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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 07, 2024 |
| Title |
CO_01 |
| Sample type |
SRA |
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| Source name |
Cerebral hemisphere
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Cerebral hemisphere
treatment: Carbon monoxide poisoning
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| Extracted molecule |
total RNA |
| Extraction protocol |
Under sterile conditions, fresh rat brain tissue is first placed in pre-cooled phosphate-buffered saline (PBS) and transferred to a sterile workbench for processing. Then, the tissue is digested with PBS containing 0.25% trypsin and 0.1% DNAse I, gently shaking in a 37°C water bath for 15-30 minutes, with the time adjusted based on the actual digestion results. To terminate digestion, an equal volume of DMEM culture medium containing 10% fetal bovine serum (FBS) is added, and the mixture is filtered through a 40-70μm cell strainer to remove undigested tissue and cell clumps. Subsequently, the cells are centrifuged at 1300 rpm at 4°C for 5 minutes and resuspended in pre-cooled PBS, repeating the washing until the supernatant is clear. Cell density is measured using a cell counting plate or an automatic cell counter, and cell viability is assessed using a 0.4% trypan blue exclusion test, ensuring a viability rate of over 90%. This series of meticulous operations aims to obtain high-quality single-cell suspensions from rat brain tissue, laying the foundation for subsequent single-cell transcriptome analysis.
The key technology of the 10x Genomics Chromium™ system leverages millions of unique Barcodes to tag different samples (long DNA molecules/single cells). Initially, Gel beads containing Barcode sequences are mixed with a mixture of samples and enzymes, then combined with an oil surfactant to form GEMs (Gel Bead-In-Emulsions, meaning oil droplets encapsulating Gel beads, samples, and enzyme mixture). The GEMs are collected and flow into a reservoir, where Gel beads dissolve to release Barcode sequences, starting the sample tagging process. The products containing Barcode information from each droplet are mixed together to construct a standard sequencing library.
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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 raw data was mapped to the Rnor_6.0 rat reference genome using CellRanger (10x Genomics).
Assembly: Rnor_6.0
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Apr 02, 2024 |
| Last update date |
Apr 07, 2024 |
| Contact name |
Xudong Zhou |
| E-mail(s) |
haipizxd@gmail.com
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| Organization name |
Shandong University of Traditional Chinese Medicine
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| Department |
First Clinical College
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| Street address |
4655 University Road, University Science and Technology Park, Changqing District, Jinan City, Shandong Province, China
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| City |
Jinan |
| ZIP/Postal code |
264000 |
| Country |
China |
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| Platform ID |
GPL20084 |
| Series (1) |
| GSE262987 |
CLCF1/NF-κB Signaling Pathway Regulates Macrophage Efferocytosis to Ameliorate Neural Damage and Cognitive Dysfunction After CO Poisoning. |
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| Relations |
| BioSample |
SAMN40722935 |
| SRA |
SRX24126792 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8182738_CO_01_barcodes.tsv.gz |
34.9 Kb |
(ftp)(http) |
TSV |
| GSM8182738_CO_01_features.tsv.gz |
117.4 Kb |
(ftp)(http) |
TSV |
| GSM8182738_CO_01_matrix.mtx.gz |
33.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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