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Sample GSM3790166 Query DataSets for GSM3790166
Status Public on Apr 07, 2020
Title Hi-C_HSPC_BMT_DKO_rep2
Sample type SRA
 
Source name bone marrow cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: bone marrow
cell type: HSPC
genotype: DKO
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).
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description Hi-C_DKO_loop.bedpe
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
 
Submission date May 21, 2019
Last update date Apr 07, 2020
Contact name Yotaro Ochi
Organization name Kyoto Univiersity
Department Department of Pathology and Tumor Biology
Street address Yoshida-Konoe-cho
City Kyoto
ZIP/Postal code 606-8501
Country Japan
 
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
Relations
BioSample SAMN11808014
SRA SRX5877922

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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