|
| Status |
Public on Aug 28, 2020 |
| Title |
KPC PDA tumour 6 CD105neg CAFs |
| Sample type |
SRA |
| |
|
| Source name |
KPC GEMM mouse Pdx1-Cre; KrasLSL-G12D/+; Trp53LSL-R172H/+ (KPC)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spontaneous pancreatic tumours
cell type: CD105neg
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FACS isolated CAFs were centrifuged at 400g for 5 min, carefully aspirated and cells lysed in RLT buffer. Lysis and subsequent RNA isolation was conudcted as per instructions ffor the Qiagen RNeasy micro kits
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
6neg
|
| Data processing |
Sequencing reads (76bp, paired-end) were aligned to the mouse reference genome GRCm38.mm10 using STAR aligner version 2.5.1b
Gene annotation was taken from Ensembl build 92
Read counts were determined by using the featureCounts function from Bioconductor package Rsubread version 1.28.1
Expression of a gene was calculated as Transcipts Per Kilobase Million (TPM) using standard calculation
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with TPM values for every gene and every sample
|
| |
|
| Submission date |
Aug 27, 2020 |
| Last update date |
Aug 28, 2020 |
| Contact name |
Alexander Kononov |
| E-mail(s) |
[email protected]
|
| Organization name |
Cancer Research UK Manchester Institute
|
| Lab |
System Oncology
|
| Street address |
Oglesby Building, 555 Wilmslow Rd,
|
| City |
MANCHESTER |
| ZIP/Postal code |
SK10 4TG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE156985 |
Gene expression profiles of CD105pos and CD105neg cancer-associated fibroblasts (CAFs) from KPC mice |
|
| Relations |
| BioSample |
SAMN15923916 |
| SRA |
SRX9023324 |
