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| Status |
Public on Jan 17, 2023 |
| Title |
DMG5_short read spatial transcriptomics |
| Sample type |
SRA |
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| Source name |
DMG5
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| Organism |
Homo sapiens |
| Characteristics |
replicates: DMG5
integrated diagnosis: Diffuse midline glioma, H3K27M-mutant
primary/ recurrent: Primary
who grade: IV
p53 ihc: Positive
idh1 mutant: No
tert mutant (c228t or c250t): No
mgmt promoter methylation: No
h3f3a mutant: Yes
hist1h3b mutant: No
gfap ihc: Positive
oligo2 ihc: Positive
ki_67 labeling index (cc): 30%
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| Extracted molecule |
total RNA |
| Extraction protocol |
Surgically removed human glioma samples were snap-frozen in isopentane/liquid nitrogen, embedded in pre-chilled OCT (Tissue-Tek O.C.T. Compound, SAKURA), and then cryosectioned into 10 μm sections at -20℃. Sections with obvious tumor areas were collected. Frozen tissue sections on Visium Tissue Optimization Slides were fixed with pre-chilled methanol. H&E staining was performed according to the Tissue Optimization Guide (CG000238 Rev A, 10X Genomics), and subjected to bright-field imaging under a Leica DM6B microscope. Sections were permeabilized with 0.1N HCl at different durations. The released mRNA was captured by probes on the slides, and reverse transcribed to cDNA marked by fluorescently labeled nucleotides. Tissue was then removed from the slides with a digestive enzyme, leaving the fluorescently labeled cDNA, which was visualized under a Leica DM6B microscope. Based on the signal intensity, we determined the optimal permeabilization duration for human brain tumor samples was 12min
Follwed by protocol of spatial transcriptomics based 10X technology
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
ST RNA-seq alignment process was completed by spaceranger (version 1.1.0)
Seurat V4 workflow
Genome_build: hg38
Supplementary_files_format_and_content: spaceranger workflow outcome
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| Submission date |
Jan 25, 2022 |
| Last update date |
Jan 17, 2023 |
| Contact name |
Yuan Wang |
| E-mail(s) |
wangyuan@scu.edu.cn
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| Organization name |
Sichuan university
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| Street address |
No.17 People's South Road
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| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE194329 |
Spatial multi-omics reveals vulnerabilities of radial glia-like cancer-initiating cells within distinct ecosystems of pediatric and adult malignant gliomas |
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| Relations |
| BioSample |
SAMN25259538 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5833532_DMG5_spaceranger_out.tar.gz |
167.2 Mb |
(ftp)(http) |
TAR |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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