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Sample GSM7422461 Query DataSets for GSM7422461
Status Public on Jun 07, 2023
Title pancreas , Dox_25wks
Sample type SRA
 
Source name p48-Cre;LSL-KrasG12D;Rosa26R-LSL-rtTA-TetO-GnasR201C, on 0.0060% doxycycline diet
Organism Mus musculus
Characteristics tissue: pancreas
genotype: p48-Cre;LSL-KrasG12D;Rosa26R-LSL-rtTA-TetO-GnasR201C
treatment: 0.0060% doxycycline diet
age: 33 weeks
Extracted molecule total RNA
Extraction protocol Samples were flash frozen in liquid nitrogen, cryo-sectioned and H&E stained. After sectioning onto the Visium slides, sample processing was performed as described in the Visium 10x Genomics protocol for fresh-frozen tissue samples (15 minutes were used for permealization time)
Library preparation was performed as described in the Visium 10x genomics protocol for fresh-frozen tissue samples. After library preparation, samples were pooled and sequenced using a NextSeq 550 (Ilumina, CA, USA).
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model NextSeq 550
 
Description GNASmouse_onlydox_merge.rds
Data processing The sequencing outputs for all Visium datasets were preprocessed using SpaceRanger-v1.2.1 and mapped to either the latest human or mouse reference genome and the filtered matrices were converted to Seurat objects in R and used for downstream analyses.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz : Compressed tar archives include Filtered feature-barcode matrices from Space Ranger
Supplementary files format and content: spatial.tar.gz : Compressed tar archives include processed output from Space Ranger with spatial information
Supplementary files format and content: filtered_feature_bc_matrix.h5 : Filtered feature-barcode matrices in HDF5 format
Supplementary files format and content: GNASmouse_onlydox_merge.rds : RDS file both samples merged
Library strategy: Spatial Transcriptomics Visium 10x genomics
 
Submission date May 24, 2023
Last update date Jun 07, 2023
Contact name Anirban Maitra
E-mail(s) AMaitra@mdanderson.org
Organization name The University of Texas MD Anderson Cancer Center
Department Translational Molecular Pathology
Lab Maitra laboratory
Street address 6565 MD Anderson Blvd
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL21626
Series (2)
GSE233254 Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 Expression as a Driver of Gastric Differentiation and Indolent Biological Potential
GSE233317 Visium Spatial Transcriptomics of a murine model of IPMN
Relations
BioSample SAMN35345558
SRA SRX20502081

Supplementary file Size Download File type/resource
GSM7422461_25wksDox_filtered_feature_bc_matrix.h5 11.6 Mb (ftp)(http) H5
GSM7422461_25wksDox_filtered_feature_bc_matrix.tar.gz 30.6 Mb (ftp)(http) TAR
GSM7422461_25wksDox_spatial.tar.gz 11.6 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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