|
| Status |
Public on May 04, 2022 |
| Title |
Comma1D basal population |
| Sample type |
SRA |
| |
|
| Source name |
Comma-1D
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Comma1D, Sca-1(H), EpCAM (L)
|
| Treatment protocol |
n/a
|
| Growth protocol |
Cell lines were obtained from the American Type Culture Collection. Comma1-D cells were grown in DMEM:F12 (Gibco) supplemented with 2% FCS, 5 ng/mL murine EGF (Sigma), 10 μg/mL human insulin (Sigma), and 50 μg/mL gentamicin (Gibco).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were captured with the Chromium Controller (10x Genomics).
Library preparation was performed with Chromium Single Cell Gene Expression 3′ Kits (10x Genomics)
scRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
C1D_B
|
| Data processing |
Read processing including demultiplexing, barcode assignment, and UMI quantification was performed by the Cell Ranger analysis pipeline.
This pipeline performed de-multiplexing, alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample
|
| |
|
| Submission date |
Aug 18, 2021 |
| Last update date |
May 05, 2022 |
| Contact name |
Jiyang Yu |
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Department of Computational Biology
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE182352 |
Single-cell dissection of Comma-1D cultures reveals cell populations with unique differentiation and transformation properties [scRNA-Seq] |
| GSE182354 |
Single-cell dissection of Comma-1D cultures reveals cell populations with unique differentiation and transformation properties |
|
| Relations |
| BioSample |
SAMN20848328 |
| SRA |
SRX11809422 |
