|
| Status |
Public on Jun 07, 2023 |
| Title |
PCN organoid 3 of 3 |
| Sample type |
SRA |
| |
|
| Source name |
esophagus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: organoid
cell type: epithelial cell
genotype: Trp53;Cdkn2a;Notch1 KO
treatment: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
organoids from WT, PN, and PCN were collected 7 days after seeding and lysed with Rneasy Mini Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
diffgene_PCN1_WT
PCN3
|
| Data processing |
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files which contain sequences of reads and corresponding base quality.
Assembly: GRCm38/mm10
Supplementary files format and content: DESEQ output files comparing 2 groups, counts, fpkms
|
| |
|
| Submission date |
Sep 21, 2022 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Jae-Il Park |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE213904 |
Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion [bulkRNAseq] |
| GSE213929 |
Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion |
|
| Relations |
| BioSample |
SAMN30954069 |
| SRA |
SRX17663528 |
