|
| Status |
Public on Dec 21, 2022 |
| Title |
Human postmortem brain MTG region, control 1, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Human postmortem brain
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human postmortem brain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Human postmortem brain tissue from MTG region was cryosectioned at 10 µm using the Cryostat
Spatially resoved transcriptomics (SRT) was performed using the 10x Genomics Visium Spatial Gene Expression Kit (Slide Kit, Part# 1000188. Reagent Kit, Par# 1000189) by following established 10x protocal (CG000239 Rev A)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics Visium platform
|
| Data processing |
Raw sequencing data of six human MTG samples were obtained from Visium (BCL files) and processed with the SpaceRanger (v.1.2.2) software to generate FASTQ files via the SpaceRanger “mkfastq” function. FASTQ files were then aligned to and quantified to the expression matrix by using GRCh38 Reference-2020-A and the SpaceRanger “count” function. The two functions SpaceRanger “mkfastq” and “count” were used for demultiplexing sample and transcriptome alignment using default parameters.
Assembly: hg38
Supplementary files format and content: csv and png for spatial images, count matrix, and metadata
|
| |
|
| Submission date |
Dec 07, 2022 |
| Last update date |
Dec 21, 2022 |
| Contact name |
Cankun Wang |
| E-mail(s) |
cankun.wang@osumc.edu
|
| Phone |
6143784915
|
| Organization name |
The Ohio State University Wexner Medical Center
|
| Lab |
BMBL
|
| Street address |
281 W Lane Ave, Columbus, OH 43210
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE220442 |
Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer’s disease |
|
| Relations |
| BioSample |
SAMN32093362 |
| SRA |
SRX18525083 |
