5.clean.3dg.txt

value: WT


title: WT,Ly49HposNK,d4,Spleen,2,11821


title: cell_161


title: Synoviocytes,ORC,CTRLUntreated

value: ORC


title: WT,Ly49HposNK,d2,Spleen,4,11821

value: d2 post MCMV infection


title: WT,Ly49HposNK,d2,Spleen,3,11821


title: cell_164

value: blood


title: GM12878, 600U, Cell 91

description:
GM-600U_091.allValidPairs.txt
GM-600U_091.hic
GM-600U_091.mcool
GM-600U_091.clean.smooth.bw
GM-600U_091_20kb_1.3dg.txt
GM-600U_091_20kb_2.3dg.txt
GM-600U_091_20kb_3.3dg.txt
GM-600U_091_20kb_4.3dg.txt
GM-600U_091_20kb_5.3dg.txt
GM-600U_091_10kb_1.3dg.txt
GM-600U_091_10kb_2.3dg.txt
GM-600U_091_10kb_3.3dg.txt
GM-600U_091_10kb_4.3dg.txt
GM-600U_091_10kb_5.3dg.txt
GM-600U_091_5kb_1.3dg.txt
GM-600U_091_5kb_2.3dg.txt
GM-600U_091_5kb_3.3dg.txt
GM-600U_091_5kb_4.3dg.txt
GM-600U_091_5kb_5.3dg.txt
GM-600U_091_20kb_1.clean.3dg.txt
GM-600U_091_20kb_2.clean.3dg.txt
GM-600U_091_20kb_3.clean.3dg.txt
GM-600U_091_20kb_4.clean.3dg.txt
GM-600U_091_20kb_5.clean.3dg.txt
GM-600U_091_10kb_1.clean.3dg.txt
GM-600U_091_10kb_2.clean.3dg.txt
GM-600U_091_10kb_3.clean.3dg.txt
GM-600U_091_10kb_4.clean.3dg.txt
GM-600U_091_10kb_5.clean.3dg.txt
GM-600U_091_5kb_1.clean.3dg.txt
GM-600U_091_5kb_2.clean.3dg.txt
GM-600U_091_5kb_3.clean.3dg.txt
GM-600U_091_5kb_4.clean.3dg.txt
GM-600U_091_5kb_5.clean.3dg.txt

value: lymphoblastoid


title: Synoviocytes,PC,STNGTreated


title: GM12878, 600U, Cell 92

description:
GM-600U_092.allValidPairs.txt
GM-600U_092.hic
GM-600U_092.mcool
GM-600U_092.clean.smooth.bw
GM-600U_092_20kb_1.3dg.txt
GM-600U_092_20kb_2.3dg.txt
GM-600U_092_20kb_3.3dg.txt
GM-600U_092_20kb_4.3dg.txt
GM-600U_092_20kb_5.3dg.txt
GM-600U_092_10kb_1.3dg.txt
GM-600U_092_10kb_2.3dg.txt
GM-600U_092_10kb_3.3dg.txt
GM-600U_092_10kb_4.3dg.txt
GM-600U_092_10kb_5.3dg.txt
GM-600U_092_5kb_1.3dg.txt
GM-600U_092_5kb_2.3dg.txt
GM-600U_092_5kb_3.3dg.txt
GM-600U_092_5kb_4.3dg.txt
GM-600U_092_5kb_5.3dg.txt
GM-600U_092_20kb_1.clean.3dg.txt
GM-600U_092_20kb_2.clean.3dg.txt
GM-600U_092_20kb_3.clean.3dg.txt
GM-600U_092_20kb_4.clean.3dg.txt
GM-600U_092_20kb_5.clean.3dg.txt
GM-600U_092_10kb_1.clean.3dg.txt
GM-600U_092_10kb_2.clean.3dg.txt
GM-600U_092_10kb_3.clean.3dg.txt
GM-600U_092_10kb_4.clean.3dg.txt
GM-600U_092_10kb_5.clean.3dg.txt
GM-600U_092_5kb_1.clean.3dg.txt
GM-600U_092_5kb_2.clean.3dg.txt
GM-600U_092_5kb_3.clean.3dg.txt
GM-600U_092_5kb_4.clean.3dg.txt
GM-600U_092_5kb_5.clean.3dg.txt


title: Chondrocytes,PC,CTRLUntreated


title: cell_160


title: GM12878, 600U, Cell 89

description:
GM-600U_089.allValidPairs.txt
GM-600U_089.hic
GM-600U_089.mcool
GM-600U_089.clean.smooth.bw
GM-600U_089_20kb_1.3dg.txt
GM-600U_089_20kb_3.3dg.txt
GM-600U_089_20kb_5.3dg.txt
GM-600U_089_10kb_1.3dg.txt
GM-600U_089_10kb_3.3dg.txt
GM-600U_089_10kb_5.3dg.txt
GM-600U_089_5kb_1.3dg.txt
GM-600U_089_5kb_3.3dg.txt
GM-600U_089_5kb_5.3dg.txt
GM-600U_089_20kb_1.clean.3dg.txt
GM-600U_089_20kb_3.clean.3dg.txt
GM-600U_089_20kb_5.clean.3dg.txt
GM-600U_089_10kb_1.clean.3dg.txt
GM-600U_089_10kb_3.clean.3dg.txt
GM-600U_089_10kb_5.clean.3dg.txt
GM-600U_089_5kb_1.clean.3dg.txt
GM-600U_089_5kb_3.clean.3dg.txt
GM-600U_089_5kb_5.clean.3dg.txt


title: cell_158


title: cell_159


title: GM12878, 600U, Cell 90

description:
GM-600U_090.allValidPairs.txt
GM-600U_090.hic
GM-600U_090.mcool
GM-600U_090.clean.smooth.bw
GM-600U_090_20kb_1.3dg.txt
GM-600U_090_20kb_2.3dg.txt
GM-600U_090_20kb_3.3dg.txt
GM-600U_090_20kb_4.3dg.txt
GM-600U_090_20kb_5.3dg.txt
GM-600U_090_10kb_1.3dg.txt
GM-600U_090_10kb_2.3dg.txt
GM-600U_090_10kb_3.3dg.txt
GM-600U_090_10kb_4.3dg.txt
GM-600U_090_10kb_5.3dg.txt
GM-600U_090_5kb_1.3dg.txt
GM-600U_090_5kb_2.3dg.txt
GM-600U_090_5kb_3.3dg.txt
GM-600U_090_5kb_4.3dg.txt
GM-600U_090_5kb_5.3dg.txt
GM-600U_090_20kb_1.clean.3dg.txt
GM-600U_090_20kb_2.clean.3dg.txt
GM-600U_090_20kb_3.clean.3dg.txt
GM-600U_090_20kb_4.clean.3dg.txt
GM-600U_090_20kb_5.clean.3dg.txt
GM-600U_090_10kb_1.clean.3dg.txt
GM-600U_090_10kb_2.clean.3dg.txt
GM-600U_090_10kb_3.clean.3dg.txt
GM-600U_090_10kb_4.clean.3dg.txt
GM-600U_090_10kb_5.clean.3dg.txt
GM-600U_090_5kb_1.clean.3dg.txt
GM-600U_090_5kb_2.clean.3dg.txt
GM-600U_090_5kb_3.clean.3dg.txt
GM-600U_090_5kb_4.clean.3dg.txt
GM-600U_090_5kb_5.clean.3dg.txt


title: WT,Ly49HposNK,d2,Spleen,2,11821

value: Spleen


title: WT,Ly49HposNK,d1,Spleen,4,11821

value: d1 post MCMV infection


title: Chondrocytes,AG1,STNGTreated


title: cell_157


title: cell_181


title: GM12878, 600U, Cell 88

description:
GM-600U_088.allValidPairs.txt
GM-600U_088.hic
GM-600U_088.mcool
GM-600U_088.clean.smooth.bw
GM-600U_088_20kb_1.3dg.txt
GM-600U_088_20kb_2.3dg.txt
GM-600U_088_20kb_3.3dg.txt
GM-600U_088_20kb_4.3dg.txt
GM-600U_088_20kb_5.3dg.txt
GM-600U_088_10kb_1.3dg.txt
GM-600U_088_10kb_2.3dg.txt
GM-600U_088_10kb_3.3dg.txt
GM-600U_088_10kb_4.3dg.txt
GM-600U_088_10kb_5.3dg.txt
GM-600U_088_5kb_1.3dg.txt
GM-600U_088_5kb_2.3dg.txt
GM-600U_088_5kb_3.3dg.txt
GM-600U_088_5kb_4.3dg.txt
GM-600U_088_5kb_5.3dg.txt
GM-600U_088_20kb_1.clean.3dg.txt
GM-600U_088_20kb_2.clean.3dg.txt
GM-600U_088_20kb_3.clean.3dg.txt
GM-600U_088_20kb_4.clean.3dg.txt
GM-600U_088_20kb_5.clean.3dg.txt
GM-600U_088_10kb_1.clean.3dg.txt
GM-600U_088_10kb_2.clean.3dg.txt
GM-600U_088_10kb_3.clean.3dg.txt
GM-600U_088_10kb_4.clean.3dg.txt
GM-600U_088_10kb_5.clean.3dg.txt
GM-600U_088_5kb_1.clean.3dg.txt
GM-600U_088_5kb_2.clean.3dg.txt
GM-600U_088_5kb_3.clean.3dg.txt
GM-600U_088_5kb_4.clean.3dg.txt
GM-600U_088_5kb_5.clean.3dg.txt


title: cell_156

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz


title: WT,Ly49HposNK,d1,Spleen,2,11821


title: Synoviocytes,AG1,STNGTreated

value: Synoviocytes


title: TNFR2KO,Ly49HposNK,d4,Spleen,4,11821


title: cell_155


title: Chondrocytes,ORC,TNFTreated

value: TNF


title: Macrophage,PC,CTRLUntreated


title: cell_154


title: TNFR2KO,Ly49HposNK,d4,Spleen,3,11821


title: Chondrocytes,ORC,CTRLUntreated


title: TNFR2KO,Ly49HposNK,d4,Spleen,2,11821


title: Macrophage,AG1,STNGTreated


title: GM12878, 600U, Cell 85

description:
GM-600U_085.allValidPairs.txt
GM-600U_085.hic
GM-600U_085.mcool
GM-600U_085.clean.smooth.bw
GM-600U_085_20kb_1.3dg.txt
GM-600U_085_20kb_2.3dg.txt
GM-600U_085_20kb_3.3dg.txt
GM-600U_085_20kb_4.3dg.txt
GM-600U_085_20kb_5.3dg.txt
GM-600U_085_10kb_1.3dg.txt
GM-600U_085_10kb_2.3dg.txt
GM-600U_085_10kb_3.3dg.txt
GM-600U_085_10kb_4.3dg.txt
GM-600U_085_10kb_5.3dg.txt
GM-600U_085_5kb_1.3dg.txt
GM-600U_085_5kb_2.3dg.txt
GM-600U_085_5kb_3.3dg.txt
GM-600U_085_5kb_4.3dg.txt
GM-600U_085_5kb_5.3dg.txt
GM-600U_085_20kb_1.clean.3dg.txt
GM-600U_085_20kb_2.clean.3dg.txt
GM-600U_085_20kb_3.clean.3dg.txt
GM-600U_085_20kb_4.clean.3dg.txt
GM-600U_085_20kb_5.clean.3dg.txt
GM-600U_085_10kb_1.clean.3dg.txt
GM-600U_085_10kb_2.clean.3dg.txt
GM-600U_085_10kb_3.clean.3dg.txt
GM-600U_085_10kb_4.clean.3dg.txt
GM-600U_085_10kb_5.clean.3dg.txt
GM-600U_085_5kb_1.clean.3dg.txt
GM-600U_085_5kb_2.clean.3dg.txt
GM-600U_085_5kb_3.clean.3dg.txt
GM-600U_085_5kb_4.clean.3dg.txt
GM-600U_085_5kb_5.clean.3dg.txt


