|
| Status |
Public on Apr 24, 2022 |
| Title |
MC38 RT replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Tumor
cell line: MC38
cell type: Sorted CD45+ cells
genotype: C57BL/6J
treatment: Radiation 12Gy in vivo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions were processed on a 10X Chromium controller using the 10X Single Cell 3’ Reagent kit (v3.0) according to manufacturer's instructions
scRNA-seq libraries were prepared using the 10X Single Cell 3’ Reagent kit (v3.0) according to manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Data were processed using the Cell Ranger pipeline (v3.1.0) and subsequently analyzed with the Loupe Browser from 10X Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/what-is-loupe-cell-browser).
BCL to fastq conversion using cellranger mkfastq with cellranger v3.1.0 and dependency bcl2fastq2 v2.20.0
cellranger count with default settings run on each sample individually to generate single cell features counts
cellranger aggr with default settings (--normalize=mapped) to aggregate all samples into a single .cloupe file for exploration in Loupe Cell Browser
Assembly: mm10
Supplementary files format and content: Processed files pertaining to each individual samples are the tab seperated values and matrix files output from running cellranger count
Supplementary files format and content: The "Allsamples" supplemental files are te tab seperated values, barcodes, and matrix files output from running cellranger aggr on all 16 samples.
|
| |
|
| Submission date |
Apr 19, 2022 |
| Last update date |
Apr 25, 2022 |
| Contact name |
Michael Gough |
| Organization name |
Earle A Chiles Research Institute
|
| Street address |
4805 NW Glisan St, Suite 2N35
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97213 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE201026 |
Fluorescent tracking identifies tumor migratory dendritic cells as critical for cross-presentation in the lymph node following radiation therapy induced maturation |
|
| Relations |
| BioSample |
SAMN27630594 |
| SRA |
SRX14909829 |
