|
| Status |
Public on Jul 23, 2020 |
| Title |
SW480_singlecell_EpCAMhigh |
| Sample type |
SRA |
| |
|
| Source name |
colon cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon
tissue: SW480
rna isolation date: 2018-11-23
|
| Growth protocol |
Cell populations were sorted from established colon cancer cell lines grown in standard culture medium.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were lysed in droplets using Single Cell 3' v2 chemistry (10X Genomics).
RNA-Seq was performed at the Erasmus MC Center for Biomics (Rotterdam, The Netherlands). For each sample, between 50k-100k EpCAMlo cells and EpCAMhi cells were FACS sorted and processed using the 10X Genomics Chromium Single Cell Controller. Samples were sequenced (Illumina) to a depth ranging 49k-65k reads/cells.
single cell RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
single cell
|
| Data processing |
Gene-cell matrices were obtained by conversion of the raw data using the Cell Ranger pipeline (v2.1.1).
Filtered gene-cell matrices were merged in R, and processed for downstream analysis using the Seurat package (v3).
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene-cell matrices include hgnc symbols and read counts
|
| |
|
| Submission date |
Jul 22, 2020 |
| Last update date |
Jul 23, 2020 |
| Contact name |
Mathijs Verhagen |
| E-mail(s) |
m.p.verhagen@erasmusmc.nl
|
| Organization name |
Erasmus Medical Center
|
| Street address |
Doctor Molewaterplein 40
|
| City |
Rotterdam |
| ZIP/Postal code |
3015 GD |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE154930 |
Phenotypic plasticity underlies local invasion and distant metastasis in colon cancer (Single cell RNA-Seq) |
|
| Relations |
| BioSample |
SAMN15608675 |
| SRA |
SRX8801288 |
