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Status |
Public on Dec 19, 2023 |
Title |
RMS2_O_P7* [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 organoid 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: cryopreserved medium: M3 passage number: P7 culture type: 3D
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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 |
RMS187_S37
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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 |
SAMN38303350 |
SRA |
SRX22561033 |
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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