title: TNFR2KO,Ly49HposNK,d2,Spleen,3,11821


title: TNFR2KO,Ly49HposNK,d2,Spleen,4,11821


title: GM12878, 600U, Cell 86

description:
GM-600U_086.allValidPairs.txt
GM-600U_086.hic
GM-600U_086.mcool
GM-600U_086.clean.smooth.bw
GM-600U_086_20kb_1.3dg.txt
GM-600U_086_20kb_2.3dg.txt
GM-600U_086_20kb_3.3dg.txt
GM-600U_086_20kb_4.3dg.txt
GM-600U_086_20kb_5.3dg.txt
GM-600U_086_10kb_1.3dg.txt
GM-600U_086_10kb_2.3dg.txt
GM-600U_086_10kb_3.3dg.txt
GM-600U_086_10kb_4.3dg.txt
GM-600U_086_10kb_5.3dg.txt
GM-600U_086_5kb_1.3dg.txt
GM-600U_086_5kb_2.3dg.txt
GM-600U_086_5kb_3.3dg.txt
GM-600U_086_5kb_4.3dg.txt
GM-600U_086_5kb_5.3dg.txt
GM-600U_086_20kb_1.clean.3dg.txt
GM-600U_086_20kb_2.clean.3dg.txt
GM-600U_086_20kb_3.clean.3dg.txt
GM-600U_086_20kb_4.clean.3dg.txt
GM-600U_086_20kb_5.clean.3dg.txt
GM-600U_086_10kb_1.clean.3dg.txt
GM-600U_086_10kb_2.clean.3dg.txt
GM-600U_086_10kb_3.clean.3dg.txt
GM-600U_086_10kb_4.clean.3dg.txt
GM-600U_086_10kb_5.clean.3dg.txt
GM-600U_086_5kb_1.clean.3dg.txt
GM-600U_086_5kb_2.clean.3dg.txt
GM-600U_086_5kb_3.clean.3dg.txt
GM-600U_086_5kb_4.clean.3dg.txt
GM-600U_086_5kb_5.clean.3dg.txt


title: Synoviocytes,ORC,PICTreated

value: PIC


title: GM12878, 600U, Cell 84

description:
GM-600U_084.allValidPairs.txt
GM-600U_084.hic
GM-600U_084.mcool
GM-600U_084.clean.smooth.bw
GM-600U_084_20kb_1.3dg.txt
GM-600U_084_20kb_2.3dg.txt
GM-600U_084_20kb_3.3dg.txt
GM-600U_084_20kb_5.3dg.txt
GM-600U_084_10kb_1.3dg.txt
GM-600U_084_10kb_2.3dg.txt
GM-600U_084_10kb_3.3dg.txt
GM-600U_084_10kb_5.3dg.txt
GM-600U_084_5kb_1.3dg.txt
GM-600U_084_5kb_2.3dg.txt
GM-600U_084_5kb_3.3dg.txt
GM-600U_084_5kb_5.3dg.txt
GM-600U_084_20kb_1.clean.3dg.txt
GM-600U_084_20kb_2.clean.3dg.txt
GM-600U_084_20kb_3.clean.3dg.txt
GM-600U_084_20kb_5.clean.3dg.txt
GM-600U_084_10kb_1.clean.3dg.txt
GM-600U_084_10kb_2.clean.3dg.txt
GM-600U_084_10kb_3.clean.3dg.txt
GM-600U_084_10kb_5.clean.3dg.txt
GM-600U_084_5kb_1.clean.3dg.txt
GM-600U_084_5kb_2.clean.3dg.txt
GM-600U_084_5kb_3.clean.3dg.txt
GM-600U_084_5kb_5.clean.3dg.txt


title: GM12878, 600U, Cell 83

description:
GM-600U_083.allValidPairs.txt
GM-600U_083.hic
GM-600U_083.mcool
GM-600U_083.clean.smooth.bw
GM-600U_083_20kb_1.3dg.txt
GM-600U_083_20kb_2.3dg.txt
GM-600U_083_20kb_3.3dg.txt
GM-600U_083_20kb_4.3dg.txt
GM-600U_083_20kb_5.3dg.txt
GM-600U_083_10kb_1.3dg.txt
GM-600U_083_10kb_2.3dg.txt
GM-600U_083_10kb_3.3dg.txt
GM-600U_083_10kb_4.3dg.txt
GM-600U_083_10kb_5.3dg.txt
GM-600U_083_5kb_1.3dg.txt
GM-600U_083_5kb_2.3dg.txt
GM-600U_083_5kb_3.3dg.txt
GM-600U_083_5kb_4.3dg.txt
GM-600U_083_5kb_5.3dg.txt
GM-600U_083_20kb_1.clean.3dg.txt
GM-600U_083_20kb_2.clean.3dg.txt
GM-600U_083_20kb_3.clean.3dg.txt
GM-600U_083_20kb_4.clean.3dg.txt
GM-600U_083_20kb_5.clean.3dg.txt
GM-600U_083_10kb_1.clean.3dg.txt
GM-600U_083_10kb_2.clean.3dg.txt
GM-600U_083_10kb_3.clean.3dg.txt
GM-600U_083_10kb_4.clean.3dg.txt
GM-600U_083_10kb_5.clean.3dg.txt
GM-600U_083_5kb_1.clean.3dg.txt
GM-600U_083_5kb_2.clean.3dg.txt
GM-600U_083_5kb_3.clean.3dg.txt
GM-600U_083_5kb_4.clean.3dg.txt
GM-600U_083_5kb_5.clean.3dg.txt


title: cell_152


title: cell_151


title: Chondrocytes,ORC,STNGTreated


title: Macrophage,ORC,STNGTreated


title: GM12878, 600U, Cell 81

description:
GM-600U_081.allValidPairs.txt
GM-600U_081.hic
GM-600U_081.mcool
GM-600U_081.clean.smooth.bw
GM-600U_081_20kb_1.3dg.txt
GM-600U_081_20kb_2.3dg.txt
GM-600U_081_20kb_3.3dg.txt
GM-600U_081_20kb_4.3dg.txt
GM-600U_081_20kb_5.3dg.txt
GM-600U_081_10kb_1.3dg.txt
GM-600U_081_10kb_2.3dg.txt
GM-600U_081_10kb_3.3dg.txt
GM-600U_081_10kb_4.3dg.txt
GM-600U_081_10kb_5.3dg.txt
GM-600U_081_5kb_1.3dg.txt
GM-600U_081_5kb_2.3dg.txt
GM-600U_081_5kb_3.3dg.txt
GM-600U_081_5kb_4.3dg.txt
GM-600U_081_5kb_5.3dg.txt
GM-600U_081_20kb_1.clean.3dg.txt
GM-600U_081_20kb_2.clean.3dg.txt
GM-600U_081_20kb_3.clean.3dg.txt
GM-600U_081_20kb_4.clean.3dg.txt
GM-600U_081_20kb_5.clean.3dg.txt
GM-600U_081_10kb_1.clean.3dg.txt
GM-600U_081_10kb_2.clean.3dg.txt
GM-600U_081_10kb_3.clean.3dg.txt
GM-600U_081_10kb_4.clean.3dg.txt
GM-600U_081_10kb_5.clean.3dg.txt
GM-600U_081_5kb_1.clean.3dg.txt
GM-600U_081_5kb_2.clean.3dg.txt
GM-600U_081_5kb_3.clean.3dg.txt
GM-600U_081_5kb_4.clean.3dg.txt
GM-600U_081_5kb_5.clean.3dg.txt


title: GM12878, 600U, Cell 82

description:
GM-600U_082.allValidPairs.txt
GM-600U_082.hic
GM-600U_082.mcool
GM-600U_082.clean.smooth.bw
GM-600U_082_20kb_1.3dg.txt
GM-600U_082_20kb_2.3dg.txt
GM-600U_082_20kb_3.3dg.txt
GM-600U_082_20kb_5.3dg.txt
GM-600U_082_10kb_1.3dg.txt
GM-600U_082_10kb_2.3dg.txt
GM-600U_082_10kb_3.3dg.txt
GM-600U_082_10kb_5.3dg.txt
GM-600U_082_5kb_1.3dg.txt
GM-600U_082_5kb_2.3dg.txt
GM-600U_082_5kb_3.3dg.txt
GM-600U_082_5kb_5.3dg.txt
GM-600U_082_20kb_1.clean.3dg.txt
GM-600U_082_20kb_2.clean.3dg.txt
GM-600U_082_20kb_3.clean.3dg.txt
GM-600U_082_20kb_5.clean.3dg.txt
GM-600U_082_10kb_1.clean.3dg.txt
GM-600U_082_10kb_2.clean.3dg.txt
GM-600U_082_10kb_3.clean.3dg.txt
GM-600U_082_10kb_5.clean.3dg.txt
GM-600U_082_5kb_1.clean.3dg.txt
GM-600U_082_5kb_2.clean.3dg.txt
GM-600U_082_5kb_3.clean.3dg.txt
GM-600U_082_5kb_5.clean.3dg.txt


