|
| Status |
Public on Mar 06, 2024 |
| Title |
Donor3 |
| Sample type |
SRA |
| |
|
| Source name |
ovary
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ovary
subject id: Donor3
subject status: healthy donor
|
| Treatment protocol |
Tissue was cut in 1x1x1 mm pieces and digested in 0.5mg/ml collagenase IA with 0.01 mg/ml DNase I in PBS at 37C for 30 minutes, then strained through 70 then 30 um filters. Single cell suspension was quenched with ice cold PBS with 10% fetal bovine serum and remaining tissue from the 70 um strainer was digested using the same process for an additional 30 minutes, after which additional single cell suspension was combined with that from the first 30 minute digest. The suspension was treated with red blood cell lysis buffer, rinsed with 1% then 0.04% bovine serum albumin solutions in PBS, then immediately sent for DAPI live/dead cell sorting.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After removal of dead DAPI+ cells, the cell suspension was submitted to the University of Michigan Advanced Genomics Core and loaded into the 10X Genomics Chromium controller for droplet-based single-cell capture. Sequencing libraries were prepared according to the user guide of the 10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v2, Product Code 120237.
Library was performed according to the manufacter's instructions (single cell v2 protocol, 10x Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The barcoded processing, gene counting and aggregationi were made using Cell Ranger software v2.1.1
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Mar 01, 2024 |
| Last update date |
Mar 06, 2024 |
| Contact name |
Jun Li |
| E-mail(s) |
junzli@umich.edu
|
| Organization name |
University of Michigan
|
| Department |
Human Genetics
|
| Street address |
1141 Catherine St
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE260685 |
Cellular atlas of the human ovary using morphologically guided spatial transciptomics and single-cell sequencing [scRNA-seq] |
|
| Relations |
| BioSample |
SAMN40216521 |
| SRA |
SRX23810063 |
