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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 05, 2021 |
| Title |
MP1 |
| Sample type |
SRA |
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| Source name |
PBS treated tumor ECs from MMTV-PyMT model
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| Organism |
Mus musculus |
| Characteristics |
cell type: tumor endothelial cells
strain: c57bl/6
sorting: FACS sorted
age: Adult
treatment: PBS injected CD31+ tumor EC
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| Extracted molecule |
total RNA |
| Extraction protocol |
FACS sorted endothelial cells were processed on the 10X chromium system following the manufacturer's protocols.
Using Chromium Next GEM Single cell 3' v3 Reagent Kit (10X genomics), cDNA libraries were constructed
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
single cell RNA
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| Data processing |
Cell Ranger (v3.0.0) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mouse reference genome.
Aligned reads were then read by Seurat (v3.1.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 500 genes) and potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
Expression matrices were made after quality control. After initial clustering, contaminating cell populations were removed. Matrices were log normalized to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Cell-gene expression matrix of log normalized UMI counts for tumor ECs
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| Submission date |
Apr 04, 2021 |
| Last update date |
Apr 05, 2021 |
| Contact name |
Myung Jin Yang |
| E-mail(s) |
mjyang@kaist.ac.kr
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| Organization name |
Institute for Basic Science
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| Street address |
34141
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| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE171451 |
Transcriptomic changes of tumor endothelial cells in spontaneous breast tumour model and implanted breast tumour model |
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| Relations |
| BioSample |
SAMN18614371 |
| SRA |
SRX10510567 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5225849_MP1_expression_matrix.csv.gz |
21.8 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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