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| Status |
Public on Jan 11, 2024 |
| Title |
Spinal 7_spatial |
| Sample type |
SRA |
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| Source name |
Spinal cord
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Spinal cord
age: 51 years old
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Samples were immediately cleaned from the blood and connective tissue and frozen on dry ice. Spinal cord tissues were cut transversely, parts were embedded in optimal cutting temperature (OCT) compound for spatial transcriptomics. Cryosections were cut at 10-μm thickness and mounted onto the GEX arrays. Sections were placed on a Thermocycler Adaptor with the active surface facing up and were incubated at 37°C for 1 min. Then, sections were fixed with methyl alcohol at -20°C for 30 min, followed by staining with hematoxylin and eosin (H&E) (Eosin, Dako CS701, Hematoxylin Dako S3309, bluing buffer CS702).
Visum spatial libraries were constructed using Visum spatial Library construction kit (10x Genomics, PN-1000184) according to the manufacture’s introduction.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Basecalls performed using bcl2fastq tools
Visum spatial gene expression was processed using Visum spatial gene expression slide and Reagent Kit (10x Genomics, PN-1000184).
Assembly: GRCh38
Supplementary files format and content: Tab separated values files with barcode sequences corresponding to column indices, features corresponding to row indices
Library strategy: spatial transcriptomics
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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) |
| GSE243074 |
Spatial transcriptomics and single-nucleus RNA-sequencing reveal a transcriptomic atlas of human spinal cord [Spinal spatial] |
| GSE243077 |
Spatial transcriptomics and single-nucleus RNA-sequencing reveal a transcriptomic atlas of human spinal cord |
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| Relations |
| BioSample |
SAMN37383416 |
| SRA |
SRX21767134 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7778680_Spinal_7L_ch00.jpg.gz |
38.6 Mb |
(ftp)(http) |
JPG |
| GSM7778680_Spinal_spatial_7_filtered_feature_bc_matrix.tar.gz |
32.2 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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