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| Status |
Public on May 22, 2024 |
| Title |
P18 |
| Sample type |
SRA |
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| Source name |
DSRCT, frozen tumor samples, RNA-seq
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Desmoplastic Small Round Cell Tumor
patient id: ID17
sample id: P18
ewsr1 breakpoint_exon: 7
wt1 breakpoint_exon: 8
sampling site: Peritoneum
age: 25
gender: M
deceased: 1
follow-up duration_(months): 30
prior chemotherapy: 1
number of_prior_chemotherapy_lines: 1
chemotherapy regimens: L1: AI
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Ribbon sections of frozen samples were cut using a cryostat microtome after embedding within O.C.T. Next, frozen tissue was lyzed using Qiagen TissueLyser II with 3 mm tungsten carbide beads according to manufacturer protocol. RNA extraction was then performed using the Qiagen AllPrep DNA/RNA kit standard protocol.
After the QC procedure, rRNA was removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs(dUTP, dATP, dGTP and dCTP), RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Then followed by purification by AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection and degradation of second-strand U-contained cDNA by the USER enzyme. The strand-specific cDNA library was generated after the final PCR enrichment.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Count matrix in transcript per million for all RNA-seq samples (N=29: GR129T01, GR111T01, GR130T01, GR131T01, GR113T01, GR114T01, GR133T01, GR115T01, GR116T01, GR117T01, GR134T01, GR118T01, GR119T01, GR120T01, GR121T01, GR122T01, GR135T01, GR123T01, GR124T01, GR125T01, GR136T01, GR128T01, GR108T01, GR109T01, GR110T01, GR101T01, GR103T01, GR106T01, GR107T01)
Patient raw data cannot be provided due to privacy concerns
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| Data processing |
RNA-seq data were analyzed according to nf-core/rnaseq pipeline
Raw reads quality control (QC) was performed using FastQC
Adapter trimming was done with Trim Galore!
Alignment to the reference genome and transcript quatification were performed using Salmon
Assembly: hg19 (GENCODE version 19)
Supplementary files format and content: Count matrix in transcript per million
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| Submission date |
May 18, 2024 |
| Last update date |
May 22, 2024 |
| Contact name |
Clémence Henon |
| E-mail(s) |
clemence.henon@gustaveroussy.fr
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| Organization name |
Gustave Roussy
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| Street address |
114 rue Edouard Vaillant
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| City |
Villejuif |
| ZIP/Postal code |
94800 |
| Country |
France |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE263523 |
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors |
| GSE267805 |
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors [Patient_bulkRNA-seq] |
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| Supplementary data files not provided |
| Raw data not provided for this record |
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