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Sample GSM4293555 Query DataSets for GSM4293555
Status Public on Jul 31, 2020
Title Human PDAC
Sample type SRA
 
Source name Pancreas tumor cells
Organism Homo sapiens
Characteristics cell type: Pancreas tumor cells
Extracted molecule total RNA
Extraction protocol The pancreas was removed and washed and the acinar cells were isolated using 10mg collagenase P and 0.2mg trypsin inhibitor live cells were isolated by using MACS dead cells removal kit (Miltenyi Biotech #130-090-101) with MACS MS columns. The stomach was removed and the cells isolated first with dissociation buffer containing 2mg collagenase P and then with dissociation buffer containing 5 mg Dispase II (Roche #D4693) at 37C.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing The Illumina bcl2fastq (v1.8.3) was used to convert Illumina base call files (bcl) to FASTQ files. Alignment of FASTQs to the mm10/hg19 reference was done by Cell Ranger (v3.0, 10X Genomics). mm10/hg19 reference downloaded from 10x (v1.2.0, 10X Genomics) and a tdTomato sequence gene was added to mm10. Library constriction was performed according to standard 3’ 10x genomics kit and sequence using illumine Hi-Seq and Next-seq machine.
First analysis of the data was done using R package Seurat(v2.3.4). Raw transcript counts gene-cell matrices were filtered to remove cells with: (i) fewer than 200 transcripts, (ii) total UMI counts lower then 1000,(iii) cells with more than 5% or 10% mitochondrial genes for 10x chemistry v2 or v3, respectively. In addition, genes that expressed in less than 3 cells were removed. The gene-cell matrices were then normalized such that the number of UMIs in each cell was divided by the total UMI counts, multiplied by 10,000 and log transformed. Data was scaled using ScaleData Function from Seurat to remove unwanted sources of variation, so that cell-cycle heterogeneity or UMI counts does not contribute to PCA or downstream analysis.
Genome_build: mm10 and added tdTomato gene
Genome_build: hg19
Supplementary_files_format_and_content: All processed data merged are tab-delimited csv file from raw data of the Seurat [email protected] and can be distinguish by barcode name.
Supplementary_files_format_and_content: rows are genes, columns are cell barcodes and the values are normalized and log transformed
 
Submission date Feb 03, 2020
Last update date Jul 31, 2020
Contact name Oren Parnas
E-mail(s) [email protected]
Organization name Hebrew University
Department Immunology
Lab Oren Parnas Lab
Street address Faculty of Medicine, Ein-Kerem medical center
City Jerusalem
ZIP/Postal code 91120
Country Israel
 
Platform ID GPL16791
Series (1)
GSE141017 Single cell transcriptomes of pancreatic pre-invasive lesions and cancer reveal acinar metaplastic cells’ heterogeneity
Relations
BioSample SAMN13978880
SRA SRX7670020

Supplementary file Size Download File type/resource
GSM4293555_Human.csv.gz 12.6 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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