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| Status |
Public on Jun 02, 2021 |
| Title |
ATRT, INI293 |
| Sample type |
SRA |
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| Source name |
tumor sample
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| Organism |
Homo sapiens |
| Characteristics |
tumor type: ATRT
tissue: CNS
age: NA
genotype: SMARCB1-mutated
Sex: M
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were obtained from tumor frozen samples using Qiagen RNAeasy kit, according to the manufacturer's procedures (Qiage, Venlo, Netherlands)
Barcoded Illumina compatible libraries were generated from 750 ng of total RNA for each sample using TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, California, U.S.)
Library werer sequenced using the Illumina HiSeq 2500 platform in the 100 bp paired-end mode
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Quality control: sequenced reads quality were assessed using fastqc v0.11.5
Mapping: sequenced reads were aligned with hg19 human genome reference using STAR v2.5.3a
Reads counting: reads aligned in each gene are counted using STAR v2.5.3a and the and the refFlat table gene annotation (downloaded in GTF format on October 2nd, 2018 from UCSC website)
Transcript Per Million (TPM) normalized count were calculated based on library size and gene length using an in-house script
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with TPM normalized gene count for every gene and every sample in tab-delimited text file
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample in tab-delimited text file
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| Submission date |
Jun 01, 2021 |
| Last update date |
Aug 29, 2023 |
| Contact name |
Nicolas Servant |
| E-mail(s) |
Nicolas.Servant@curie.fr
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| Organization name |
Institut Curie
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| Street address |
26 rue d'ulm
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| City |
Paris Cedex 05 |
| ZIP/Postal code |
75248 |
| Country |
France |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE175891 |
High-throughput gene expression profilng of SMARCA4-mutated extra-cranial rhabdoid tumours (ECRT-SMARCA4), SMARCB1-mutated ECRT, ATRT and SCCOHT tumours by RNA sequencing |
| GSE175893 |
SMARCA4-deficient rhabdoid tumours show intermediate molecular features between SMARCB1-deficient rhabdoid tumours and small cell carcinomas of the ovary, hypercalcaemic type. |
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| Relations |
| Reanalyzed by |
GSE241831 |
| BioSample |
SAMN19487468 |
| SRA |
SRX11037879 |
| 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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