|
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 |