title: TNFR2KO,Ly49HposNK,d1,Spleen,4,11821


title: Chondrocytes,PC,PICTreated

value: PC


title: cell_150


title: cell_149


title: GM12878, 600U, Cell 80

description:
GM-600U_080.allValidPairs.txt
GM-600U_080.hic
GM-600U_080.mcool
GM-600U_080.clean.smooth.bw
GM-600U_080_20kb_1.3dg.txt
GM-600U_080_20kb_2.3dg.txt
GM-600U_080_20kb_3.3dg.txt
GM-600U_080_20kb_4.3dg.txt
GM-600U_080_20kb_5.3dg.txt
GM-600U_080_10kb_1.3dg.txt
GM-600U_080_10kb_2.3dg.txt
GM-600U_080_10kb_3.3dg.txt
GM-600U_080_10kb_4.3dg.txt
GM-600U_080_10kb_5.3dg.txt
GM-600U_080_5kb_1.3dg.txt
GM-600U_080_5kb_2.3dg.txt
GM-600U_080_5kb_3.3dg.txt
GM-600U_080_5kb_4.3dg.txt
GM-600U_080_5kb_5.3dg.txt
GM-600U_080_20kb_1.clean.3dg.txt
GM-600U_080_20kb_2.clean.3dg.txt
GM-600U_080_20kb_3.clean.3dg.txt
GM-600U_080_20kb_4.clean.3dg.txt
GM-600U_080_20kb_5.clean.3dg.txt
GM-600U_080_10kb_1.clean.3dg.txt
GM-600U_080_10kb_2.clean.3dg.txt
GM-600U_080_10kb_3.clean.3dg.txt
GM-600U_080_10kb_4.clean.3dg.txt
GM-600U_080_10kb_5.clean.3dg.txt
GM-600U_080_5kb_1.clean.3dg.txt
GM-600U_080_5kb_2.clean.3dg.txt
GM-600U_080_5kb_3.clean.3dg.txt
GM-600U_080_5kb_4.clean.3dg.txt
GM-600U_080_5kb_5.clean.3dg.txt

value: 600U MNase


title: GM12878, 600U, Cell 87

description:
GM-600U_087.allValidPairs.txt
GM-600U_087.hic
GM-600U_087.mcool
GM-600U_087.clean.smooth.bw
GM-600U_087_20kb_1.3dg.txt
GM-600U_087_20kb_2.3dg.txt
GM-600U_087_20kb_3.3dg.txt
GM-600U_087_20kb_4.3dg.txt
GM-600U_087_20kb_5.3dg.txt
GM-600U_087_10kb_1.3dg.txt
GM-600U_087_10kb_2.3dg.txt
GM-600U_087_10kb_3.3dg.txt
GM-600U_087_10kb_4.3dg.txt
GM-600U_087_10kb_5.3dg.txt
GM-600U_087_5kb_1.3dg.txt
GM-600U_087_5kb_2.3dg.txt
GM-600U_087_5kb_3.3dg.txt
GM-600U_087_5kb_4.3dg.txt
GM-600U_087_5kb_5.3dg.txt
GM-600U_087_20kb_1.clean.3dg.txt
GM-600U_087_20kb_2.clean.3dg.txt
GM-600U_087_20kb_3.clean.3dg.txt
GM-600U_087_20kb_4.clean.3dg.txt
GM-600U_087_20kb_5.clean.3dg.txt
GM-600U_087_10kb_1.clean.3dg.txt
GM-600U_087_10kb_2.clean.3dg.txt
GM-600U_087_10kb_3.clean.3dg.txt
GM-600U_087_10kb_4.clean.3dg.txt
GM-600U_087_10kb_5.clean.3dg.txt
GM-600U_087_5kb_1.clean.3dg.txt
GM-600U_087_5kb_2.clean.3dg.txt
GM-600U_087_5kb_3.clean.3dg.txt
GM-600U_087_5kb_4.clean.3dg.txt
GM-600U_087_5kb_5.clean.3dg.txt


title: cell_148


title: Synoviocytes,ORC,ADDTreated

value: ADD


title: cell_153


title: GM12878, 600U, Cell 79

description:
GM-600U_079.allValidPairs.txt
GM-600U_079.hic
GM-600U_079.mcool
GM-600U_079.clean.smooth.bw
GM-600U_079_20kb_1.3dg.txt
GM-600U_079_20kb_2.3dg.txt
GM-600U_079_20kb_3.3dg.txt
GM-600U_079_20kb_4.3dg.txt
GM-600U_079_20kb_5.3dg.txt
GM-600U_079_10kb_1.3dg.txt
GM-600U_079_10kb_2.3dg.txt
GM-600U_079_10kb_3.3dg.txt
GM-600U_079_10kb_4.3dg.txt
GM-600U_079_10kb_5.3dg.txt
GM-600U_079_5kb_1.3dg.txt
GM-600U_079_5kb_2.3dg.txt
GM-600U_079_5kb_3.3dg.txt
GM-600U_079_5kb_4.3dg.txt
GM-600U_079_5kb_5.3dg.txt
GM-600U_079_20kb_1.clean.3dg.txt
GM-600U_079_20kb_2.clean.3dg.txt
GM-600U_079_20kb_3.clean.3dg.txt
GM-600U_079_20kb_4.clean.3dg.txt
GM-600U_079_20kb_5.clean.3dg.txt
GM-600U_079_10kb_1.clean.3dg.txt
GM-600U_079_10kb_2.clean.3dg.txt
GM-600U_079_10kb_3.clean.3dg.txt
GM-600U_079_10kb_4.clean.3dg.txt
GM-600U_079_10kb_5.clean.3dg.txt
GM-600U_079_5kb_1.clean.3dg.txt
GM-600U_079_5kb_2.clean.3dg.txt
GM-600U_079_5kb_3.clean.3dg.txt
GM-600U_079_5kb_4.clean.3dg.txt
GM-600U_079_5kb_5.clean.3dg.txt


title: Synoviocytes,ORC,STNGTreated


title: osteoclast-conditioned media, replicate 4

city: Crawley

first: Benjamin

last: Mullin

state: WA

address: 35 Stirling Hwy

institute: University of Western Australia

data_processing:
Sequence reads were trimmed using AGeNT trimmer (v2.0.3): -v2
Trimmed reads were aligned to the mouse genome using STAR v2.7.5a
Raw read counts were summarised at the gene level using featureCounts v2.0.1 (mm10 GENCODE Genes M25)
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw read counts for each sample

extract_protocol:
RNeasy Plus Mini Kit (Qiagen, Germany)
RNA libraries for RNAseq were prepared using the Sureselect HS2 library preparation kit following manufacturer's protocols.

value: Leukaemia cells

value: Osteoclast-conditioned media


title: cell_147


title: GM12878, 600U, Cell 78

description:
GM-600U_078.allValidPairs.txt
GM-600U_078.hic
GM-600U_078.mcool
GM-600U_078.clean.smooth.bw
GM-600U_078_20kb_1.3dg.txt
GM-600U_078_20kb_4.3dg.txt
GM-600U_078_20kb_5.3dg.txt
GM-600U_078_10kb_1.3dg.txt
GM-600U_078_10kb_4.3dg.txt
GM-600U_078_10kb_5.3dg.txt
GM-600U_078_5kb_1.3dg.txt
GM-600U_078_5kb_4.3dg.txt
GM-600U_078_5kb_5.3dg.txt
GM-600U_078_20kb_1.clean.3dg.txt
GM-600U_078_20kb_4.clean.3dg.txt
GM-600U_078_20kb_5.clean.3dg.txt
GM-600U_078_10kb_1.clean.3dg.txt
GM-600U_078_10kb_4.clean.3dg.txt
GM-600U_078_10kb_5.clean.3dg.txt
GM-600U_078_5kb_1.clean.3dg.txt
GM-600U_078_5kb_4.clean.3dg.txt
GM-600U_078_5kb_5.clean.3dg.txt


title: osteoclast-conditioned media, replicate 3


title: TNFR2KO,Ly49HposNK,d2,Spleen,2,11821


title: Macrophage,AG1,PICTreated

value: Macrophage


title: GM12878, 600U, Cell 77

description:
GM-600U_077.allValidPairs.txt
GM-600U_077.hic
GM-600U_077.mcool
GM-600U_077.clean.smooth.bw
GM-600U_077_20kb_1.3dg.txt
GM-600U_077_20kb_2.3dg.txt
GM-600U_077_20kb_3.3dg.txt
GM-600U_077_20kb_4.3dg.txt
GM-600U_077_20kb_5.3dg.txt
GM-600U_077_10kb_1.3dg.txt
GM-600U_077_10kb_2.3dg.txt
GM-600U_077_10kb_3.3dg.txt
GM-600U_077_10kb_4.3dg.txt
GM-600U_077_10kb_5.3dg.txt
GM-600U_077_5kb_1.3dg.txt
GM-600U_077_5kb_2.3dg.txt
GM-600U_077_5kb_3.3dg.txt
GM-600U_077_5kb_4.3dg.txt
GM-600U_077_5kb_5.3dg.txt
GM-600U_077_20kb_1.clean.3dg.txt
GM-600U_077_20kb_2.clean.3dg.txt
GM-600U_077_20kb_3.clean.3dg.txt
GM-600U_077_20kb_4.clean.3dg.txt
GM-600U_077_20kb_5.clean.3dg.txt
GM-600U_077_10kb_1.clean.3dg.txt
GM-600U_077_10kb_2.clean.3dg.txt
GM-600U_077_10kb_3.clean.3dg.txt
GM-600U_077_10kb_4.clean.3dg.txt
GM-600U_077_10kb_5.clean.3dg.txt
GM-600U_077_5kb_1.clean.3dg.txt
GM-600U_077_5kb_2.clean.3dg.txt
GM-600U_077_5kb_3.clean.3dg.txt
GM-600U_077_5kb_4.clean.3dg.txt
GM-600U_077_5kb_5.clean.3dg.txt


title: cell_145


title: osteoclast-conditioned media, replicate 2


title: Chondrocytes,ORC,PICTreated

value: Chondrocytes


title: GM12878, 600U, Cell 76

description:
GM-600U_076.allValidPairs.txt
GM-600U_076.hic
GM-600U_076.mcool
GM-600U_076.clean.smooth.bw
GM-600U_076_20kb_1.3dg.txt
GM-600U_076_20kb_2.3dg.txt
GM-600U_076_20kb_3.3dg.txt
GM-600U_076_20kb_4.3dg.txt
GM-600U_076_20kb_5.3dg.txt
GM-600U_076_10kb_1.3dg.txt
GM-600U_076_10kb_2.3dg.txt
GM-600U_076_10kb_3.3dg.txt
GM-600U_076_10kb_4.3dg.txt
GM-600U_076_10kb_5.3dg.txt
GM-600U_076_5kb_1.3dg.txt
GM-600U_076_5kb_2.3dg.txt
GM-600U_076_5kb_3.3dg.txt
GM-600U_076_5kb_4.3dg.txt
GM-600U_076_5kb_5.3dg.txt
GM-600U_076_20kb_1.clean.3dg.txt
GM-600U_076_20kb_2.clean.3dg.txt
GM-600U_076_20kb_3.clean.3dg.txt
GM-600U_076_20kb_4.clean.3dg.txt
GM-600U_076_20kb_5.clean.3dg.txt
GM-600U_076_10kb_1.clean.3dg.txt
GM-600U_076_10kb_2.clean.3dg.txt
GM-600U_076_10kb_3.clean.3dg.txt
GM-600U_076_10kb_4.clean.3dg.txt
GM-600U_076_10kb_5.clean.3dg.txt
GM-600U_076_5kb_1.clean.3dg.txt
GM-600U_076_5kb_2.clean.3dg.txt
GM-600U_076_5kb_3.clean.3dg.txt
GM-600U_076_5kb_4.clean.3dg.txt
GM-600U_076_5kb_5.clean.3dg.txt

