|
Status |
Public on Jun 07, 2023 |
Title |
pancreas, Dox_15wks |
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: 23 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 |
SAMN35345559 |
SRA |
SRX20502080 |