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Sample GSM7211463 Query DataSets for GSM7211463
Status Public on Aug 11, 2023
Title WT-old-LSK-MicroC
Sample type SRA
 
Source name Bone marrow
Organism Mus musculus
Characteristics tissue: Bone marrow
cell type: Lin-cKit+Sca1+
genotype: WT
Treatment protocol No treatment
Growth protocol 6-8 weeks WT mice were used as WT-young; 12-24 months WT mice were used as WT-old; 6-8 weeks Tet2KO mice were used as Tet2KO-young; 12-24 months Tet2KO mice were used as Tet2KO-old;
Extracted molecule genomic DNA
Extraction protocol 0.5 million LSK (Lin-cKit+Sca1+) cells were harvested from WT-young, WT-old, T2KO-young and T2KO-old mice
micro-C data were generated using Dovetail® Micro-C Kit. In briefly, the cells were crosslinked with FA in the presence of DSG, followed by in situ MNase Nuclease digestion and cell lysis. Then chromatins were captured by chromatin bind beads for future end polishing, bridge ligation, intra-aggregate ligation and reverse crosslinking. The purified DNA were proceeded with library generation.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Micro-C pipeline (https://micro-c.readthedocs.io/en/latest/) was used to analysis the Micro-C data. Specifically, we used bwa (0.17.17) to align raw reads on mm10 genome and the proper mapped read pairs were retained to downstream analysis. For each sample, mapped.pairs file was used as input for juicer_tools_1.22.01 to generate contact maps (hic format file). hicPCA function from HiCExplorer (3.7.2) with H3K4me3 ChIPseq tracks of young (4 month old) mice HSCs as correction for PCA values was applied to determine A/B compartment regions.
Assembly: mm10
Supplementary files format and content: hic format include contact matrix
 
Submission date Apr 21, 2023
Last update date Aug 11, 2023
Contact name Jia Li
E-mail(s) jiali@tamu.edu
Organization name Texas A&M U Health Science Center
Department CEDP
Lab Jia Li Lab
Street address 2121 W HOLCOMBE BLVD
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
 
Platform ID GPL24247
Series (1)
GSE183675 Tet2 deficiency altered hematopoietic stem and progenitor cells ageing process
Relations
BioSample SAMN34299588
SRA SRX20051588

Supplementary file Size Download File type/resource
GSM7211463_WO.contact_map.hic 1.2 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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