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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 04, 2024 |
| Title |
Ctrl, snRNAseq |
| Sample type |
SRA |
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| Source name |
Cerebral cortex
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| Organism |
Mus musculus |
| Characteristics |
tissue: Cerebral cortex
cell type: Nerve cell
genotype: none
treatment: PBS were injected into male Balb/c mice subjected to controlled cortical impact injury through the tail vein. Next, we extracted the damaged cerebral cortex tissue.
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
The damaged cerebral cortex tissues were harvested from Balb/c mice and were washed in pre-cooled PBSE (PBS buffer containing 2 mM EGTA). Nuclei isolation was carried out using GEXSCOPE® Nucleus Separation Solution (Singleron Biotechnologies, Nanjing, China) refer to the manufacturer's product manual. Isolated nuclei were resuspended in PBSE to 106 nuclei per 400μl, fltered through a 40μm cell strainer, and counted with Trypan blue. Nuclei enriched in PBSE were stained with DAPI (1:1,000) (TermoFisher Scientifc, D1306). Nuclei were defned as DAPI-positive singlets.
The concentration of singlenucleus suspension was adjusted to 3-4 × 10^5 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies). The resulting snRNA-seq libraries were sequenced on an Illumina novaseq 6000 instrument with 150 bp paired end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
none
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| Data processing |
Raw reads were processed to generate gene expression profiles using CeleScope v1.15.0 (Singleron Biotechnologies) with default parameters. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCm38 (mm10)transcriptome using STAR(v2.6.1b). Uniquely mapped reads were then assigned to geneswith FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis.
Assembly: mm10
Supplementary files format and content: UMI count for each cell in mtx format and cell barcodes/genes/metadata in csv format
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| Submission date |
Aug 30, 2024 |
| Last update date |
Sep 04, 2024 |
| Contact name |
xiangyu Gao |
| E-mail(s) |
gaoxiangyu@fmmu.edu.cn
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| Phone |
86-029-84775567
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| Organization name |
Fourth Military Medical University
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| Department |
Department of Neurosurgery, Xijing Hospital
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| Street address |
Changle Xi Road
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| City |
Xi'an |
| ZIP/Postal code |
710032 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE276065 |
Gene expression file at single cell level of nerve cells in damaged areas of the cerebral cortex in mice with traumatic brain injury |
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| Relations |
| BioSample |
SAMN43429902 |
| SRA |
SRX25920426 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8490539_Ctrl.loom.gz |
121.9 Mb |
(ftp)(http) |
LOOM |
| GSM8490539_Ctrl_barcodes.tsv.gz |
78.0 Kb |
(ftp)(http) |
TSV |
| GSM8490539_Ctrl_genes.tsv.gz |
246.5 Kb |
(ftp)(http) |
TSV |
| GSM8490539_Ctrl_matrix.mtx.gz |
34.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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