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Sample GSM8714861 Query DataSets for GSM8714861
Status Public on Jan 14, 2025
Title OAd-IFN, Less-responder-2
Sample type SRA
 
Source name HP-1 pancreatic cancer cell line-derived tumor
Organism Mesocricetus auratus
Characteristics tissue: HP-1 pancreatic cancer cell line-derived tumor
treatment: OAd-IFN
Treatment protocol Twelve days after tumor cell inoculation, tumors were treated intratumorally with OAd-IFN or OAd-Luc (2.5x10^9 pfu/50 µL/injection) every three days for a total of four injections.
Growth protocol HP-1 pancreatic cancer tumors were established by injecting 2 x 10^6 cells in the left flanks of 6-7-week-old male Syrian hamsters.
Extracted molecule total RNA
Extraction protocol Tumors were snap-frozen in isopentane and liquid nitrogen, embedded in O.C.T. compound. A 10 µm section from each sample was placed within a capture area on the Visium Spatial slide.
Library construction was performed following the manufacturer’s instruction (CG000239, Visium Spatial Gene Expression Reagent Kits, 10x Genomics).
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description Library name: V13F06-354_D1
Fresh frozen spatial transcriptome sequencing
Data processing A reference was created using the combined MesAur1.0 and the Human Adenovirus 5 isolate HAdV-C5/USA/26107/2012 (accession GCA_029237105.1) genomes with SpaceRanger 2.0.0
Raw fastq files were aligned to the reference and the gene expression was estimated using SpaceRanger 2.0.0 with default parameters
Gene - barcode matrices of the SpaceRanger filtered data were merged and analyzed with custom R scripts
Assembly: MesAur1.0
Supplementary files format and content: aligned_fiducials.jpg: generated by SpaceRanger
Supplementary files format and content: barcodes.tsv.gz : SpaceRanger filtered barcodes
Supplementary files format and content: detected_tissue_image.jpg: generated by SpaceRanger
Supplementary files format and content: features.tsv.gz: genes included in the SpaceRanger count command
Supplementary files format and content: matrix.mtx.gz: resulting gene by barcode count matrix
Supplementary files format and content: scalefactors_json.json: generated by SpaceRanger
Supplementary files format and content: tissue_hires_image.png: high resolution image of the tissue section
Supplementary files format and content: tissue_lowres_image.png: low resolution image of the tissue section
Supplementary files format and content: tissue_positions.csv: lilst of barcode coordinates
Supplementary files format and content: merged.rds: compressed object containing the 4 tissue samples merged and analyzed with Seurat 4.3.0.1
Library strategy: Spatial Transcriptomics
 
Submission date Jan 07, 2025
Last update date Jan 14, 2025
Contact name Julia Davydova
E-mail(s) davyd003@umn.edu
Organization name University of Minnesota
Department Surgery
Lab Davydova Lab
Street address 420 Delaware St. SE, MMC 195
City Minneapolis
State/province MN
ZIP/Postal code 55455
Country USA
 
Platform ID GPL28997
Series (1)
GSE286008 Spatial transcriptomics reveals the immunomodulatory activities of an oncolytic adenovirus armed with a type I interferon in a replication-permissive immunocompetent pancreatic cancer model
Relations
BioSample SAMN46126735
SRA SRX27271441

Supplementary file Size Download File type/resource
GSM8714861_OAd_IFN_3.aligned_fiducials.jpg.gz 1.7 Mb (ftp)(http) JPG
GSM8714861_OAd_IFN_3.barcodes.tsv.gz 20.8 Kb (ftp)(http) TSV
GSM8714861_OAd_IFN_3.detected_tissue_image.jpg.gz 751.6 Kb (ftp)(http) JPG
GSM8714861_OAd_IFN_3.features.tsv.gz 155.0 Kb (ftp)(http) TSV
GSM8714861_OAd_IFN_3.matrix.mtx.gz 31.5 Mb (ftp)(http) MTX
GSM8714861_OAd_IFN_3.scalefactors_json.json.gz 176 b (ftp)(http) JSON
GSM8714861_OAd_IFN_3.tissue_hires_image.png.gz 5.6 Mb (ftp)(http) PNG
GSM8714861_OAd_IFN_3.tissue_lowres_image.png.gz 508.0 Kb (ftp)(http) PNG
GSM8714861_OAd_IFN_3.tissue_positions.csv.gz 57.0 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA

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