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| Status |
Public on Dec 19, 2023 |
| Title |
DMEM_2D_P16 [Exome panel] |
| Sample type |
SRA |
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| Source name |
N/A
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| 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: P16
culture type: 2D
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| 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.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA (gDNA) 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), following manufacturer’s instructions.
For DNA‑seq library construction, a total of 200 ng input gDNA per sample was used for SureSelect XT low input library preparation (Agilent, Santa Clara, CA).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
RMS85_S46
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| Data processing |
Unique Molecular Identifiers (UMIs) were extracted and deduplicated using UMI-tools(v.1.1.2) with default parameters.
Reads from each sequencing lane were mapped separately to thehg38human genome using bwa-mem2 (v.2.2.1) with default parameters.
Optical duplicates were removed using Picard MarkDuplicates(v.2.27.4) with default parameters.
GATK (v.4.3.0.0) BaseRecalibrator and ApplyBQSR were used with default parameters.
GATK (v.4.3.0.0) Mutect2 (with parameter ‘--callable-depth 1’) in multi-sample tumor-only mode (with sample groups as RMS1, RMS2)
Variant filtering with GATK (v.4.3.0.0) LearnReadOrientationModel, GetPileupSummaries, CalculateContamination and FilterMutectCalls, with default parameters.
Germline variants were filtered with vcftools (v.0.1.16) ‘vcf-isec’ (using germline variants from gnomAD and 1000 Genomes VCF files), with default parameters.
vcftools (v.0.1.16) ‘vcf-merge’ was used to merge all samples into a single VCF file, with default parameters.
A custom Python script was used to re-annotate variants whose FILTER value was wrongly modified by vcf-merge.
Variants were annotated using Ensembl Variant Effect Predictor (VEP,v.108.1) with default parameters.
Assembly: hg38
Supplementary files format and content: VCF file includes germline-filtered variants 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
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| Street address |
28 Rue Laennec
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| City |
Lyon |
| ZIP/Postal code |
69008 |
| Country |
France |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE248176 |
Modeling the next-generation of rhabdomyosarcoma organoids to predict effective drug combinations [Exome panel] |
| GSE248183 |
Modeling the next-generation of rhabdomyosarcoma organoids to predict effective drug combinations |
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| Relations |
| BioSample |
SAMN38303341 |
| SRA |
SRX22561042 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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