|
| Status |
Public on Sep 30, 2019 |
| Title |
CJ4_06_T_rep_1 |
| Sample type |
SRA |
| |
|
| Source name |
Murine pancreatic fibroblasts_Co-cultured with Clone T
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
experimental condition: Co-cultured with Clone T
cell type: Murine pancreatic fibroblasts
|
| Growth protocol |
Tumour sub-clones and fibroblasts were co-cultured for 48hours before resolving according to tumour cell-specific GFP expression by FACS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Isolated fibroblasts were pelleted and lysed in QIAgen RLT buffer. RNA was extracted using a Qiagen RNeasy plus kit.
Indexed PolyA libraries were prepared using 200ng of total RNA and 14 cycles of amplification with the Agilent SureSelect Strand Specific RNA Library Prep Kit for Illumina Sequencing.
Paired-end 76 base-pair sequencing was carried out by clustering 2pM of the pooled libraries on a Illumina NextSeq 500 sequencer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CJ4_06_T_rep_1_S6
|
| Data processing |
NB Dataset consists of two RNA sequencing runs, each containing 4 lanes. Each sample was sequenced within each lane of each run i.e. 8 times in total.
Sequencing reads were aligned to the mouse reference genome using the BCBio-NextGen RNA-seq pipeline using the STAR aligner.
Gene annotation was taken from Ensembl build 83. Read counts were determined by using the featureCounts function from the Bioconductor package Rsubread (version 1.16.1).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the EdgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files contain aligned read counts per sample, and normalised RPKM values.
|
| |
|
| Submission date |
Aug 06, 2019 |
| Last update date |
Sep 30, 2019 |
| Contact name |
Claus Jorgensen |
| E-mail(s) |
claus.jorgensen@cruk.manchester.ac.uk
|
| Organization name |
Cancer Research UK Manchester Institute
|
| Lab |
Systems Oncology
|
| Street address |
Alderley Park
|
| City |
Macclesfield |
| State/province |
Lancs |
| ZIP/Postal code |
SK10 4TG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE135434 |
Tumour Cell Heterogeneity Instructs Fibroblast Diversity and Reciprocal Signalling [dataset 2] |
| GSE135436 |
Tumour Cell Heterogeneity Instructs Fibroblast Diversity and Reciprocal Signalling |
|
| Relations |
| BioSample |
SAMN12501394 |
| SRA |
SRX6658661 |
