|
| Status |
Public on Mar 06, 2023 |
| Title |
RMC Treated Tumor |
| Sample type |
SRA |
| |
|
| Source name |
Captured single cell RNA
|
| Organism |
Homo sapiens |
| Characteristics |
patient treatment: High-dose methotrexate; vinblastine, doxorubicin, cisplatin (MVAC)
isolation column: Tumor dissociation kit (Miltenyi, 130-095-929); Dead cell removal kit (Miltenyi, 130-090-101), CD45 elimination column (Miltenyi, 130-045-801)
pdx specificitiescharacteristics: : /
patient: Patient 1 (nephrectomy)
sample type: Primary Tumour
tissue: Kidney
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single Cell 3สน 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 |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
LRHX2
rmc_treated_raw_counts.tsv
|
| 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 (or combined hg19-mm10 for the PDX) and gene quantification for each cell was done using CellRanger.
Data are imported into R and analyzed using Seurat v3.
Genome_build: hg19
Supplementary_files_format_and_content: Tabulated text files containing raw UMI counts for each cell.
|
| |
|
| Submission date |
Jul 28, 2021 |
| Last update date |
Mar 06, 2023 |
| Contact name |
Guillaume Davidson |
| E-mail(s) |
davidsoy@igbmc.fr
|
| Organization name |
IGBMC
|
| Street address |
1 Rue Laurent Fries
|
| City |
Strasbourg |
| ZIP/Postal code |
67404 |
| Country |
France |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE181000 |
SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance.. [scRNAseq] |
| GSE181001 |
SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance. |
|
| Relations |
| BioSample |
SAMN20456181 |
| SRA |
SRX11582725 |
