|
Status |
Public on Jan 14, 2025 |
Title |
OAd-IFN, Less-responder-1 |
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_B1 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
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|
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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 |
SAMN46126737 |
SRA |
SRX27271439 |
Supplementary file |
Size |
Download |
File type/resource |
GSM8714859_OAd_IFN_1.aligned_fiducials.jpg.gz |
1.7 Mb |
(ftp)(http) |
JPG |
GSM8714859_OAd_IFN_1.barcodes.tsv.gz |
16.4 Kb |
(ftp)(http) |
TSV |
GSM8714859_OAd_IFN_1.detected_tissue_image.jpg.gz |
789.5 Kb |
(ftp)(http) |
JPG |
GSM8714859_OAd_IFN_1.features.tsv.gz |
155.0 Kb |
(ftp)(http) |
TSV |
GSM8714859_OAd_IFN_1.matrix.mtx.gz |
22.6 Mb |
(ftp)(http) |
MTX |
GSM8714859_OAd_IFN_1.scalefactors_json.json.gz |
177 b |
(ftp)(http) |
JSON |
GSM8714859_OAd_IFN_1.tissue_hires_image.png.gz |
5.6 Mb |
(ftp)(http) |
PNG |
GSM8714859_OAd_IFN_1.tissue_lowres_image.png.gz |
512.1 Kb |
(ftp)(http) |
PNG |
GSM8714859_OAd_IFN_1.tissue_positions.csv.gz |
56.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
Raw data are available in SRA |