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| Status |
Public on Aug 24, 2023 |
| Title |
HiC_HPC5-2 |
| Sample type |
SRA |
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| Source name |
Bone Marrow
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| Organism |
Mus musculus |
| Characteristics |
tissue: Bone Marrow
cell line: HPC5
cell type: BM-derived HPC
genotype: Etv6+/+
treatment: Hi-C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C was performed using 5 million HPC5 according to the manufacturer’s instructions (Arima Hi-C kit(#A410030). Cells were crosslinked with 2% formaldehyde for 10 min at room temperature, followed by quenching using Arima Stop solution. After washing with PBS, the cell pellet was collected and stored at -80C until use. Nuclei were permeabilized using Arima lysis buffer and crosslinked chromatin was digested using the Arima restriction enzyme (RE) cocktail. The ends of restriction fragments were labeled with biotinylated nucleotides and ligated using a Arima enzymes A1, A2, B, C, and D. After reversal of crosslinks using Arima conditioning solution, the ligated DNA was purified with AMPure® XP Beads (#A63880) and sheared to a size of ∼400 bp with a Covaris M220 ultrasonicator (500295). After enrichment using Arima enrichment beads, DNA fragments were used for constructing a sequencing library using NEBNext® Ultra II DNA library prep kit (#E7103) which was then subjected to Illumina sequencing.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Hi-C analysis was performed using the HemTools pipeline hicpro as described previously11. HiC-Pro (v2.11.1) was used with default parameters; for global read mapping: --very-sensitive --L 30 --score-min L,−0.6,−0.2 --end-to-end --reorder; for local read mapping: --very-sensitive --L 20 --score-min L,−0.6,−0.2 --end-to-end --reorder; cutoffs for minimal and maximal values were not defined for FRAG_SIZE, INSERT_SIZE and CIS_DIST; for read pair filtering: RM_SINGLETON = 1, RM_MULTI = 1 and RM_DUP = 1. Then, all Hi-C data were downsampled to 200 million valid read pairs based on.allValidPairs files. HiC-Pro was used for iced matrix generation with default parameters of BIN_SIZE = 10,000, MAX_ITER = 100, FILTER_LOW_COUNT_PERC = 0.02, FILTER_HIGH_COUNT_PERC = 0 and EPS = 0.1. HicFindTADs from HiCExplorer (v3.5.1) was used for topologically associating domain (TAD) calling with default parameters after converting HiC-Pro iced matrix to H5 format (hicConvertFormat).
Assembly: mm10
Supplementary files format and content: bedj files- TAD boundaries, chromatin loops (medium and high confidence)
Supplementary files format and content: bigwig files- AB compartments (50K and 250K)
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| Submission date |
Sep 18, 2022 |
| Last update date |
Feb 28, 2024 |
| Contact name |
Kim Nichols |
| E-mail(s) |
kim.nichols@stjude.org
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| Organization name |
St. Jude Children's Research Hospital
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| Department |
Oncology
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| Lab |
Nichols Lab
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| Street address |
262 Danny Thomas Pl
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| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE213595 |
ETV6 Represses Inflammatory Response Genes and Regulates HSPC Function During Stress Hematopoiesis in Mice [Hi-C] |
| GSE213597 |
ETV6 Represses Inflammatory Response Genes and Regulates HSPC Function During Stress Hematopoiesis in Mice |
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| Relations |
| BioSample |
SAMN30874538 |
| SRA |
SRX17595631 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6589571_Loop_hic_HPC5-2-2326675.inter_30_defhigh_merged_loops.bedpe.bed12.loops.bedj.bed.gz |
80.7 Kb |
(ftp)(http) |
BED |
| GSM6589571_Loop_hic_HPC5-2-2326675.inter_30_defhigh_merged_loops.bedpe.bed12.loops.bedj.gz.tbi.gz |
16.5 Kb |
(ftp)(http) |
TBI |
| GSM6589571_Loop_hic_HPC5-2-2326675.inter_30_defmed_merged_loops.bedpe.bed12.loops.bedj.bed.gz |
142.6 Kb |
(ftp)(http) |
BED |
| GSM6589571_Loop_hic_HPC5-2-2326675.inter_30_defmed_merged_loops.bedpe.bed12.loops.bedj.gz.tbi.gz |
18.0 Kb |
(ftp)(http) |
TBI |
| GSM6589571_TAD_hic_HPC5-2-2326675.inter_30_5000_blocks.tad_TAD_bedj.bed.gz |
5.7 Kb |
(ftp)(http) |
BED |
| GSM6589571_TAD_hic_HPC5-2-2326675.inter_30_5000_blocks.tad_TAD_bedj.gz.tbi.gz |
5.2 Kb |
(ftp)(http) |
TBI |
| GSM6589571_hic_HPC5-2-2326675.inter_30.AB.NONE.250K.bw |
190.1 Kb |
(ftp)(http) |
BW |
| GSM6589571_hic_HPC5-2-2326675.inter_30.AB.NONE.50K.bw |
95.7 Kb |
(ftp)(http) |
BW |
| GSM6589571_hic_HPC5-2-2326675.inter_30.hic |
4.9 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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