value: WT


title: Chondrocytes,ORC,ADDTreated

value: ORC


title: control media, replicate 4

value: Control


title: GM12878, 600U, Cell 75

description:
GM-600U_075.allValidPairs.txt
GM-600U_075.hic
GM-600U_075.mcool
GM-600U_075.clean.smooth.bw
GM-600U_075_20kb_1.3dg.txt
GM-600U_075_20kb_2.3dg.txt
GM-600U_075_20kb_3.3dg.txt
GM-600U_075_20kb_4.3dg.txt
GM-600U_075_20kb_5.3dg.txt
GM-600U_075_10kb_1.3dg.txt
GM-600U_075_10kb_2.3dg.txt
GM-600U_075_10kb_3.3dg.txt
GM-600U_075_10kb_4.3dg.txt
GM-600U_075_10kb_5.3dg.txt
GM-600U_075_5kb_1.3dg.txt
GM-600U_075_5kb_2.3dg.txt
GM-600U_075_5kb_3.3dg.txt
GM-600U_075_5kb_4.3dg.txt
GM-600U_075_5kb_5.3dg.txt
GM-600U_075_20kb_1.clean.3dg.txt
GM-600U_075_20kb_2.clean.3dg.txt
GM-600U_075_20kb_3.clean.3dg.txt
GM-600U_075_20kb_4.clean.3dg.txt
GM-600U_075_20kb_5.clean.3dg.txt
GM-600U_075_10kb_1.clean.3dg.txt
GM-600U_075_10kb_2.clean.3dg.txt
GM-600U_075_10kb_3.clean.3dg.txt
GM-600U_075_10kb_4.clean.3dg.txt
GM-600U_075_10kb_5.clean.3dg.txt
GM-600U_075_5kb_1.clean.3dg.txt
GM-600U_075_5kb_2.clean.3dg.txt
GM-600U_075_5kb_3.clean.3dg.txt
GM-600U_075_5kb_4.clean.3dg.txt
GM-600U_075_5kb_5.clean.3dg.txt

value: blood


title: GM12878, 600U, Cell 74

description:
GM-600U_074.allValidPairs.txt
GM-600U_074.hic
GM-600U_074.mcool
GM-600U_074.clean.smooth.bw
GM-600U_074_20kb_1.3dg.txt
GM-600U_074_20kb_2.3dg.txt
GM-600U_074_20kb_3.3dg.txt
GM-600U_074_20kb_4.3dg.txt
GM-600U_074_20kb_5.3dg.txt
GM-600U_074_10kb_1.3dg.txt
GM-600U_074_10kb_2.3dg.txt
GM-600U_074_10kb_3.3dg.txt
GM-600U_074_10kb_4.3dg.txt
GM-600U_074_10kb_5.3dg.txt
GM-600U_074_5kb_1.3dg.txt
GM-600U_074_5kb_2.3dg.txt
GM-600U_074_5kb_3.3dg.txt
GM-600U_074_5kb_4.3dg.txt
GM-600U_074_5kb_5.3dg.txt
GM-600U_074_20kb_1.clean.3dg.txt
GM-600U_074_20kb_2.clean.3dg.txt
GM-600U_074_20kb_3.clean.3dg.txt
GM-600U_074_20kb_4.clean.3dg.txt
GM-600U_074_20kb_5.clean.3dg.txt
GM-600U_074_10kb_1.clean.3dg.txt
GM-600U_074_10kb_2.clean.3dg.txt
GM-600U_074_10kb_3.clean.3dg.txt
GM-600U_074_10kb_4.clean.3dg.txt
GM-600U_074_10kb_5.clean.3dg.txt
GM-600U_074_5kb_1.clean.3dg.txt
GM-600U_074_5kb_2.clean.3dg.txt
GM-600U_074_5kb_3.clean.3dg.txt
GM-600U_074_5kb_4.clean.3dg.txt
GM-600U_074_5kb_5.clean.3dg.txt

value: lymphoblastoid


title: Macrophage,ORC,ADDTreated


title: TNFR2KO,Ly49HposNK,d1,Spleen,2,11821

value: Spleen


title: cell_143


title: Chondrocytes,AG1,PICTreated


title: cell_142


title: GM12878, 600U, Cell 73

description:
GM-600U_073.allValidPairs.txt
GM-600U_073.hic
GM-600U_073.mcool
GM-600U_073.clean.smooth.bw
GM-600U_073_20kb_1.3dg.txt
GM-600U_073_20kb_2.3dg.txt
GM-600U_073_20kb_3.3dg.txt
GM-600U_073_20kb_4.3dg.txt
GM-600U_073_20kb_5.3dg.txt
GM-600U_073_10kb_1.3dg.txt
GM-600U_073_10kb_2.3dg.txt
GM-600U_073_10kb_3.3dg.txt
GM-600U_073_10kb_4.3dg.txt
GM-600U_073_10kb_5.3dg.txt
GM-600U_073_5kb_1.3dg.txt
GM-600U_073_5kb_2.3dg.txt
GM-600U_073_5kb_3.3dg.txt
GM-600U_073_5kb_4.3dg.txt
GM-600U_073_5kb_5.3dg.txt
GM-600U_073_20kb_1.clean.3dg.txt
GM-600U_073_20kb_2.clean.3dg.txt
GM-600U_073_20kb_3.clean.3dg.txt
GM-600U_073_20kb_4.clean.3dg.txt
GM-600U_073_20kb_5.clean.3dg.txt
GM-600U_073_10kb_1.clean.3dg.txt
GM-600U_073_10kb_2.clean.3dg.txt
GM-600U_073_10kb_3.clean.3dg.txt
GM-600U_073_10kb_4.clean.3dg.txt
GM-600U_073_10kb_5.clean.3dg.txt
GM-600U_073_5kb_1.clean.3dg.txt
GM-600U_073_5kb_2.clean.3dg.txt
GM-600U_073_5kb_3.clean.3dg.txt
GM-600U_073_5kb_4.clean.3dg.txt
GM-600U_073_5kb_5.clean.3dg.txt


title: cell_141


title: control media, replicate 2


title: GM12878, 600U, Cell 72

description:
GM-600U_072.allValidPairs.txt
GM-600U_072.hic
GM-600U_072.mcool
GM-600U_072.clean.smooth.bw
GM-600U_072_20kb_1.3dg.txt
GM-600U_072_20kb_2.3dg.txt
GM-600U_072_20kb_3.3dg.txt
GM-600U_072_20kb_4.3dg.txt
GM-600U_072_20kb_5.3dg.txt
GM-600U_072_10kb_1.3dg.txt
GM-600U_072_10kb_2.3dg.txt
GM-600U_072_10kb_3.3dg.txt
GM-600U_072_10kb_4.3dg.txt
GM-600U_072_10kb_5.3dg.txt
GM-600U_072_5kb_1.3dg.txt
GM-600U_072_5kb_2.3dg.txt
GM-600U_072_5kb_3.3dg.txt
GM-600U_072_5kb_4.3dg.txt
GM-600U_072_5kb_5.3dg.txt
GM-600U_072_20kb_1.clean.3dg.txt
GM-600U_072_20kb_2.clean.3dg.txt
GM-600U_072_20kb_3.clean.3dg.txt
GM-600U_072_20kb_4.clean.3dg.txt
GM-600U_072_20kb_5.clean.3dg.txt
GM-600U_072_10kb_1.clean.3dg.txt
GM-600U_072_10kb_2.clean.3dg.txt
GM-600U_072_10kb_3.clean.3dg.txt
GM-600U_072_10kb_4.clean.3dg.txt
GM-600U_072_10kb_5.clean.3dg.txt
GM-600U_072_5kb_1.clean.3dg.txt
GM-600U_072_5kb_2.clean.3dg.txt
GM-600U_072_5kb_3.clean.3dg.txt
GM-600U_072_5kb_4.clean.3dg.txt
GM-600U_072_5kb_5.clean.3dg.txt


title: Synoviocytes,AG1,PICTreated


title: control media, replicate 3


title: Macrophage,ORC,TNFTreated


title: control media, replicate 1


title: cell_140

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz


title: cell_146


title: osteoclast-conditioned media, replicate 1


title: KO3

city: Hangzhou

first: Xiang

last: Lin

state: Zhejiang province

address: No. 3 Qingchun East Road, Shangcheng District, Hangzhou, 310000, China

department: Assisted Reproduction Unit, Department of Obstetrics and Gynecology;

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine;

data_processing:
Raw fastq sequences were treated with Trimmomatictools(v 0.36) using the following options: :TRAILING:20, SLIDINGWINDOW:4:15 MINLEN:52, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 52).
Paired-end reads were aligned to the mouse reference genome mm10 with HISAT2. HTSeq v0.12.4 was used to count the reads numbers mapped to each gene.
The statistically significant DE genes were obtained by an adjusted P-value threshold of <0.05 and |log2(foldchange)| > 1 using theDEseq/DESeq2/edgeR/DEGseq software. Finally, a hierarchical clustering analysis was performed using the R language package gplots according to the RPKM values of differential genes in different groups. And colors represent different clustering information, such as the similar expression pattern in the same group, including similar functions or participating in the same biological process.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values and counts for each Sample/xlsx

source_name: ovary

extract_protocol:
Three weeks old female mice were intraperitoneally injected with 5 IU of PMSG (Ningbo San Sheng Biotech, Ningbo, China) for 48 h to stimulate follicle development, followed by injection with 5 IU human chorionic gonadotropin (HCG; Ningbo San Sheng Biotech) to induce ovulation. Fresh ovary granulosa cells were extracted from mice ovary and used for RNA-seq
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the manufac- turer’s protocol, The quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately. Briefly, the mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA).And then fragmented to approximately 200bp. Subsequently, theRNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to in- structions ofNEBNext® UltraTM RNA Library Prep Kit for Illumina. The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp

treatment_protocol: Group KO  knock down  the EZH2 gene

value: ovary

value: primary granulosa cell

value: Ezh2flox/flox; Cyp19-Cre

value: Knock down  the EZH2 gene


title: GM12878, 600U, Cell 71

description:
GM-600U_071.allValidPairs.txt
GM-600U_071.hic
GM-600U_071.mcool
GM-600U_071.clean.smooth.bw
GM-600U_071_20kb_1.3dg.txt
GM-600U_071_20kb_2.3dg.txt
GM-600U_071_20kb_4.3dg.txt
GM-600U_071_20kb_5.3dg.txt
GM-600U_071_10kb_1.3dg.txt
GM-600U_071_10kb_2.3dg.txt
GM-600U_071_10kb_4.3dg.txt
GM-600U_071_10kb_5.3dg.txt
GM-600U_071_5kb_1.3dg.txt
GM-600U_071_5kb_2.3dg.txt
GM-600U_071_5kb_4.3dg.txt
GM-600U_071_5kb_5.3dg.txt
GM-600U_071_20kb_1.clean.3dg.txt
GM-600U_071_20kb_2.clean.3dg.txt
GM-600U_071_20kb_4.clean.3dg.txt
GM-600U_071_20kb_5.clean.3dg.txt
GM-600U_071_10kb_1.clean.3dg.txt
GM-600U_071_10kb_2.clean.3dg.txt
GM-600U_071_10kb_4.clean.3dg.txt
GM-600U_071_10kb_5.clean.3dg.txt
GM-600U_071_5kb_1.clean.3dg.txt
GM-600U_071_5kb_2.clean.3dg.txt
GM-600U_071_5kb_4.clean.3dg.txt
GM-600U_071_5kb_5.clean.3dg.txt


