|
| Status |
Public on May 15, 2024 |
| Title |
O2_AThi |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell type: purified hematopoietic stem cell
age: Old
autophagy status: AThi (GFPlo)
genotype: Gfp-lc3/Gfp-Lc3
treatment: steady state isolation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell pellets containing ~ 10,000 HSCs per sample were frozen dry and sent to the Memorial Sloan Kettering Cancer Center Sequencing Core Facility (New York, NY) or to Genewiz (South Plainfield, NJ).
DNA was prepared for whole exome capture and sequencing by these services.
AThi and ATlo oHSC DNA samples were sequenced to 150X coverage and tail control DNA from each biological replicate was sequenced to 30X depth with paired end sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Bowtie2 was used to align Fastq files to mouse genome.
Somatic mutations relative to tail control were called with MuTect2.
|
| |
|
| Submission date |
Apr 21, 2023 |
| Last update date |
May 15, 2024 |
| Contact name |
Paul Vincent Dellorusso |
| E-mail(s) |
paul.dellorusso@gmail.com
|
| Phone |
5166552491
|
| Organization name |
Columbia University Irving Medical Center
|
| Department |
Genetics and Development
|
| Lab |
Passegue Lab
|
| Street address |
701 West 168th Street, 724 Hammer Health Sciences Center
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE229137 |
Autophagy engaging and non-engaging hematopoietic stem cells |
| GSE230270 |
AThi oHSC ATlo oHSC WES - Identifying clonal differences or differences in mutation burden between autophagy engaging and non-engaging hematopoietic stem cells during mouse aging. |
|
| Relations |
| BioSample |
SAMN34284728 |
| SRA |
SRX20044820 |
