|
| Status |
Public on Dec 19, 2023 |
| Title |
DMEM_2D_P5 [RNAseq] |
| Sample type |
SRA |
| |
|
| Source name |
N/A
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: N/A
cell line: RMS2 cell line
cell type: Rhabdomyosarcoma
age in_years: 7
Sex: M
histological subtype: Embryonal
disease state: Relapse/metastatic
sample location: Lung
primary tumor_location: Ischioanal
fresh/cryopreserved: fresh
medium: DMEM
passage number: P5
culture type: 2D
|
| 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 |
polyA RNA |
| Extraction protocol |
RNA from both RMS tissues and matched in vitro models cultured in 2D or 3D conditions with DMEM, M3 and M5 media were extracted using the Allprep DNA/RNA/miRNA universal kit (Qiagen, cat. no. 80224) and Arcturus® PicoPure® RNA Isolation Kit (ThermoFisher Scientific, cat. no. KIT0204) only for small tumor pieces, following manufacturer’s instructions.
For RNA‑seq library construction, 100 to 1 000 ng of total RNAs were used. Libraries were prepared with Illumina Stranded mRNA Prep (Illumina, cat. no. 20040534) following recommendations.
ssRNA-seq (stranded RNA-seq)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Trimming of adapter sequences was done with Cutadapt (v.3.4) using -a CTGTCTCTTATACACATCT and -A CTGTCTCTTATACACATCT parameters.
Reads were mapped using STAR (v.2.7.9) to the human reference genome assembly GRCh38.p13 with --seedSearchStartLmax 38 --outFilterMatchNminOverLread 0.66 --outReadsUnmapped Fastx --outSAMmultNmax -1 --outMultimapperOrder Random --outFilterScoreMinOverLread 0.66 --quantMode TranscriptomeSAM --outSAMstrandField intronMotif --twopassMode Basic --limitSjdbInsertNsj 1324910 parameters.
Gene expression data was generated with HTseq-count (v.0.13.5) using --order pos --stranded reverse parameters.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
|
| |
|
| 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) |
| GSE248177 |
Modeling the next-generation of rhabdomyosarcoma organoids to predict effective drug combinations [RNAseq] |
| GSE248183 |
Modeling the next-generation of rhabdomyosarcoma organoids to predict effective drug combinations |
|
| Relations |
| BioSample |
SAMN38303370 |
| SRA |
SRX22561079 |
