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Sample GSM7871986 Query DataSets for GSM7871986
Status Public on Nov 04, 2023
Title Sample2: Atm intact, status post focal brain irradiation
Sample type RNA
 
Source name Primary p53/H3.3K27M diffuse midline glioma-bearing mouse brain
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
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.
Label Xenium Mouse Probe Set
Label protocol Xenium Mouse Probe Set
 
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.
Scan protocol Xenium In Situ Analyzer
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
 
Submission date Oct 30, 2023
Last update date Nov 04, 2023
Contact name Zachary J Reitman
E-mail(s) zjr@duke.edu
Phone 4847168416
Organization name Duke University
Street address B227 LSRC, 308 Research Dr
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL33896
Series (1)
GSE246584 Ataxia-telangiectasia mutated (Atm) disruption sensitizes spatially-directed H3.3K27M/TP53 diffuse midline gliomas to radiation therapy

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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