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| Status |
Public on Mar 18, 2024 |
| Title |
CT_2_L |
| Sample type |
SRA |
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| Source name |
cortex
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: cortex
treatment: unilateral ACES, for the ipsilateral hemisphere collection
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Cartilage were lysesd and pelleted by centrifugation at 300 g for 3 minutes at 4 °C and washed with cold PBS. Tissues were resuspended in 1 mL pre-warmed (37 °C) TrypLE, and rotated at 37 °C for 15 to 30 minutes until tissues were dissociated into single cells via microscope). Cells were pelleted at 300 g for 3 minutes at 4 °C, and washed with cold PBS.
Chromium Single Cell 3' Reagents Kits version 2
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Data processing |
The gene expression matrices were generated from raw reads using scopetools (https://anaconda.org/singleronbio/scopetools). The first step involved filtering out reads without polyT tails and extracting cell barcodes and unique molecular identifiers (UMIs). Adapters and polyA tails were trimmed before aligning the reads to the pre-mRNA reference. Then reads with the same cell barcode, UMI, and gene were grouped together to count the number of UMIs per gene per cell.
Assembly: scRNA-seq: mm39
Supplementary files format and content: scRNA-seq: tar file containing barcodes.tsv, genes.tsv, and matrix.mtx
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| Submission date |
Jan 19, 2024 |
| Last update date |
Mar 18, 2024 |
| Contact name |
Yan WANG |
| E-mail(s) |
winstonwang37@gmail.com
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| Organization name |
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences
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| Street address |
1068 Xueyuan Ave
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| City |
Shenzhen |
| ZIP/Postal code |
518055 |
| Country |
China |
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| Platform ID |
GPL32190 |
| Series (1) |
| GSE253672 |
Single-nucleus RNA diverse brain regions after electrical brain stimulation (EBS) |
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| Relations |
| BioSample |
SAMN39507481 |
| SRA |
SRX23313852 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8025492_CT_2_L_matrix.tar.gz |
43.4 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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