title: cell_144


title: cell_139


title: cell_138


title: KO2


title: Macrophage,ORC,PICTreated

value: PIC


title: GM12878, 600U, Cell 69

description:
GM-600U_069.allValidPairs.txt
GM-600U_069.hic
GM-600U_069.mcool
GM-600U_069.clean.smooth.bw
GM-600U_069_20kb_1.3dg.txt
GM-600U_069_20kb_2.3dg.txt
GM-600U_069_20kb_3.3dg.txt
GM-600U_069_20kb_4.3dg.txt
GM-600U_069_20kb_5.3dg.txt
GM-600U_069_10kb_1.3dg.txt
GM-600U_069_10kb_2.3dg.txt
GM-600U_069_10kb_3.3dg.txt
GM-600U_069_10kb_4.3dg.txt
GM-600U_069_10kb_5.3dg.txt
GM-600U_069_5kb_1.3dg.txt
GM-600U_069_5kb_2.3dg.txt
GM-600U_069_5kb_3.3dg.txt
GM-600U_069_5kb_4.3dg.txt
GM-600U_069_5kb_5.3dg.txt
GM-600U_069_20kb_1.clean.3dg.txt
GM-600U_069_20kb_2.clean.3dg.txt
GM-600U_069_20kb_3.clean.3dg.txt
GM-600U_069_20kb_4.clean.3dg.txt
GM-600U_069_20kb_5.clean.3dg.txt
GM-600U_069_10kb_1.clean.3dg.txt
GM-600U_069_10kb_2.clean.3dg.txt
GM-600U_069_10kb_3.clean.3dg.txt
GM-600U_069_10kb_4.clean.3dg.txt
GM-600U_069_10kb_5.clean.3dg.txt
GM-600U_069_5kb_1.clean.3dg.txt
GM-600U_069_5kb_2.clean.3dg.txt
GM-600U_069_5kb_3.clean.3dg.txt
GM-600U_069_5kb_4.clean.3dg.txt
GM-600U_069_5kb_5.clean.3dg.txt

value: 600U MNase


title: KO1


title: GM12878, 600U, Cell 68

description:
GM-600U_068.allValidPairs.txt
GM-600U_068.hic
GM-600U_068.mcool
GM-600U_068.clean.smooth.bw
GM-600U_068_20kb_1.3dg.txt
GM-600U_068_20kb_2.3dg.txt
GM-600U_068_20kb_4.3dg.txt
GM-600U_068_20kb_5.3dg.txt
GM-600U_068_10kb_1.3dg.txt
GM-600U_068_10kb_2.3dg.txt
GM-600U_068_10kb_4.3dg.txt
GM-600U_068_10kb_5.3dg.txt
GM-600U_068_5kb_1.3dg.txt
GM-600U_068_5kb_2.3dg.txt
GM-600U_068_5kb_4.3dg.txt
GM-600U_068_5kb_5.3dg.txt
GM-600U_068_20kb_1.clean.3dg.txt
GM-600U_068_20kb_2.clean.3dg.txt
GM-600U_068_20kb_4.clean.3dg.txt
GM-600U_068_20kb_5.clean.3dg.txt
GM-600U_068_10kb_1.clean.3dg.txt
GM-600U_068_10kb_2.clean.3dg.txt
GM-600U_068_10kb_4.clean.3dg.txt
GM-600U_068_10kb_5.clean.3dg.txt
GM-600U_068_5kb_1.clean.3dg.txt
GM-600U_068_5kb_2.clean.3dg.txt
GM-600U_068_5kb_4.clean.3dg.txt
GM-600U_068_5kb_5.clean.3dg.txt


title: Yak_18m_testis4

city: Lanzhou

first: Xingdong

last: Wang

state: 未选择

address: No.335 Jiangouyan, Qilihe District

institute: CAAS: Chinese Academy of Agricultural Sciences

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Yak, LU_Bosgru_v3.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos grunniens

source_name: Testicular tissue of yak before sexual maturity for single-cell RNA sequencing

extract_protocol:
The frozen testicular tissue was removed and immediately placed in a 37 ℃ water bath for 2 min. After the tissue was melted, take it out with tweezers, place it in the resuscitation solution (DMEM/F12 medium+0.5mol/L sucrose+20% FBS), place it in a 37 ℃ water bath for 2min, preheat the DPBS to wash the tissue block for 2-3 times, place the tissue block in DMEM/F12 medium (Gibco, Waltham, MA, USA), and cut the tissue with ophthalmic scissors. Transfer the testicular tissue of cutted to a 15mL centrifuge tube, and add a solution with 0.2% collagenase IV (2 mg/mL) (Sigma, City of Saint Louis, USA) and hyaluronidase (2 mg/mL) solution (Sigma, City of Saint Louis, USA) (1:1) of 8~10 times the total amount of tissue. The centrifuge tube was placed in a 37℃ constant temperature shaker at 120 rpm (30 min, after 15min, 200μL tissue digestive fluid was taken every 3min to observe the digestive condition under the microscope until the free tubules with no mass tissue could be clearly observed), centrifuge at 1000 r/min for 5 min and drain the supernatant. 0.25% trypsin solution (2.5 mg/mL) (Gibco, Waltham, MA, USA), 8-10 times the total amount of tissue blocks, was added again. Finally, the tissue digestible solution was placed in a constant temperature shaker at 37℃ at 120 rpm (40 min, after 15min, 200μL tissue digestible solution was taken every 3min to observe the digestion condition under the microscope until the single cell suspension could be clearly observed). Fetal bovine serum was added to terminate digestion. The mixed cell suspension was blown evenly and filtered through 70μm and 40μm screens successively. The filtrate was collected and centrifuged at 300×g 4℃ for 5 min, the supernatant was abandoned, and the cells were re-suspended in DMEM/F12 complete medium containing 10% FBS, and cultured at 37 ℃ with 5% CO2. Part of the cell suspension was stained with Trypan blue and counted by automatic counter to calculate the number of cells and viability. The concentration was ~1000 cells/uL and cell viability>90% were used for scRNA seq.
The Cell suspension was loaded onto the Chromium Single Cell Controller instrument (10x Genomics, Pleasanton, CA, USA) and the bead and cells with Cell Barcode were wrapped in the droplet. The droplet containing cells was collected, and then the cells were lysed in the droplet, so that the mRNA in the cells combined with the bead Cell Barcode to form a Single Cell GEMs, and the reverse transcription reaction was performed in the droplet to construct the cDNA library. GEM-RT-PCR was performed with a 96-hole reaction module (Bio-Rad; CT022510) in the C1000 Touch thermal cycler to generate barcode cDNA using the following procedures: 53°C for 45 min; 85°C for 5 minutes; Maintain at 4°C. The sample index on the library sequence is used to distinguish the source of the target sequence.

value: testis

value: Germ cell

tag: developmental stage

value: adolescence


title: WT4

value: Ezh2flox/+; Cyp19-Cre


title: GM12878, 600U, Cell 67

description:
GM-600U_067.allValidPairs.txt
GM-600U_067.hic
GM-600U_067.mcool
GM-600U_067.clean.smooth.bw
GM-600U_067_20kb_1.3dg.txt
GM-600U_067_20kb_3.3dg.txt
GM-600U_067_20kb_4.3dg.txt
GM-600U_067_20kb_5.3dg.txt
GM-600U_067_10kb_1.3dg.txt
GM-600U_067_10kb_3.3dg.txt
GM-600U_067_10kb_4.3dg.txt
GM-600U_067_10kb_5.3dg.txt
GM-600U_067_5kb_1.3dg.txt
GM-600U_067_5kb_3.3dg.txt
GM-600U_067_5kb_4.3dg.txt
GM-600U_067_5kb_5.3dg.txt
GM-600U_067_20kb_1.clean.3dg.txt
GM-600U_067_20kb_3.clean.3dg.txt
GM-600U_067_20kb_4.clean.3dg.txt
GM-600U_067_20kb_5.clean.3dg.txt
GM-600U_067_10kb_1.clean.3dg.txt
GM-600U_067_10kb_3.clean.3dg.txt
GM-600U_067_10kb_4.clean.3dg.txt
GM-600U_067_10kb_5.clean.3dg.txt
GM-600U_067_5kb_1.clean.3dg.txt
GM-600U_067_5kb_3.clean.3dg.txt
GM-600U_067_5kb_4.clean.3dg.txt
GM-600U_067_5kb_5.clean.3dg.txt


title: Yak_18m_testis3

description: 10x Genomics


title: cell_136


title: cell_135


title: WT2


title: WT3


title: cell_134


title: Yak_6m_testis2

description: 10x Genomics

value: prepubertal


title: WT1


title: GM12878, 600U, Cell 66

description:
GM-600U_066.allValidPairs.txt
GM-600U_066.hic
GM-600U_066.mcool
GM-600U_066.clean.smooth.bw
GM-600U_066_20kb_1.3dg.txt
GM-600U_066_20kb_2.3dg.txt
GM-600U_066_20kb_4.3dg.txt
GM-600U_066_20kb_5.3dg.txt
GM-600U_066_10kb_1.3dg.txt
GM-600U_066_10kb_2.3dg.txt
GM-600U_066_10kb_4.3dg.txt
GM-600U_066_10kb_5.3dg.txt
GM-600U_066_5kb_1.3dg.txt
GM-600U_066_5kb_2.3dg.txt
GM-600U_066_5kb_4.3dg.txt
GM-600U_066_5kb_5.3dg.txt
GM-600U_066_20kb_1.clean.3dg.txt
GM-600U_066_20kb_2.clean.3dg.txt
GM-600U_066_20kb_4.clean.3dg.txt
GM-600U_066_20kb_5.clean.3dg.txt
GM-600U_066_10kb_1.clean.3dg.txt
GM-600U_066_10kb_2.clean.3dg.txt
GM-600U_066_10kb_4.clean.3dg.txt
GM-600U_066_10kb_5.clean.3dg.txt
GM-600U_066_5kb_1.clean.3dg.txt
GM-600U_066_5kb_2.clean.3dg.txt
GM-600U_066_5kb_4.clean.3dg.txt
GM-600U_066_5kb_5.clean.3dg.txt

