|
| Status |
Public on Jul 20, 2023 |
| Title |
Patinet 7 Adjacent Normal Tissue |
| Sample type |
SRA |
| |
|
| Source name |
Human Pancreatic Biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
pathology: Adjacent Normal Tissue
tissue: Pancreatic
treatment: None
cell type: CD45+ Single cells from Pancreas
|
| Treatment protocol |
Human Pancreatic tissue samples were collected from treatmnet naïve patinets.
|
| Growth protocol |
Pancreatic tumor tissues were immediately processed, Single cells were isolated, quantified and stored in FBS+20%DMSO till further processing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929). Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing.
Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequencing was performed on an Illumina HiSeq 4000.
De-multiplexing and barcode processing were performed using the Cell Ranger Software Suite (Version 4.0.0). Specifically, the reads were aligned to the human hg19 using CellRanger v4.0.0. Finally, a gene-barcode matrix containing the cell barcodes and gene expression counts for each individual sample was generated by counting the single-cell 3’ UMIs.
The gene barcode matrix was then imported to Seurat v3 in R (v4.0.2). Data were filtered to include cells with at least 100 genes and no more than 25% mitochondrial genes. Then, the data was normalized, scaled and integrated within Seurat v3 to remove batch effects across samples.
Assembly: hg19
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 |
May 29, 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 |
GPL20301 |
| Series (1) |
| GSE205049 |
Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer |
|
| Relations |
| BioSample |
SAMN28741194 |
| SRA |
SRX15494112 |
