|
| Status |
Public on Apr 21, 2023 |
| Title |
hematopoietic stem and progenitor cells, old diet restricted mice , scATACseq |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell type: hematopoietic stem and progenitor cells (LSK)
strain: C57BL/6J
diet: diet restricted
age: old (25-26.7 months)
|
| Treatment protocol |
mice were single caged, their food consumptionw as measured over the course of a week after which the dietary restricted mice were fed once a day shortly before lights out with a food allotment corresponding to 70% of their normal food intake by weight.
|
| Growth protocol |
female mice were kept in groups of 3-5 littermates, in 12:12 hour light:dark cycle in 20-24°C and 40-60% air humidity, had adlibitum access to gamma-irradiated chow and autoclaved, unacidified drinking water until ~6 months old (young mice) or ~25 months old (old mice)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We were able to isolated 50,000 hematopoietic stem and multipotent progenitor cells from each mouse using antibody staining and FACS. Cell suspensions from two mice were pooled for nuclei isolation. Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing was performed according to protocol (PROTOCOL VERSION, lysis time 3 minutes).
Nuclei suspensions were loaded into separate channels of the Chromium Controller (10x Genomics) and processed with Single Cell Multiome ATAC + Gene Expression (v1 chemistry) following the manufacturer's protocol (Document Number CG000338 Rev E). ATAC libraries: 7 cycles in sample index PCR reaction and evaluated using D5000 ScreenTape (Agilent 4200 TapeStation System) and DNA 7500 (Agilent 2100 Bioanalyzer). Gene Expression libraries: cDNA was amplified in 7 cycles, total cDNA was assessed on high sensitivity DNA assay (Agilent 2100 Bioanalyzer), another 6 cycles of sample index PCR were performed and final libraries were evaluated using D5000 ScreenTape (Agilent 4200 TapeStation System). Each type of library was pooled and sequenced using Illumina NovaSeq 6000 platform and two SP Reagent Kits v1.5 (100 cycles). scATAC-seq: Read 1 and Read 2 53 bp for DNA Insert, i7 8 bp for sample index and i5 24 bp for 10x Barcode and Spacer. scRNA-seq: Read 1 28 bp for 10x Barcode and UMI; Read 2 90 bp for Insert, i7 and i5 10 bp for sample index.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
multiome nulcear RNA and nuclear ATAC
|
| Data processing |
base calling: cellranger-arc mkfastq (cellranger-arc-2.0.0; bcl2FastQ v2.20.0.422)
Assembly: mm10
Supplementary files format and content: Folders containing the raw gene by cell gene expression matrix
Supplementary files format and content: Folders containing the filtered gene by cell gene expression matrix
Supplementary files format and content: Tab-separated files containing fragment information
Supplementary files format and content: Index of the tab-separated files
|
| |
|
| Submission date |
Apr 17, 2023 |
| Last update date |
Apr 21, 2023 |
| Contact name |
Pura Muñoz-Cánoves |
| Organization name |
Altos Labs
|
| Lab |
Muñoz-Cánoves
|
| Street address |
5510 Morehouse Dr
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92121 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE229892 |
Paired single nucleus RNA and ATAC sequencing on the role of diet and aging in hematopoietic stem and progenitor cells |
|
| Relations |
| BioSample |
SAMN34224264 |
| SRA |
SRX19992866 |
