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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 22, 2020 |
| Title |
WT Intestinal stromal single cell_rep2 |
| Sample type |
SRA |
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| Source name |
PDGFRb+-CreERT2-Tomato+
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J
age: Adult
genotype/variation: wild type
cell preparation: FACS sorted
cell type: PDGFRb+ intestinal stromal single cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
FACS sorted stromal cells were processed on the 10X chromium system following the manufacturer's protocols.
Using Chromium 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 |
HiSeq X Ten |
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| Description |
WT_int_stroma2_S1_L003
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| Data processing |
Cell Ranger (v3.0.2) 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 (v3.0.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 1000 genes) and potential doublets (expressing more than 6000 genes) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control, expression matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat 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 WT and LATS1/2 KO datasets
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| Submission date |
Jun 03, 2019 |
| Last update date |
Jul 22, 2020 |
| Contact name |
Hyunsoo Cho |
| E-mail(s) |
hyunsooj325@kaist.ac.kr
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| Organization name |
IBS/KAIST
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| Street address |
Yuseonggu
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| City |
Daejeon |
| ZIP/Postal code |
Daejeon |
| Country |
South Korea |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE124488 |
Bulk RNA-sequencing and Single-cell RNA-sequencing of adult mice intestinal stromal cells and lacteal LECs with PDGFRb-specific deletion of LATS1/2 |
| GSE132092 |
Bulk RNA-sequencing and Single-cell RNA-sequencing of adult mice intestinal stromal cells and lacteal LECs with PDGFRb-specific deletion of LATS1/2 [scRNA-seq 2] |
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| Relations |
| BioSample |
SAMN11936765 |
| SRA |
SRX5953136 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3842418_WT_int_stroma_2_expression_matrix.csv.gz |
106.9 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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