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| Status |
Public on Jan 11, 2024 |
| Title |
Spinal_snRNA-seq_4 |
| Sample type |
SRA |
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| Source name |
Spinal cord
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Spinal cord
age: 59 years old
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Nuclei were isolated using a Nucleus Isolation Kit (catalogue no. 52009-10, SHBIO, China) according to the manufacturer’s instructions. Nuclei suspension was loaded onto a Chromium single cell controller (10x Genomics) to generate single-nucleus gel beads in the emulsion (GEM) using single cell 3' Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074) according to the manufacturer’s protocols.
The 10x snRNA-seq library was established using Single Cell 3’ Library and Gel Bead Kit V3.1, according to the manufacturer’s instructions.
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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 |
220719A_spinal_4L
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| Data processing |
Basecalls performed using bcl2fastq.gz tools
Raw single-cell RNA-seq data were processed using 10X Genomics Cell Ranger (v5.0.1), including demultiplexing the fastq.gz reads, aligning them to the human reference genome (GRCh38, v3.0.0, from 10X Genomics), and counting the unique molecular identifier (UMI) (by using ‘cellranger count’ function).
Assembly: GRCh38
Supplementary files format and content: Tab separated values files with barcode sequences corresponding to column indices, features corresponding to row indices
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| Submission date |
Sep 13, 2023 |
| Last update date |
Jan 11, 2024 |
| Contact name |
Donghang Zhang |
| Organization name |
West China Hospital of Sichuan University
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| Street address |
No.37, guoxue lane, wuhou district, chengdu city, sichuan province
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| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE243076 |
Spatial transcriptomics and single-nucleus RNA-sequencing reveal a transcriptomic atlas of human spinal cord [Spinal snRNA-seq] |
| GSE243077 |
Spatial transcriptomics and single-nucleus RNA-sequencing reveal a transcriptomic atlas of human spinal cord |
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| Relations |
| BioSample |
SAMN37385915 |
| SRA |
SRX21771589 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7779046_Spinal_4_filtered_feature_bc_matrix.tar.gz |
75.7 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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