|
| Status |
Public on Nov 27, 2023 |
| Title |
acinar_organoid_RNAseq_4 |
| Sample type |
SRA |
| |
|
| Source name |
exocrine pancreas
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: exocrine pancreas
cell type: acinar
genotype: WT
condition: organoid culture
|
| Treatment protocol |
"K" genotype cells have enforced expression of oncogenic KRAS-G12V and "KPTS" genotype cells have KRAS-G12V and CRISPR/Cas9 knockout of P16, P53, and SMAD4 .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Zymo Direct-zol RNA Miniprep Kit as per manufacturer instructions.
RNAseq libraries prepared using Illumina Stranded mRNA Prep Ligation kit as per manufacturer instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Alignment was performed using TopHat 2.1.1 and gene expression was quantified using HTSeq 0.11.1.
Assembly: hg38
Supplementary files format and content: read_table.txt.gz is tab delimited table of read counts per gene for all samples.
Supplementary files format and content: TPM_table.txt.gz is tab delimited table of transcripts per million per gene for all samples
|
| |
|
| Submission date |
Jan 16, 2023 |
| Last update date |
Nov 27, 2023 |
| Contact name |
Pei Wang |
| E-mail(s) |
wangp3@uthscsa.edu
|
| Organization name |
University of Texas Health San Antonio
|
| Department |
Cell Systems & Anatomy
|
| Street address |
7703 Floyd Curl Dr
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE222990 |
RNA sequencing of human pancreatic acinar and ductal cells |
| GSE222991 |
Functional Genomics of human pancreatic acinar and ductal cells |
|
| Relations |
| BioSample |
SAMN32758603 |
| SRA |
SRX19047829 |
