|
| Status |
Public on Dec 19, 2023 |
| Title |
RMS1_O_P13 [scRNAseq] |
| Sample type |
SRA |
| |
|
| Source name |
N/A
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: N/A
cell line: RMS1 organoid
cell type: Rhabdomyosarcoma
age in_years: 8
Sex: M
histological subtype: Embryonal
disease state: Relapse
sample location: Parameningeal
primary tumor_location: N/A
fresh/cryopreserved: fresh
medium: M3
passage number: P13
culture type: 3D
|
| Growth protocol |
Culture medium was changed twice a week, and RMS_O were split every 2 weeks on average. Finally, culture medium was changed 24 to 48 h before extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FNRMS-derived organoids were dissociated using TrypLE Express Enzyme (ThermoFisher Scientific, cat. no. 12605010) preheated to 37 °C for 3 min. Cells were then filtered through a 30-µm strainer (Miltenyi Biotec, cat. no. 130 098 458), centrifuged at 500 × g for 5 min, resuspended in complete culture medium and sorted using a FACSAria (BD Biosciences). Cells were centrifuged again at 500 × g for 8 min and resuspended in PBS (Gibco, cat. no. 14190-094) with 0.04% BSA (Sigma-Aldrich, cat. no. A7030) for a final cell concentration of 1 000 cells/µL.
Approximately 20 µL of isolated cells were loaded on a 10X Genomic chip and run on the Chromium Controller system (10X Genomics) to target 10 000 cells per sample. Gene expression data were generated with the Chromium Single Cell 5’ v3.1 assay (10X Genomics) and sequenced on the NovaSeq 6000 platform (S1 flow cell, Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
gene-barcode count matrices were generated from raw sequencing reads using Cell Ranger (v.3.1.0, 10x Genomics) mkfastq and count.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Nov 17, 2023 |
| Last update date |
Dec 19, 2023 |
| Contact name |
Thomas Diot |
| Organization name |
Cancer Research Center of Lyon
|
| Street address |
28 Rue Laennec
|
| City |
Lyon |
| ZIP/Postal code |
69008 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE248178 |
Modeling the next-generation of rhabdomyosarcoma organoids to predict effective drug combinations [scRNAseq] |
| GSE248183 |
Modeling the next-generation of rhabdomyosarcoma organoids to predict effective drug combinations |
|
| Relations |
| BioSample |
SAMN38303400 |
| SRA |
SRX22561131 |
