|
| Status |
Public on Jun 07, 2023 |
| Title |
LG_3 |
| Sample type |
SRA |
| |
|
| Source name |
Low grade IPMN
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Low grade IPMN
gender: M
age: 56
|
| 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).
Spatial Transcriptomics Visium 10x genomics
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
10x Genomics
scMC.merge.all.final.rds
scMC.all.3areas.final.rds
All_RCTD.final.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.
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: scMC.merge.all.final.rds : RDS file with all the samples combined
Supplementary files format and content: scMC.all.3areas.final.rds : RDS file with selected spots covering the epithelial lining of the IPMN and cancer lesions (“epilesional”); the adjacent PME (‘juxtalesional”), corresponding to two layers of spots (~200 µm) surrounding the lesion; and an additional two layers of spots located further out of the lesions (“perilesional”)
Supplementary files format and content: All_RCTD.final.rds : RDS file with RCTD weights
|
| |
|
| 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 |
GPL18573 |
| 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 |
| GSE233293 |
Visium Spatial Transcriptomics expression profiles from IPMN samples of the pancreas |
|
| Relations |
| BioSample |
SAMN35345997 |
| SRA |
SRX20502564 |
