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| Status |
Public on Apr 15, 2024 |
| Title |
GR2 patient, site 1, scRNAseq |
| Sample type |
SRA |
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| Source name |
Tumor
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Tumor
patient: GR2 patient, site 1
disease: Desmoplastic Small Round Cell Tumor
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| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, fresh DSRCT tumor and peritumor material was collected into RPMI 1640 medium with GlutaMAXTM Supplement (GibcoTM, reference 61870010) or MACS Tissue Storage Solution (Miltenyi Biotec, reference 130-100-008) with a delay of less than 30 minutes after surgery. Tissue samples were further cut into small chunks and incubated at 37°C in RPMI medium containing DNAse I (Sigma, reference DN25-100MG) at 2.2 µg/mL (final concentration) and LiberaseTM Thermolysin Low (TL) (Roche, reference 5401020001) at 4.5 µg/mL (final concentration) during 20 to 30 minutes. After tissue dissociation, the mixture was washed in 1x PBS + 0.04% BSA before centrifugation. To obtain a single-cell suspension, cells resuspended in 1x PBS + 0.04% BSA were filtered twice with a 70 mm and 30 mm cell strainer. After another round of centrifugation, cells were resuspended in 1x PBS + 0.04% BSA. When necessary, red blood cell lysis was performed with a 2 to 3 minutes incubation in 1X Red Blood Cell Lysis buffer (BioLegend, reference 420301) protected from light before washing in 10 mL PBS and performing a last round of centrifugation.
Cell concentration and viability were controlled with an automated cell counter using trypan blue, and cells were loaded into the 10x Genomics cassette for a targeted cell recovery of 5,000 cells per sample following the recommendations from the manufacturer’s protocol. Cell encapsulation, reverse transcription, and library generation were performed according to 10x Genomics standard protocols. Paired-end sequencing was performed on the Illumina NovaSeq 6000 sequencer for a targeted depth of 400 million reads per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcode processing, gene counting were performed using CellRanger software (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Apr 09, 2024 |
| Last update date |
Apr 15, 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) |
| GSE263521 |
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors [scRNA-Seq] |
| GSE263523 |
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM8193966_GR2_1_barcodes.tsv.gz |
20.0 Mb |
(ftp)(http) |
TSV |
| GSM8193966_GR2_1_features.tsv.gz |
297.6 Kb |
(ftp)(http) |
TSV |
| GSM8193966_GR2_1_matrix.mtx.gz |
46.6 Mb |
(ftp)(http) |
MTX |
| Raw data not provided for this record |
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