|
| Status |
Public on Jun 07, 2023 |
| Title |
PC organoid 2 of 2 |
| Sample type |
SRA |
| |
|
| Source name |
esophagus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: organoid
cell type: epithelial cell
genotype: Trp53;Cdkn2a KO
treatment: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
organoids from WT, PC, PN, and PCN were collected 7 days after seeding and digested with 0.05% trypsin-EDTA at 37 ℃ for 30 min.
Each group was tagged with 2 CMO tags from CellPlex kit (10x Genomics). The tagged cells of each group were pooled together with same number of cells after counting cells. cDNA library was prepared with the 10x Genomics 3’ v2 kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Multiplexed
|
| Data processing |
The demultiplexing, barcoded processing, and gene counting were performed using the Cell Ranger ( v6.1.2)
Assembly: GRCm38/mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)
|
| |
|
| Submission date |
Sep 22, 2022 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Jae-Il Park |
| E-mail(s) |
jaeil@mdanderson.org
|
| Organization name |
M.D. Anderson Cancer Center
|
| Department |
Dept. of Experimental Radiation Oncology
|
| Street address |
6565 MD Anderson BLVD
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE213927 |
Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion [scRNAseq] |
| GSE213929 |
Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion |
|
| Relations |
| BioSample |
SAMN30961501 |
| SRA |
SRX17673798 |
