|
| Status |
Public on Jun 20, 2024 |
| Title |
colon, orthotopic MC38 tumor, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
colonic tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: colonic tumor
cell line: MC38
Sex: male
cell type: immune cells from tumors
genotype: WT
time: 21days after tumor injection
treatment: intra-colonic MC38 injection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell suspensions of orthotopic murine tumors were processed with a 10x Chromium Next GEM Single Cell 5’ kit and loaded on a 10x chromium controller to create Single Cell Gel beads in Emulsion (GEM).
A cDNA library was created using a 10x 5’ library kit acording to manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sample demultiplexing and data analysis was performed using 10x's Cellranger suite using the standard parameters.
The count matrices obtained after pre-processing with Cellranger were concatenated to obtain a combined raw count matrix which was then analyzed using the Seurat R package (v3.1.3).
immune cells were selected based on canonical markers and used for downstream analysis
Assembly: mm10
Supplementary files format and content: Raw files are files obtained as output from cellranger in .bam format. Processed files are counts file of the cells included in the analysis aafter QC in tab separated format
|
| |
|
| Submission date |
May 05, 2023 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Gianluca Matteoli |
| Organization name |
KU Leuven
|
| Street address |
Herestraat 49
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE231803 |
IL-1R signaling drives enteric glia-macrophage interaction in colorectal cancer progression [scRNA-Seq] |
| GSE231804 |
IL-1R signaling drives enteric glia-macrophage interactions in colorectal cancer |
|
| Relations |
| BioSample |
SAMN34718974 |
| SRA |
SRX20233656 |
