|
| Status |
Public on Sep 10, 2021 |
| Title |
scRNA-seq of liver metastases of colorectal cancer:COL15 liver metastases |
| Sample type |
SRA |
| |
|
| Source name |
the tumor microenvironment of liver metastases of CRC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: matched liver metastases
age: 35
Sex: Female
tumor stage: IVA
treatment: treated
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Fresh biopsies of the primary colorectal cancer and the matched liver metastases were collected during surgery. Venous blood was collected before surgery in EDTA anticoagulant tubes and used to isolate PBMC immediately. Once the specimens were separated from body, they were processed for scRNA-seq immediately.
10x single-cell RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw base call (BCL) files were demultiplexed into FASTQ file by bsl2fastq.
Droplet-based sequencing data were qualified by FastQC software. Then reads were aligned against GRCh38 human reference genome provided by Cell Ranger (version 2.0, 10x Genomics).
The raw gene expression matrix generated from each sample were aggregated using CellRanger (version 2.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes.tsv.gz (barcode_#, where # corresponds to patient sample name); features.tsv.gz; matrix.mtx.gz. The files contain aggregated information about unique barcodes, features and gene-cell matrix.
|
| |
|
| Submission date |
Jun 16, 2021 |
| Last update date |
Sep 10, 2021 |
| Contact name |
liheng che |
| E-mail(s) |
cheliheng@126.com
|
| Organization name |
Sun Yat sen university
|
| Street address |
Xin gang road
|
| City |
Guangzhou |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE178318 |
A Single-Cell Atlas of Liver Metastases of Colorectal Cancer Reveals the Reprogramming of the Tumor Microenvironment in Response to Preoperative Chemotherapy |
|
| Relations |
| BioSample |
SAMN18876204 |
| SRA |
SRX11048626 |
