|
| Status |
Public on Jan 14, 2021 |
| Title |
15783X2 HC569-A8-18-Control rep2 |
| Sample type |
SRA |
| |
|
| Source name |
pancreas
|
| Organism |
Mus musculus |
| Characteristics |
strain: mixed 129/B6
hnf4a status: Negative
agent: Control
|
| Growth protocol |
Cells were grown in DMEM + 10% FBS and treated with 1mg/ml of doxycycline or vehicle for 7 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol extraction followed by PureLink RNA Mini Kit purification
TruSeq Stranded RNA kit with Ribo-Zero Gold (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Single cell clone from 2D cultures derived from murine pancreatic tumors, cultured in control condition
15783X2
|
| Data processing |
The human GRCh38 FASTA and GTF files were downloaded from Ensembl release 92.
The reference database was created using STAR version 2.5.4a with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2.
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).
|
| |
|
| Submission date |
Sep 30, 2019 |
| Last update date |
May 16, 2022 |
| Contact name |
Eric Snyder |
| E-mail(s) |
eric.snyder@hci.utah.edu
|
| Organization name |
University of Utah, Huntsman Cancer Institute
|
| Department |
Pathology
|
| Street address |
2000 Circle of Hope Drive
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84103 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE138143 |
Hnf4a regulated transcriptome in 2D cell lines derived from murine pancreatic tumors [2D cell lines] |
| GSE138145 |
Hnf4a regulated transcriptome |
|
| Relations |
| BioSample |
SAMN12871813 |
| SRA |
SRX6922455 |