value: WT


title: cell_133


title: GM12878, 600U, Cell 65

description:
GM-600U_065.allValidPairs.txt
GM-600U_065.hic
GM-600U_065.mcool
GM-600U_065.clean.smooth.bw
GM-600U_065_20kb_1.3dg.txt
GM-600U_065_20kb_2.3dg.txt
GM-600U_065_20kb_3.3dg.txt
GM-600U_065_20kb_4.3dg.txt
GM-600U_065_20kb_5.3dg.txt
GM-600U_065_10kb_1.3dg.txt
GM-600U_065_10kb_2.3dg.txt
GM-600U_065_10kb_3.3dg.txt
GM-600U_065_10kb_4.3dg.txt
GM-600U_065_10kb_5.3dg.txt
GM-600U_065_5kb_1.3dg.txt
GM-600U_065_5kb_2.3dg.txt
GM-600U_065_5kb_3.3dg.txt
GM-600U_065_5kb_4.3dg.txt
GM-600U_065_5kb_5.3dg.txt
GM-600U_065_20kb_1.clean.3dg.txt
GM-600U_065_20kb_2.clean.3dg.txt
GM-600U_065_20kb_3.clean.3dg.txt
GM-600U_065_20kb_4.clean.3dg.txt
GM-600U_065_20kb_5.clean.3dg.txt
GM-600U_065_10kb_1.clean.3dg.txt
GM-600U_065_10kb_2.clean.3dg.txt
GM-600U_065_10kb_3.clean.3dg.txt
GM-600U_065_10kb_4.clean.3dg.txt
GM-600U_065_10kb_5.clean.3dg.txt
GM-600U_065_5kb_1.clean.3dg.txt
GM-600U_065_5kb_2.clean.3dg.txt
GM-600U_065_5kb_3.clean.3dg.txt
GM-600U_065_5kb_4.clean.3dg.txt
GM-600U_065_5kb_5.clean.3dg.txt


title: Patient10_MyleoidCell_POST

type: RNA

city: Barcelona

first: Cristina

last: Sole Marce

address: Pg Vall Hebron 119-129

country: Spain

institute: Vall Hebron Institute Research

hyb_protocol: For mRNA:Following fragmentation, 5,5ug of ds-cDNA were hybridized for 16hr at 45ºC on GeneChip Clariom S human array cartridge. Array cartridge was washed and stained in the Affymetrix GCS300 System. For miRNA: 130 ng of biotin-labeled RNA were hybridized for 40 hr at 4ºC on GeneChip miR4.0 cartridge. Array cartridge was washed and stained in the Affymetrix GCS300 System.

scan_protocol: Array cartridge was scanned using the GCS300System, 7G with autoloder.

data_processing: Raw expression values were obtained directly from .CEL file and were preocessed using the RMA method in oligo R package to get normalizae expression values.

label: biotin

source_name: Myeloid cell

label_protocol: For mRNA samples: Biotinylated ds-cDNA were prepared according to the standard Affymetric, ThermoFisher, protocol from 1ng total RNA, GeneChip Pico Kit manual workflow, user guide. For miRNA samples: biotinylated RNA were prepared according to the standard Affymetrix, ThermoFisher, protocol from 130ng total RNA, GeneChip FlashTag Biotin HSR RNA.

extract_protocol: Peripheral blood mononuclear cells (PBMCs) and serum were collected pre- and post-belimumab treatment (6 months). PBMCs were isolated via Ficoll-Hypaque gradient centrifugation (Vacutainer CPT, BD Biosciences) and B, T and myeloid cell subset were sorted using spectral cytometry. RNA and miRNA were obtained using using the RNeasy Mini Kit following the manufacturer’s instructions, with quality and concentration assessed via Bioanalyzer PicoChip.

tag: group

value: Post-treatment


title: GM12878, 600U, Cell 70

description:
GM-600U_070.allValidPairs.txt
GM-600U_070.hic
GM-600U_070.mcool
GM-600U_070.clean.smooth.bw
GM-600U_070_20kb_1.3dg.txt
GM-600U_070_20kb_2.3dg.txt
GM-600U_070_20kb_3.3dg.txt
GM-600U_070_10kb_1.3dg.txt
GM-600U_070_10kb_2.3dg.txt
GM-600U_070_10kb_3.3dg.txt
GM-600U_070_5kb_1.3dg.txt
GM-600U_070_5kb_2.3dg.txt
GM-600U_070_5kb_3.3dg.txt
GM-600U_070_20kb_1.clean.3dg.txt
GM-600U_070_20kb_2.clean.3dg.txt
GM-600U_070_20kb_3.clean.3dg.txt
GM-600U_070_10kb_1.clean.3dg.txt
GM-600U_070_10kb_2.clean.3dg.txt
GM-600U_070_10kb_3.clean.3dg.txt
GM-600U_070_5kb_1.clean.3dg.txt
GM-600U_070_5kb_2.clean.3dg.txt
GM-600U_070_5kb_3.clean.3dg.txt


title: Yak_6m_testis1

description: 10x Genomics


title: Yak_4Y_testis5

description: 10x Genomics

source_name: Testicular tissue of yak after sexual maturity for single-cell RNA sequencing

value: Postsexual maturity


title: Patient10_Bcell_POST

source_name: B cell


title: cell_137

value: blood


title: GM12878, 600U, Cell 64

description:
GM-600U_064.allValidPairs.txt
GM-600U_064.hic
GM-600U_064.mcool
GM-600U_064.clean.smooth.bw
GM-600U_064_20kb_1.3dg.txt
GM-600U_064_20kb_2.3dg.txt
GM-600U_064_20kb_3.3dg.txt
GM-600U_064_20kb_5.3dg.txt
GM-600U_064_10kb_1.3dg.txt
GM-600U_064_10kb_2.3dg.txt
GM-600U_064_10kb_3.3dg.txt
GM-600U_064_10kb_5.3dg.txt
GM-600U_064_5kb_1.3dg.txt
GM-600U_064_5kb_2.3dg.txt
GM-600U_064_5kb_3.3dg.txt
GM-600U_064_5kb_5.3dg.txt
GM-600U_064_20kb_1.clean.3dg.txt
GM-600U_064_20kb_2.clean.3dg.txt
GM-600U_064_20kb_3.clean.3dg.txt
GM-600U_064_20kb_5.clean.3dg.txt
GM-600U_064_10kb_1.clean.3dg.txt
GM-600U_064_10kb_2.clean.3dg.txt
GM-600U_064_10kb_3.clean.3dg.txt
GM-600U_064_10kb_5.clean.3dg.txt
GM-600U_064_5kb_1.clean.3dg.txt
GM-600U_064_5kb_2.clean.3dg.txt
GM-600U_064_5kb_3.clean.3dg.txt
GM-600U_064_5kb_5.clean.3dg.txt

value: lymphoblastoid


title: KO-H4h IP

data_processing:
Raw fastq sequences were treated with Trimmomatic tools (v 0.36) using the following options: TRAIL- ING: 20, MINLEN: 235 and CROP: 235, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 52).
Genomic alignment (version from UCSC genome browser) was using bowtie2 (version: 2.4.2) to get uniquely mapping reads.
MACS2 (version 2.2.7) was employed to perform peak calling with the corresponding input sample serving as control. Then using mm10  to annotate the Peaks.. Motif central enrichment was performed by CentriMo (version: 5.3.0).
Assembly: mm10
Supplementary files format and content: bigWig/bw

growth_protocol: Group KO-H4h  knock down  the EZH2 gene

extract_protocol:
Three weeks old female mice were intraperitoneally injected with 5 IU of PMSG (Ningbo San Sheng Biotech, Ningbo, China) for 48 h to stimulate follicle development, followed by injection with 5 IU human chorionic gonadotropin (HCG; Ningbo San Sheng Biotech) to induce ovulation. Fresh ovary granulosa cells were extracted from mice ovary and a ChIP assay was performed using a Simple ChIP® Enzymatic Chromatin IP Kit (9003, Cell Signaling Technology) in accordance with the manufacturer’s instructions.
The CHIP DNA was assessed by Agilent 2200 TapeStation(Agilent Technologies, USA) and Qubit(Thermo Fisher Scientifc,USA) .The ChIP-Seq libraries were constructed following the Illumina ChIP-Seq library gener- ation protocol. Briefly, chip DNA was fragmented to approximately 200bp , Subsequently, the fragments were repaired end and added A-tailing following by adaptor ligation. The adaptor-ligated DNA was enrichment with a low-cycle according to instructions of NEBNext® UltraTMDNA Library Prep Kit for Illumina (NEB, USA). The DNA library products were assessed using the Agilent 2200 TapeStation(Agilent Technologies, USA) and Qubit (Thermo Fisher Scientific, USA), the libraries were then sequenced with pair-end 150 bp by Illumina platform  (Illumina,USA)

treatment_protocol: ChIP-grade anti-H3K27Me3 (9733, Cell Signaling Technology) were used for IP in WT-H4h group and KO-H4h group.


title: GM12878, 600U, Cell 63

description:
GM-600U_063.allValidPairs.txt
GM-600U_063.hic
GM-600U_063.mcool
GM-600U_063.clean.smooth.bw
GM-600U_063_20kb_2.3dg.txt
GM-600U_063_20kb_3.3dg.txt
GM-600U_063_20kb_4.3dg.txt
GM-600U_063_10kb_2.3dg.txt
GM-600U_063_10kb_3.3dg.txt
GM-600U_063_10kb_4.3dg.txt
GM-600U_063_5kb_2.3dg.txt
GM-600U_063_5kb_3.3dg.txt
GM-600U_063_5kb_4.3dg.txt
GM-600U_063_20kb_2.clean.3dg.txt
GM-600U_063_20kb_3.clean.3dg.txt
GM-600U_063_20kb_4.clean.3dg.txt
GM-600U_063_10kb_2.clean.3dg.txt
GM-600U_063_10kb_3.clean.3dg.txt
GM-600U_063_10kb_4.clean.3dg.txt
GM-600U_063_5kb_2.clean.3dg.txt
GM-600U_063_5kb_3.clean.3dg.txt
GM-600U_063_5kb_4.clean.3dg.txt


title: cell_131


title: cell_132


title: Patient10_Tcell_POST

source_name: T cell


title: KO-H4h Input


title: WT-H4h IP

value: ChIP-grade anti-H3K27Me3 (9733, Cell Signaling Technology)


title: GM12878, 600U, Cell 61

description:
GM-600U_061.allValidPairs.txt
GM-600U_061.hic
GM-600U_061.mcool
GM-600U_061.clean.smooth.bw
GM-600U_061_20kb_1.3dg.txt
GM-600U_061_20kb_2.3dg.txt
GM-600U_061_20kb_3.3dg.txt
GM-600U_061_20kb_4.3dg.txt
GM-600U_061_20kb_5.3dg.txt
GM-600U_061_10kb_1.3dg.txt
GM-600U_061_10kb_2.3dg.txt
GM-600U_061_10kb_3.3dg.txt
GM-600U_061_10kb_4.3dg.txt
GM-600U_061_10kb_5.3dg.txt
GM-600U_061_5kb_1.3dg.txt
GM-600U_061_5kb_2.3dg.txt
GM-600U_061_5kb_3.3dg.txt
GM-600U_061_5kb_4.3dg.txt
GM-600U_061_5kb_5.3dg.txt
GM-600U_061_20kb_1.clean.3dg.txt
GM-600U_061_20kb_2.clean.3dg.txt
GM-600U_061_20kb_3.clean.3dg.txt
GM-600U_061_20kb_4.clean.3dg.txt
GM-600U_061_20kb_5.clean.3dg.txt
GM-600U_061_10kb_1.clean.3dg.txt
GM-600U_061_10kb_2.clean.3dg.txt
GM-600U_061_10kb_3.clean.3dg.txt
GM-600U_061_10kb_4.clean.3dg.txt
GM-600U_061_10kb_5.clean.3dg.txt
GM-600U_061_5kb_1.clean.3dg.txt
GM-600U_061_5kb_2.clean.3dg.txt
GM-600U_061_5kb_3.clean.3dg.txt
GM-600U_061_5kb_4.clean.3dg.txt
GM-600U_061_5kb_5.clean.3dg.txt


