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| Status |
Public on Apr 07, 2020 |
| Title |
Hi-C_HSPC_BMT_RKO_rep1 |
| Sample type |
SRA |
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| Source name |
bone marrow cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
cell type: HSPC
genotype: RKO
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C experiments were performed using HSPCs obtained from WT-, SKO-, RKO-, or DKO-transplanted mice.
Briefly, two million c-Kit+ HSPCs of WT/SKO/RKO/DKO-transplanted mice were crosslinked with 1% formaldehyde for 10 min at room temperature. Cells were permeabilized and chromatin was digested with MboI restriction enzyme, and the ends of restriction fragments were labeled with biotinylated nucleotides and ligated. After crosslink reversal, DNA was purified and sheared with Covaris M220 (Covaris). Then point ligation junctions were pulled down with streptavidin beads. Then libraries were constructed with Nextera Mate Pair Sample Preparation Kit (Illumina) according to the manufacturer’s protocol, and subject to sequencing using NovaSeq (Illumina).
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Hi-C_RKO_loop.bedpe
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| Data processing |
The sequencing reads were processed using Juicer.
For comparative analysis, the valid interactions after filtering were randomly resampled and arranged in the number of the lowest sample.
Loops were called at 5kb and 10kb resolutions using HICCUPS.
Genome_build: mm10
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| Submission date |
May 21, 2019 |
| Last update date |
Apr 07, 2020 |
| Contact name |
Yotaro Ochi |
| Organization name |
Kyoto Univiersity
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| Department |
Department of Pathology and Tumor Biology
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| Street address |
Yoshida-Konoe-cho
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| City |
Kyoto |
| ZIP/Postal code |
606-8501 |
| Country |
Japan |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE131580 |
Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes [Hi-C] |
| GSE131583 |
Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes |
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| Relations |
| BioSample |
SAMN11808017 |
| SRA |
SRX5877919 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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