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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 05, 2024 |
| Title |
PreSC_KO |
| Sample type |
SRA |
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| Source name |
xenograft
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| Organism |
Mus musculus |
| Characteristics |
cell type: epithelial cells
tissue: xenograft
strain: nude mice
age: 6-8 weeks old
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse xenograft tumors were transferred to a dry dish and minced into pieces with blades. The tissue was digested in Leibovitz’s medium (Gibco, 21083-027) with 2 mg/mL Collagenase Type I (Worthington, CLS-1 LS004197), 2 mg/mL Elastase (Worthington, ESL LS002294) and 2 mg/mL DNaseI (Worthington, D LS002007) at 37 °C for 45 min. The tissue was triturated with pipet every 15 min of digestion until homogenous. The digestion was stopped with FBS (Invitrogen, 10082-139) to a final concentration of 20%. The cells were filtered with a 70 μm cell strainer (Falcon, 352350) and spun down at 5000 rpm for 1 min. The cell pellet was resuspended in red blood cell lysing buffer (Sigma, R7757) for 3 min, spun down at 5000 rpm for 1 min and washed with 1 mL ice-cold Leibovitz’s medium with 10% FBS. Cells were resuspended in 1 mL ice-cold Leibovitz’s medium with 10% FBS and filtered with a cell strainer (20 μm). Dead cells were removed with Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) according to the manufacturer's instructions. Live cells were collected for 10x Genomics library preparation.
Single cell Gene Expression Library was prepared using Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics, PN-1000121).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
May 05, 2022 |
| Last update date |
May 05, 2024 |
| Contact name |
Shengzhe Zhang |
| E-mail(s) |
zhangshengzhe@gmail.com
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| Organization name |
MD Anderson Cancer Center
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| Department |
Experimental Radiation Oncology
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| Street address |
6565 MD Anderson Blvd
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE202311 |
Gene expression profile at single cell level of xenograft tumors |
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| Relations |
| BioSample |
SAMN28101830 |
| SRA |
SRX15165627 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6108265_KO_barcodes.tsv.gz |
78.1 Kb |
(ftp)(http) |
TSV |
| GSM6108265_KO_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM6108265_KO_matrix.mtx.gz |
152.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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