|
| Status |
Public on Sep 02, 2020 |
| Title |
IRAK4 KO + rescue 1 |
| Sample type |
SRA |
| |
|
| Source name |
KP2
|
| Organism |
Mus musculus |
| Characteristics |
cell line: KP2
genotype: IRAK4 KO + rescue
cell type: Pancreatic cancer line from KPC mouse
passages: <10 from being generated
strain: C57BL/6J
|
| Treatment protocol |
KO of IRAK4 was achieved by infection of KP2 cells with plentiCRISPR vectors encoding sgRNAs against IRAK4
|
| Growth protocol |
All cells were cultured in DMEM/10% FBS, 1% Pen/Strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
oligo-dT
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45. RPKM and CPM calculated from gene counts with custom R scripting.
Genome_build: Ensembl Release 76 GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format
|
| |
|
| Submission date |
Apr 10, 2020 |
| Last update date |
Sep 02, 2020 |
| Contact name |
Kian-Huat Lim |
| E-mail(s) |
kian-huat.lim@wustl.edu
|
| Phone |
3143627009
|
| Organization name |
Washington University School of Medicine
|
| Department |
Internal Medicine/Oncology
|
| Street address |
4566 Scott Avenue, Room 502
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE148442 |
Transcriptomic analysis of IRAK4 in murine pancreatic cancer cells (KP2) |
|
| Relations |
| BioSample |
SAMN14573159 |
| SRA |
SRX8094281 |