title: Patient9_Bcell_POST


title: WT-H4h Input

value: ovary


title: cell_129


title: cell_130


title: GM12878, 600U, Cell 60

description:
GM-600U_060.allValidPairs.txt
GM-600U_060.hic
GM-600U_060.mcool
GM-600U_060.clean.smooth.bw
GM-600U_060_20kb_1.3dg.txt
GM-600U_060_20kb_2.3dg.txt
GM-600U_060_20kb_3.3dg.txt
GM-600U_060_20kb_4.3dg.txt
GM-600U_060_20kb_5.3dg.txt
GM-600U_060_10kb_1.3dg.txt
GM-600U_060_10kb_2.3dg.txt
GM-600U_060_10kb_3.3dg.txt
GM-600U_060_10kb_4.3dg.txt
GM-600U_060_10kb_5.3dg.txt
GM-600U_060_5kb_1.3dg.txt
GM-600U_060_5kb_2.3dg.txt
GM-600U_060_5kb_3.3dg.txt
GM-600U_060_5kb_4.3dg.txt
GM-600U_060_5kb_5.3dg.txt
GM-600U_060_20kb_1.clean.3dg.txt
GM-600U_060_20kb_2.clean.3dg.txt
GM-600U_060_20kb_3.clean.3dg.txt
GM-600U_060_20kb_4.clean.3dg.txt
GM-600U_060_20kb_5.clean.3dg.txt
GM-600U_060_10kb_1.clean.3dg.txt
GM-600U_060_10kb_2.clean.3dg.txt
GM-600U_060_10kb_3.clean.3dg.txt
GM-600U_060_10kb_4.clean.3dg.txt
GM-600U_060_10kb_5.clean.3dg.txt
GM-600U_060_5kb_1.clean.3dg.txt
GM-600U_060_5kb_2.clean.3dg.txt
GM-600U_060_5kb_3.clean.3dg.txt
GM-600U_060_5kb_4.clean.3dg.txt
GM-600U_060_5kb_5.clean.3dg.txt


title: Mouse muscle Sca1+ FAPs HiCAR_WT_rep4

city: Durham

first: Yarui

last: Diao

state: NC

address: 303 Research Drive

department: Cell Biology

institute: Duke University

description:
FAP_HiCAR_WT_rep4
HiCAR for FAPs from wildtype mouse
FAP_HiCAR_accessibleFragment_wt.bw
FAP_HiCAR_HiC-Matrix_wt.hic

data_processing:
*library strategy: HiCAR
The HiCAR reads were analyzed by jianhong/hicar pipeline (v 2.0.0rc). Briefly, the 5' end adapter ' TGTGCGAACTCAGACC' was trimmed by `cutadapt` (v 4.2) and the reads will be mapped by BWA to mouse genome mm10, filtered by pairtools and used to call interactions by peakachu (v 2.1 ). The raw reads were mapped by BWA (bwa mem v 0.7.17-r1188 with parameter -SP to skip mate rescue and pairing). The enzyme was assigned as 'MseI'. The valid pairs were selected by pairtools (v 0.3.0) if the pair_type is 'UU', 'UR' or 'RU' and parsed with parameter ' --min-mapq 10 --max-molecule-size 2000 --max-inter-align-gap 50 --walks-policy 5 unique --no-flip --drop-seq --drop-sam '. The Aggregate Peak Analysis (APA) was performed by juicer_tools (v 3.0.0 ref).
The tracks and heatmaps of HiCAR signals were plotted by Bioconductor package trackViewer (v 1.33.5), ComplexHeatmap (v 2.2.0) and deepTools (v 3.1.3).
Assembly: mm10
Supplementary files format and content: Big wig files containing binarized chromatin accessibility tracks in bedgraph format.
Supplementary files format and content: hic files with binarized chromatin interaction frequency for each 10kb bin across the genome.

source_name: Muscle

extract_protocol:
Single cells were collected from mouse muscle by disection and mincing of muscle tissue, digestion using collagenase II and dispase in wash medium, and training using a 20-gauge needle and a 40 micrometer filter. FAPs were then isolated by Sca1+, propidium iodide negative FACS sorted cells.
HiCAR

value: Muscle

value: Fibro-adipogenic progenitors

value: Wildtype


title: Patient9_Tcell_POST


title: Patient8_MyleoidCell_POST


title: cell_128


title: Mouse muscle Sca1+ FAPs HiCAR_WT_rep2

description:
FAP_HiCAR_WT_rep2
HiCAR for FAPs from wildtype mouse
FAP_HiCAR_accessibleFragment_wt.bw
FAP_HiCAR_HiC-Matrix_wt.hic


title: Patient8_Bcell_POST


title: GM12878, 600U, Cell 58

description:
GM-600U_058.allValidPairs.txt
GM-600U_058.hic
GM-600U_058.mcool
GM-600U_058.clean.smooth.bw
GM-600U_058_20kb_1.3dg.txt
GM-600U_058_20kb_2.3dg.txt
GM-600U_058_20kb_3.3dg.txt
GM-600U_058_20kb_4.3dg.txt
GM-600U_058_20kb_5.3dg.txt
GM-600U_058_10kb_1.3dg.txt
GM-600U_058_10kb_2.3dg.txt
GM-600U_058_10kb_3.3dg.txt
GM-600U_058_10kb_4.3dg.txt
GM-600U_058_10kb_5.3dg.txt
GM-600U_058_5kb_1.3dg.txt
GM-600U_058_5kb_2.3dg.txt
GM-600U_058_5kb_3.3dg.txt
GM-600U_058_5kb_4.3dg.txt
GM-600U_058_5kb_5.3dg.txt
GM-600U_058_20kb_1.clean.3dg.txt
GM-600U_058_20kb_2.clean.3dg.txt
GM-600U_058_20kb_3.clean.3dg.txt
GM-600U_058_20kb_4.clean.3dg.txt
GM-600U_058_20kb_5.clean.3dg.txt
GM-600U_058_10kb_1.clean.3dg.txt
GM-600U_058_10kb_2.clean.3dg.txt
GM-600U_058_10kb_3.clean.3dg.txt
GM-600U_058_10kb_4.clean.3dg.txt
GM-600U_058_10kb_5.clean.3dg.txt
GM-600U_058_5kb_1.clean.3dg.txt
GM-600U_058_5kb_2.clean.3dg.txt
GM-600U_058_5kb_3.clean.3dg.txt
GM-600U_058_5kb_4.clean.3dg.txt
GM-600U_058_5kb_5.clean.3dg.txt


title: cell_127


title: cell_126


title: GM12878, 600U, Cell 57

description:
GM-600U_057.allValidPairs.txt
GM-600U_057.hic
GM-600U_057.mcool
GM-600U_057.clean.smooth.bw
GM-600U_057_20kb_1.3dg.txt
GM-600U_057_20kb_2.3dg.txt
GM-600U_057_20kb_3.3dg.txt
GM-600U_057_20kb_4.3dg.txt
GM-600U_057_20kb_5.3dg.txt
GM-600U_057_10kb_1.3dg.txt
GM-600U_057_10kb_2.3dg.txt
GM-600U_057_10kb_3.3dg.txt
GM-600U_057_10kb_4.3dg.txt
GM-600U_057_10kb_5.3dg.txt
GM-600U_057_5kb_1.3dg.txt
GM-600U_057_5kb_2.3dg.txt
GM-600U_057_5kb_3.3dg.txt
GM-600U_057_5kb_4.3dg.txt
GM-600U_057_5kb_5.3dg.txt
GM-600U_057_20kb_1.clean.3dg.txt
GM-600U_057_20kb_2.clean.3dg.txt
GM-600U_057_20kb_3.clean.3dg.txt
GM-600U_057_20kb_4.clean.3dg.txt
GM-600U_057_20kb_5.clean.3dg.txt
GM-600U_057_10kb_1.clean.3dg.txt
GM-600U_057_10kb_2.clean.3dg.txt
GM-600U_057_10kb_3.clean.3dg.txt
GM-600U_057_10kb_4.clean.3dg.txt
GM-600U_057_10kb_5.clean.3dg.txt
GM-600U_057_5kb_1.clean.3dg.txt
GM-600U_057_5kb_2.clean.3dg.txt
GM-600U_057_5kb_3.clean.3dg.txt
GM-600U_057_5kb_4.clean.3dg.txt
GM-600U_057_5kb_5.clean.3dg.txt


title: Patient9_MyleoidCell_POST


title: GM12878, 600U, Cell 56

description:
GM-600U_056.allValidPairs.txt
GM-600U_056.hic
GM-600U_056.mcool
GM-600U_056.clean.smooth.bw
GM-600U_056_20kb_1.3dg.txt
GM-600U_056_20kb_2.3dg.txt
GM-600U_056_20kb_3.3dg.txt
GM-600U_056_20kb_4.3dg.txt
GM-600U_056_10kb_1.3dg.txt
GM-600U_056_10kb_2.3dg.txt
GM-600U_056_10kb_3.3dg.txt
GM-600U_056_10kb_4.3dg.txt
GM-600U_056_5kb_1.3dg.txt
GM-600U_056_5kb_2.3dg.txt
GM-600U_056_5kb_3.3dg.txt
GM-600U_056_5kb_4.3dg.txt
GM-600U_056_20kb_1.clean.3dg.txt
GM-600U_056_20kb_2.clean.3dg.txt
GM-600U_056_20kb_3.clean.3dg.txt
GM-600U_056_20kb_4.clean.3dg.txt
GM-600U_056_10kb_1.clean.3dg.txt
GM-600U_056_10kb_2.clean.3dg.txt
GM-600U_056_10kb_3.clean.3dg.txt
GM-600U_056_10kb_4.clean.3dg.txt
GM-600U_056_5kb_1.clean.3dg.txt
GM-600U_056_5kb_2.clean.3dg.txt
GM-600U_056_5kb_3.clean.3dg.txt
GM-600U_056_5kb_4.clean.3dg.txt


