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| Status |
Public on Oct 24, 2024 |
| Title |
PID 0 |
| Sample type |
SRA |
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| Source name |
spinal cord
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| Organism |
Mus musculus |
| Characteristics |
tissue: spinal cord
cell line: none
cell type: microglia
genotype: wild type
treatment: sham
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| Treatment protocol |
Spared nerve injury (SNI; PID 3, PID 7, PID 14) or sham surgeries were conducted.
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| Growth protocol |
none
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| Extracted molecule |
total RNA |
| Extraction protocol |
Spinal cords were harvested from sham or SNI mice at PID 3, PID 7 and PID 14 in ice-cold PBS solution. Cells in the ipsilateral L4-L6 spinal cord dorsal horns were isolated, homogenized using loose and tight pestles in 1 mL ice-cold Ca2+/Mg2+-free HBSS for 15-20 times by simultaneously rotation. The homogenate was passed through a pre-wet 70 μm mesh cell strainer (BD Biosciences, USA) and spun down at 300 g for 5 min at 4 °C. The cell pellet was resuspended in 40% Percoll solution (GE Healthcare #GE17-0891-01) and centrifuged at 500 g for 15 min at 4 °C. Cells in pellet resuspended and incubated in ice-cold FACS buffer and then incubated in ice-cold FACS buffer containing Cd11b-PE (BioLegend, #101208) at a final dilution of 1:300 for 30 min. The cells were then washed with 1 mL of ice-cold FACS buffer. After centrifuging at 800 g for 5 min, the pellet was resuspended in ice-cold FACS buffer. Living cells exhibiting high fluorescence levels of Cd11b were sorted by FACS using a 70 μm chip on the FACSAriaTM Fusion Platform (BD Biosciences, Carlsbad, CA, USA) with Purity mode.
Single-cell RNA-Seq libraries was prepared using Chromium Single Cell 3’ Library and Gel Bead Kit v3.0 (10X Genomics #PN-1000075), Chromium Single Cell 3′ Library Construction Kit v3.0 (10X Genomics #PN-1000078), Chromium Chip B Single Cell kit (10X Genomics #PN-1000154), Chromium i7 Multiplex Kit (10X Genomics #PN-120262) and chromium controller, following manufacturer’s instruction. The samples were sequenced on an DNBSEQ-T7 sequencer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
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| Data processing |
Cell Ranger (10× Genomics, US)
Seurat suite (version 3.0.1) in R (version 3.5.1)
clustering
t-SNE, cluster visualization
DEG, GO
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell
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| Submission date |
Oct 26, 2023 |
| Last update date |
Oct 24, 2024 |
| Contact name |
Yidan ZOU |
| E-mail(s) |
zouyidan123@outlook.com
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| Phone |
92962600
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| Organization name |
The Chinese university of Hong Kong
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| Street address |
Rm902, LKS medical Sciences Bldg, PWH, Shatin , HK, 902
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| City |
Shatin |
| State/province |
State |
| ZIP/Postal code |
nil |
| Country |
Hong Kong |
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| Platform ID |
GPL28330 |
| Series (1) |
| GSE246288 |
Single-cell RNA sequencing reveals cellular heterogeneity of spinal microglia in neuropathic pain |
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| Relations |
| BioSample |
SAMN37997312 |
| SRA |
SRX22238648 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7866244_SA_raw_feature_bc_matrix.tar.gz |
101.1 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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