|
| Status |
Public on Jul 20, 2023 |
| Title |
Human Pancreatic Biopsy 1 |
| Sample type |
SRA |
| |
|
| Source name |
Pancrease
|
| Organism |
Homo sapiens |
| Characteristics |
pathology: PDAC
tissue: Pancreatic
treatment: None
|
| Treatment protocol |
Fresh tissue sections without any treatment were used for the generation of sptaial library
|
| Growth protocol |
Tissue slices approximately 10um in size were cut from fresh frozen OCT embedded tissue sections and placed on the Visium slide.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated as per the instructions described in the 10X Genomics Spatial protocols with permeabilization time of around 24 minutes
Dual indexed library was prepared as per manufacturesrs instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Reference genomes (GRCh37) were constructed and gene expression values were extracted by using the 10x Genomics Space Ranger 1.3.0 software. For the removal of ambient RNA, SpotClean(31) was utilized. The R package Seurat v.4.0.1 was used for normalization by negative binomial regression, dimensionality reduction by Uniform Manifold Approximation and Projection (UMAP), and clustering of the data by a shared nearest neighbor modularity optimization based on the Louvain algorithm(54). Cell type annotations were performed manually and by using the databases Human Primary and Blueprint Encode in SingleR(55).
Assembly: GRCh37
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample; A gene expression matrix, a document of barcodes and a document of all features are included for each sample.
|
| |
|
| Submission date |
Jun 02, 2022 |
| Last update date |
Jul 21, 2023 |
| Contact name |
MENGJIE QIU |
| E-mail(s) |
Mengjie.Qiu@med.uni-heidelberg.de
|
| Phone |
015237253115
|
| Organization name |
Universitat Heidelberg
|
| Street address |
Im Neuenheimer 672
|
| City |
Heidelberg |
| State/province |
Choose State/Province |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE205354 |
Spatially resolved multi-omics single-cell analyses inform mechanisms of immune-dysfunction in pancreatic cancer |
|
| Relations |
| BioSample |
SAMN28828543 |
| SRA |
SRX15573068 |
