|
| Status |
Public on May 18, 2020 |
| Title |
CT_dura_CD45pos |
| Sample type |
SRA |
| |
|
| Source name |
CD45+ dura single cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
sample type: FACS sorted
age: Adult
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FACS sorted CD45+ or CD45- 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
single cell RNA
CD45+ dura single cell RNA library
|
| Data processing |
Cell Ranger (v3.1.0) was used to process single cell 3' RNA-seq ouput. Breifly, first the cell ranger mkfastq was used to demultiplex 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 (v3.1.0) and cell-gene raw expression matrices were made. Potential doublets were removed by Scrublet. Low quality cells (less than 1000 detected genes) were removed. Also, cells with high mitochondrial gene associated UMI count (>7% of total UMI counts) were removed.
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
|
| |
|
| Submission date |
Feb 26, 2020 |
| Last update date |
May 19, 2020 |
| Contact name |
Bong Ihn Koh |
| Organization name |
Korea Advanced Institute of Science and Technology
|
| Street address |
291 Daehakro
|
| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE145973 |
Single-cell RNA-sequencing of CD45+ cells isolated from mouse dura mater or brain after photothrombotic injury |
|
| Relations |
| BioSample |
SAMN14212817 |
| SRA |
SRX7806099 |
