|
| Status |
Public on Jun 26, 2023 |
| Title |
Normal Adjacent Tissue 2 (N2) |
| Sample type |
SRA |
| |
|
| Source name |
Captured single cell RNA
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: clear-cell renal cell carcinoma
tissue: Kidney
sample type: Normal Adjacent Tissue
patient: Patient 4
disease stage: Stage III
tumour grade: ISUP2
prior treatment: Naive
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor dissociation kit (Miltenyi, 130-095-929); Dead cell removal kit (Miltenyi, 130-090-101)
Single Cell 3ʹ Gene Expression libraries comprise standard Illumina paired-end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1, while 8 bp sample index sequences are incorporated as the i7 index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 12 bp UMI.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment to reference genome hg19 and gene quantification for each cell was done using CellRanger v3.1.
Data are imported into R and analyzed using the Seurat package v3.1.4.
Assembly: hg19
Supplementary files format and content: TSV files containing raw UMI counts for cells used in Seurat analysis.
|
| |
|
| Submission date |
Jul 29, 2022 |
| Last update date |
Jun 26, 2023 |
| Contact name |
Guillaume Davidson |
| E-mail(s) |
davidsoy@igbmc.fr
|
| Organization name |
I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire
|
| Street address |
1 Rue Laurent Fries
|
| City |
Illkirch-Graffenstaden |
| ZIP/Postal code |
67400 |
| Country |
France |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE210038 |
Mesenchymal-like tumor cells and myofibroblastic cancer-associated fibroblasts are associated with progression and immunotherapy response of clear-cell renal cell carcinoma [scRNA-seq] |
| GSE210042 |
Mesenchymal-like tumor cells and myofibroblastic cancer-associated fibroblasts are associated with progression and immunotherapy response of clear-cell renal cell carcinoma |
|
| Relations |
| BioSample |
SAMN30050092 |
| SRA |
SRX16730774 |
