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Status |
Public on Dec 19, 2023 |
Title |
RMS1_O_P22* [RNAseq] |
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: cryopreserved medium: M3 passage number: P22 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 |
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)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
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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
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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 |
SAMN38303384 |
SRA |
SRX22561092 |