title: Patient8_Tcell_POST


title: Patient7_MyleoidCell_POST


title: cell_124

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz


title: GM12878, 600U, Cell 62

description:
GM-600U_062.allValidPairs.txt
GM-600U_062.hic
GM-600U_062.mcool
GM-600U_062.clean.smooth.bw
GM-600U_062_20kb_1.3dg.txt
GM-600U_062_20kb_2.3dg.txt
GM-600U_062_20kb_3.3dg.txt
GM-600U_062_20kb_4.3dg.txt
GM-600U_062_20kb_5.3dg.txt
GM-600U_062_10kb_1.3dg.txt
GM-600U_062_10kb_2.3dg.txt
GM-600U_062_10kb_3.3dg.txt
GM-600U_062_10kb_4.3dg.txt
GM-600U_062_10kb_5.3dg.txt
GM-600U_062_5kb_1.3dg.txt
GM-600U_062_5kb_2.3dg.txt
GM-600U_062_5kb_3.3dg.txt
GM-600U_062_5kb_4.3dg.txt
GM-600U_062_5kb_5.3dg.txt
GM-600U_062_20kb_1.clean.3dg.txt
GM-600U_062_20kb_2.clean.3dg.txt
GM-600U_062_20kb_3.clean.3dg.txt
GM-600U_062_20kb_4.clean.3dg.txt
GM-600U_062_20kb_5.clean.3dg.txt
GM-600U_062_10kb_1.clean.3dg.txt
GM-600U_062_10kb_2.clean.3dg.txt
GM-600U_062_10kb_3.clean.3dg.txt
GM-600U_062_10kb_4.clean.3dg.txt
GM-600U_062_10kb_5.clean.3dg.txt
GM-600U_062_5kb_1.clean.3dg.txt
GM-600U_062_5kb_2.clean.3dg.txt
GM-600U_062_5kb_3.clean.3dg.txt
GM-600U_062_5kb_4.clean.3dg.txt
GM-600U_062_5kb_5.clean.3dg.txt


title: Mouse muscle Sca1+ FAPs HiCAR_WT_rep1

description:
FAP_HiCAR_WT_rep1
HiCAR for FAPs from wildtype mouse
FAP_HiCAR_accessibleFragment_wt.bw
FAP_HiCAR_HiC-Matrix_wt.hic


title: cell_125


title: Mouse muscle Sca1+ FAPs HiCAR_Utrn-Mdx_rep3

description:
FAP_HiCAR_Utrn-Mdx_rep3
HiCAR for FAPs from Utrophin and Mdx double KO mouse
FAP_HiCAR_accessibleFragment_Utrn-Mdx.bw
FAP_HiCAR_HiC-Matrix_Utrn-Mdx.hic

value: Utrn-/- , Mdx


title: GM12878, 600U, Cell 54

description:
GM-600U_054.allValidPairs.txt
GM-600U_054.hic
GM-600U_054.mcool
GM-600U_054.clean.smooth.bw
GM-600U_054_20kb_1.3dg.txt
GM-600U_054_20kb_2.3dg.txt
GM-600U_054_20kb_3.3dg.txt
GM-600U_054_20kb_4.3dg.txt
GM-600U_054_20kb_5.3dg.txt
GM-600U_054_10kb_1.3dg.txt
GM-600U_054_10kb_2.3dg.txt
GM-600U_054_10kb_3.3dg.txt
GM-600U_054_10kb_4.3dg.txt
GM-600U_054_10kb_5.3dg.txt
GM-600U_054_5kb_1.3dg.txt
GM-600U_054_5kb_2.3dg.txt
GM-600U_054_5kb_3.3dg.txt
GM-600U_054_5kb_4.3dg.txt
GM-600U_054_5kb_5.3dg.txt
GM-600U_054_20kb_1.clean.3dg.txt
GM-600U_054_20kb_2.clean.3dg.txt
GM-600U_054_20kb_3.clean.3dg.txt
GM-600U_054_20kb_4.clean.3dg.txt
GM-600U_054_20kb_5.clean.3dg.txt
GM-600U_054_10kb_1.clean.3dg.txt
GM-600U_054_10kb_2.clean.3dg.txt
GM-600U_054_10kb_3.clean.3dg.txt
GM-600U_054_10kb_4.clean.3dg.txt
GM-600U_054_10kb_5.clean.3dg.txt
GM-600U_054_5kb_1.clean.3dg.txt
GM-600U_054_5kb_2.clean.3dg.txt
GM-600U_054_5kb_3.clean.3dg.txt
GM-600U_054_5kb_4.clean.3dg.txt
GM-600U_054_5kb_5.clean.3dg.txt

value: 600U MNase


title: GM12878, 600U, Cell 55

description:
GM-600U_055.allValidPairs.txt
GM-600U_055.hic
GM-600U_055.mcool
GM-600U_055.clean.smooth.bw
GM-600U_055_20kb_1.3dg.txt
GM-600U_055_20kb_2.3dg.txt
GM-600U_055_20kb_3.3dg.txt
GM-600U_055_20kb_4.3dg.txt
GM-600U_055_20kb_5.3dg.txt
GM-600U_055_10kb_1.3dg.txt
GM-600U_055_10kb_2.3dg.txt
GM-600U_055_10kb_3.3dg.txt
GM-600U_055_10kb_4.3dg.txt
GM-600U_055_10kb_5.3dg.txt
GM-600U_055_5kb_1.3dg.txt
GM-600U_055_5kb_2.3dg.txt
GM-600U_055_5kb_3.3dg.txt
GM-600U_055_5kb_4.3dg.txt
GM-600U_055_5kb_5.3dg.txt
GM-600U_055_20kb_1.clean.3dg.txt
GM-600U_055_20kb_2.clean.3dg.txt
GM-600U_055_20kb_3.clean.3dg.txt
GM-600U_055_20kb_4.clean.3dg.txt
GM-600U_055_20kb_5.clean.3dg.txt
GM-600U_055_10kb_1.clean.3dg.txt
GM-600U_055_10kb_2.clean.3dg.txt
GM-600U_055_10kb_3.clean.3dg.txt
GM-600U_055_10kb_4.clean.3dg.txt
GM-600U_055_10kb_5.clean.3dg.txt
GM-600U_055_5kb_1.clean.3dg.txt
GM-600U_055_5kb_2.clean.3dg.txt
GM-600U_055_5kb_3.clean.3dg.txt
GM-600U_055_5kb_4.clean.3dg.txt
GM-600U_055_5kb_5.clean.3dg.txt


title: Patient7_Bcell_POST


title: Mouse muscle Sca1+ FAPs HiCAR_Utrn-Mdx_rep2

description:
FAP_HiCAR_Utrn-Mdx_rep2
HiCAR for FAPs from Utrophin and Mdx double KO mouse
FAP_HiCAR_accessibleFragment_Utrn-Mdx.bw
FAP_HiCAR_HiC-Matrix_Utrn-Mdx.hic


title: GM12878, 600U, Cell 53

description:
GM-600U_053.allValidPairs.txt
GM-600U_053.hic
GM-600U_053.mcool
GM-600U_053.clean.smooth.bw
GM-600U_053_20kb_1.3dg.txt
GM-600U_053_20kb_3.3dg.txt
GM-600U_053_20kb_5.3dg.txt
GM-600U_053_10kb_1.3dg.txt
GM-600U_053_10kb_3.3dg.txt
GM-600U_053_10kb_5.3dg.txt
GM-600U_053_5kb_1.3dg.txt
GM-600U_053_5kb_3.3dg.txt
GM-600U_053_5kb_5.3dg.txt
GM-600U_053_20kb_1.clean.3dg.txt
GM-600U_053_20kb_3.clean.3dg.txt
GM-600U_053_20kb_5.clean.3dg.txt
GM-600U_053_10kb_1.clean.3dg.txt
GM-600U_053_10kb_3.clean.3dg.txt
GM-600U_053_10kb_5.clean.3dg.txt
GM-600U_053_5kb_1.clean.3dg.txt
GM-600U_053_5kb_3.clean.3dg.txt
GM-600U_053_5kb_5.clean.3dg.txt


title: Patient7_Tcell_POST


title: Mouse muscle Sca1+ FAPs HiCAR_WT_rep3

description:
FAP_HiCAR_WT_rep3
HiCAR for FAPs from wildtype mouse
FAP_HiCAR_accessibleFragment_wt.bw
FAP_HiCAR_HiC-Matrix_wt.hic


title: GM12878, 600U, Cell 59

description:
GM-600U_059.allValidPairs.txt
GM-600U_059.hic
GM-600U_059.mcool
GM-600U_059.clean.smooth.bw
GM-600U_059_20kb_1.3dg.txt
GM-600U_059_20kb_4.3dg.txt
GM-600U_059_20kb_5.3dg.txt
GM-600U_059_10kb_1.3dg.txt
GM-600U_059_10kb_4.3dg.txt
GM-600U_059_10kb_5.3dg.txt
GM-600U_059_5kb_1.3dg.txt
GM-600U_059_5kb_4.3dg.txt
GM-600U_059_5kb_5.3dg.txt
GM-600U_059_20kb_1.clean.3dg.txt
GM-600U_059_20kb_4.clean.3dg.txt
GM-600U_059_20kb_5.clean.3dg.txt
GM-600U_059_10kb_1.clean.3dg.txt
GM-600U_059_10kb_4.clean.3dg.txt
GM-600U_059_10kb_5.clean.3dg.txt
GM-600U_059_5kb_1.clean.3dg.txt
GM-600U_059_5kb_4.clean.3dg.txt
GM-600U_059_5kb_5.clean.3dg.txt


title: cell_121


title: Mouse muscle Sca1+ FAPs HiCAR_Utrn-Mdx_rep1

description:
FAP_HiCAR_Utrn-Mdx_rep1
HiCAR for FAPs from Utrophin and Mdx double KO mouse
FAP_HiCAR_accessibleFragment_Utrn-Mdx.bw
FAP_HiCAR_HiC-Matrix_Utrn-Mdx.hic


title: Patient6_Bcell_POST


title: cell_120


title: Mouse muscle Sca1+ FAPs HiCAR_Mdx_rep4

description:
FAP_HiCAR_Mdx_rep4
HiCAR for FAPs from Mdx mouse
FAP_HiCAR_accessibleFragment_Mdx.bw
FAP_HiCAR_HiC-Matrix_Mdx.hic

value: Mdx


title: cell_119


title: Mouse muscle Sca1+ FAPs HiCAR_Mdx_rep3

description:
FAP_HiCAR_Mdx_rep3
HiCAR for FAPs from Mdx mouse
FAP_HiCAR_accessibleFragment_Mdx.bw
FAP_HiCAR_HiC-Matrix_Mdx.hic


title: Patient6_Tcell_POST


title: Mouse muscle Sca1+ FAPs HiCAR_Utrn-Mdx_rep4

description:
FAP_HiCAR_Utrn-Mdx_rep4
HiCAR for FAPs from Utrophin and Mdx double KO mouse
FAP_HiCAR_accessibleFragment_Utrn-Mdx.bw
FAP_HiCAR_HiC-Matrix_Utrn-Mdx.hic


title: Patient6_MyleoidCell_POST