|
| Status |
Public on Mar 03, 2023 |
| Title |
Cells_p11 |
| Sample type |
SRA |
| |
|
| Source name |
WAG/Rij rats
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: colon carcinoma
cell line: CC-531
cell type: CC-531 cell line
|
| Treatment protocol |
To establish a 3D cell culture, CC-531 cells were cultured in matrigel in order to develop organoids.
Tumor lesions throughout the abdominal cavity were induced by intraperitoneal injections in the right lower part of the abdominal cavity with 1 mL 2 ×106 cells/mL cell suspension in culture medium in 8-10 week-old WAG/Rij rats. CC-531 cells were cultured for at least two passages after being thawed.
|
| Growth protocol |
The CC-531 cell line are colon carcinoma cells derived from WAG/Rij rats. This cell line was cultured in RPMI1640 medium (Gibco) containing 25 mM HEPES and supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin/glutamine (Gibco). Cells were maintained at 37°C in a humidified atmosphere of 5% CO2 in air.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from CC-531 cells, CC-531 organoids and CC-531 ex vivo tumor tissue grown in the peritoneum of WAG/Rij rats using the RNA isolation kit (Bioke). Three different passages per sample type were used resulting in a total of 9 samples.
Library preparation was constructed using KAPA mRNA Hyperprep following by RNAseq performed on an Illumina HiSeq 4000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Cells_p11
|
| Data processing |
To assess the quality of raw data, FastQC (v.0.11.9) and MultiQC (v.1.9) were used prior to processing the data.
The first 11 bases were trimmed from each read and low-quality bases (Phred score < 20) were removed using Cutadapt (v1.18).
To align the sequences STAR (v.2.7.4.a) was applied.
The reference genome used in this step was mRatBN7.2. Finally, the number of counts per gene was obtained by STAR.
Assembly: mRatBN7.2
Supplementary files format and content: Excel file containing raw count data for all samples
|
| |
|
| Submission date |
Mar 03, 2023 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Arezo Torang |
| E-mail(s) |
a.torang@amsterdamumc.nl
|
| Organization name |
Amsterdam UMC
|
| Street address |
Meibergdreef 9
|
| City |
Amsterdam |
| ZIP/Postal code |
1105 AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE226558 |
CMS classification of the CC-531 cells, CC-531 organoids and CC-531 ex vivo tumor tissue grown in the peritoneum of rats |
|
| Relations |
| BioSample |
SAMN33576998 |
| SRA |
SRX19556224 |
