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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 20, 2023 |
| Title |
mouse RT, R26-SHH, R26P87 |
| Sample type |
SRA |
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| Source name |
tumor sample
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| Organism |
Mus musculus |
| Characteristics |
cell type: tumor cells
tissue: tumor sample
genotype: Rosa 26-CreERT2::Smarcb1flox/flox
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor samples cut in small pieces then dissociated 30 min at 37°C in CO2-independent medium (Gibco) + 0,4 g/l of human albumin (Vialebex) with Liberase TL (Roche) 150 mg/ml and DNase 1 (Sigma) 150 mcg/ml. Dissociated cells were then filtered with a 40 mm cell strainer, then washed and resuspended with C02-independent medium + 0,4 g/l of human albumin. Cells were then continuously maintained on ice or at 4°C. In case of lot of blood cells, the Debris removal kit (Miltenyi Biotec) was used according to the manufacturer’s protocol. To enrich in tumoral cells (human samples) the Tumor Cell Isolation Kit (Miltenyi Biotec) was used according to the manufactu rer’s protocol. Cells were then resuspended in PBS + BSA 0.04%. Samples were prepared for concentration of 800 cell/mcl.
Sample preparations were loaded on a 10x Chromium instrument (10x Genomics) and libraries were prepared using a Single Cell 3’ Reagent Kit (V2 chemistry, 10X Genomics) according to the manufacturer’s protocol, targeting 1000 recovered cells per sample. Single cells were included and barcoded into droplets together with gel beads coated with unique barcodes, unique molecular identifiers (UMI), and poly(dT) sequences, followed by in droplet reverse transcription to generate barcoded full-length cDNA. cDNA was subsequently recovered from droplets, then cleaned up with Dynabead MyOne Silane Beads (Thermo Fisher Scientific), then amplified with the following protocol: 98°C- 3min; 12x (98°C-15s, 67°C-20s, 72°C-1 min); held at 4°C. Amplified cDNA product was cleaned up using the SPRI select Reagent Kit (Beckman Coulter). Indexed libraries were constructed following these steps: 1. Fragmentation, end repair and A-tailing; 2. Size selection with SPRI select beads; 3. Adaptor ligation; 4. Post-ligation cleanup with SPRI select beads; 5. Sample index PCR and final cleanup with SPRI selects beads. Library and quality assessment were achieved using dsDNA High Sensitivity Assay Kit and Bioanalyzer Agilent System. Indexed libraries were tested for quality, equimolarly pooled and sequenced on an Illumina HiSeq2500 using paired-end 26x98 bp as sequencing mode, targeting at least 50 000 reads par cell.
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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, mapping, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Aug 25, 2023 |
| Last update date |
Sep 20, 2023 |
| Contact name |
Mamy Jean de Dieu ANDRIANTERANAGNA |
| E-mail(s) |
mamy-jean-de-dieu.andrianteranagna@curie.fr
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| Phone |
+33156246274
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| Organization name |
Institut Curie
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| Department |
Centre de Recherche
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| Lab |
U900
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| Street address |
26 rue d'Ulm
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| City |
Paris |
| State/province |
Ile de France |
| ZIP/Postal code |
75005 |
| Country |
France |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE241736 |
Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups [scRNAseq_mouseRT_R26SHH] |
| GSE242090 |
Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups |
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| Relations |
| BioSample |
SAMN37182747 |
| SRA |
SRX21499960 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7734656_R26P87_barcodes.tsv.gz |
32.7 Kb |
(ftp)(http) |
TSV |
| GSM7734656_R26P87_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM7734656_R26P87_matrix.mtx.gz |
56.8 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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