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| Status |
Public on Nov 04, 2023 |
| Title |
Sample2: Atm intact, status post focal brain irradiation |
| Sample type |
RNA |
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| Source name |
Primary p53/H3.3K27M diffuse midline glioma-bearing mouse brain
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| Organism |
Mus musculus |
| Characteristics |
genotype: NestinTVA; p53FL/FL; H3f3aloxP-Stop-loxP-K27M-Tag/+;AtmFL/+
treatment: 10 Gy x 3 focal brain irradiation
strain: C57BL/6
tissue: Primary p53/H3.3K27M diffuse midline glioma-bearing mouse brain
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor-bearing brains subjected to Xenium ISS were detected by in vivo imaging 37-48 days after birth and collected seven days after tumor detection, either after three daily treatments of 10 Gy initiated within two days of tumor detection, or mock treatment.
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| Label |
Xenium Mouse Probe Set
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| Label protocol |
Xenium Mouse Probe Set
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| Hybridization protocol |
5um FFPE tissue sections are placed on a 10x Genomics Xenium slide and dried at room temperature. Once dried, tissue slides are incubated at 60C for 2 hours and then deparaffinized and decrosslinked. Briefly, sections are deparaffinized via xylene immersion to solubilize the paraffin, ethanol to remove the solubilized paraffin and slowly hydrate the tissue, and then immersed in water to remove residual ethanol. Once hydrated, tissues slides are decrosslinked. Briefly, tissue slides are inserted into 10x Genomics Xenium slide cassettes. Decrosslinking buffer is then added to the well created by the cassette and incubated. After incubation, buffer is removed and the sample is washed. Tissue is then processed through Hybridization, Ligation & Amplification protocols. Briefly, pre-designed probe panels, with optional custom probe content, are added to the tissue. Each circularizable DNA probe contains two regions that hybridize to target RNA and a third region that encodes a gene-specific barcode. The two ends of the probes bind the target RNA and are ligated to generate a circular DNA probe. Following ligation, the circularized probe is amplified, producing multiple copies of the gene-specific barcode for each target. Prepared tissue slides are then loaded for imaging on the Xenium Analyzer for in situ analysis. Fluorescently-labeled oligos bind to the amplified DNA probes. Cyclical rounds of fluorescent probe hybridization, imaging, and removal generate optical patterns specific for each barcode, which are converted into a gene identity. Identified transcripts are then visualized using Xenium Explorer software.
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| Scan protocol |
Xenium In Situ Analyzer
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| Data processing |
Image pre-processing, puncta detection, transcript decoding and quality score assignment was perofrmed via on-board analysis software Xenium Analyzer.
Xenium analyzer performed read quantification and generated cell by gene count matrix.
*matrix.mtx.gz: Gene-barcode matrix in Market Exchange Format (MEX). Columns correspond to individual cells(barcodes), while rows correspond to genes.
*features.tsv.gz: Gene feature info
*barcodes.tsv.gz: Barcode sequences that correspond to column indices in matrix.mtx.
*transcript.csv.gz: Transcript quality and localization info
*cells.csv.gz: Cell summary and transcript count info for each identified cell
*morpholoy.ome.tif.gz: Image file in tif format
*gene_panel.json: JSON file
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| Submission date |
Oct 30, 2023 |
| Last update date |
Nov 04, 2023 |
| Contact name |
Zachary J Reitman |
| E-mail(s) |
zjr@duke.edu
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| Phone |
4847168416
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| Organization name |
Duke University
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| Street address |
B227 LSRC, 308 Research Dr
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
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| Platform ID |
GPL33896 |
| Series (1) |
| GSE246584 |
Ataxia-telangiectasia mutated (Atm) disruption sensitizes spatially-directed H3.3K27M/TP53 diffuse midline gliomas to radiation therapy |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM7871986_Sample2_barcodes.tsv.gz |
570.7 Kb |
(ftp)(http) |
TSV |
| GSM7871986_Sample2_cells.csv.gz |
11.9 Mb |
(ftp)(http) |
CSV |
| GSM7871986_Sample2_features.tsv.gz |
3.9 Kb |
(ftp)(http) |
TSV |
| GSM7871986_Sample2_gene_panel.json.gz |
5.7 Kb |
(ftp)(http) |
JSON |
| GSM7871986_Sample2_matrix.mtx.gz |
70.4 Mb |
(ftp)(http) |
MTX |
| GSM7871986_Sample2_morphology.ome.tif.gz |
8.0 Gb |
(ftp)(http) |
TIFF |
| GSM7871986_Sample2_transcripts.csv.gz |
1.7 Gb |
(ftp)(http) |
CSV |
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