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Sample GSM8097057 Query DataSets for GSM8097057
Status Public on Jun 19, 2024
Title uninjure, caudal 0.5mm from epicenter
Sample type SRA
 
Source name spinal cord
Organism Mus musculus
Characteristics tissue: spinal cord
treatment: sham
Treatment protocol a complete transection of the spinal cord of C57BL/6J mice at the tenth thoracic vertebra was performed.
Growth protocol Adult female mice of 8-9 weeks old were used in the SCI.
Extracted molecule polyA RNA
Extraction protocol Four consecutive spinal cord cryosections were cut at 20-μm thickness each and attached to one of the four capture areas of the Visium Spatial Gene Expression slides (10x Genomics, 1000184).
The spatial transcriptomics library was constructed according to the Visium Spatial Gene Expression Reagent Kits User Guide (10x Genomics, CG000239 Rev D).
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description Fresh frozen Spatial transcriptome sequencing
Data processing The raw Visium spatial RNA-seq data and histological H&E images were processed using the Space Ranger pipeline (v.1.0.0, 10x Genomics) to align and summarize unique molecular identifier (UMI) counts according to the reference genome “Mouse Genome mm10”.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression count of each tissue spot in Hierarchical Data Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spot
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tiisue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcode and the coordinates specifying spots
Library strategy: Spatial Transcriptomics
 
Submission date Feb 22, 2024
Last update date Jun 19, 2024
Contact name Guangdun Peng
Organization name Chinese Academy of Sciences
Department Guangzhou Institute of Biomedicine and Health
Lab Guangdun Peng's lab
Street address Kaiyuan Ave 190
City Guangzhou
ZIP/Postal code 510530
Country China
 
Platform ID GPL24247
Series (1)
GSE256397 A spatiotemporal molecular atlas of mouse spinal cord injury identifies a distinct astrocyte subpopulation and therapeutic potential of IGFBP2
Relations
BioSample SAMN40043396
SRA SRX23708661

Supplementary file Size Download File type/resource
GSM8097057_WT_sham_T_210323-aligned_fiducials.jpg.gz 1.3 Mb (ftp)(http) JPG
GSM8097057_WT_sham_T_210323-detected_tissue_image.jpg.gz 2.0 Mb (ftp)(http) JPG
GSM8097057_WT_sham_T_210323-filtered_feature_bc_matrix.h5 5.1 Mb (ftp)(http) H5
GSM8097057_WT_sham_T_210323-scalefactors_json.json.gz 178 b (ftp)(http) JSON
GSM8097057_WT_sham_T_210323-tissue_hires_image.png.gz 3.9 Mb (ftp)(http) PNG
GSM8097057_WT_sham_T_210323-tissue_lowres_image.png.gz 368.5 Kb (ftp)(http) PNG
GSM8097057_WT_sham_T_210323-tissue_positions_list.csv.gz 57.0 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA

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