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Sample GSM7147720 Query DataSets for GSM7147720
Status Public on May 10, 2024
Title KFO-PDX_chip3
Sample type SRA
 
Source name PDAC
Organism Homo sapiens
Characteristics tissue: PDAC
Extracted molecule total RNA
Extraction protocol Lysis according to iCELL8 single cell system
Nextera based iCELL8 single nuclei
full length cDNA/ iCELL8 Takara
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Sequence images were transformed with Illumina software BaseCaller to BCL files, which were converted to fastq files with bcl2fastq v2.20.0.422
Sequences were demultiplexed using Cogent version 1.0 from TAKARA
Using cutadapt version 2.5, sequences were removed if they had more than 70% N’s, had bases with quality <20 in the 3’ end trimmed, had N bases trimmed at both ends, were trimmed for various adapters (polyA, polyT, Illumina sequencing regular and reverse complement primers, polyG, SINGV6 and SMART) and were finally discarded if the trimmed reads was shorter than 15 bases
Trimmed sequences were aligned to the genome referencehg38sequenceusing the STAR aligner 2.7.2b using default parameters
Primary, unstranded aligned sequences were counted for all genes using featureCounts version 1.6.4
Gene matrices, metadata and gene info files were generated for all cells in all samples by Cogent version 1.0 from Takara
Assembly: hg38 gene version 107
Supplementary files format and content: GeneMatrix – CSV files with read count per gene for each cell (10 files, one per chip)
Supplementary files format and content: Metadata – CSV files with sample affiliation for each cell and number of reads at different steps of the analysis (10 files, one per chip)
Supplementary files format and content: Gene_info – CSV file with gene information for which reads were counted
 
Submission date Apr 05, 2023
Last update date May 10, 2024
Contact name Gabriela Salinas
E-mail(s) Gabriela.Salinas-Riester@medizin.uni-goettingen.de
Organization name Universitaetsmedizin Goettingen
Department Department of Pathology
Lab NGS Integrative Genomics
Street address Kreuzbergring 57
City Goettingen
State/province Lower-Saxony
ZIP/Postal code 37075
Country Germany
 
Platform ID GPL11154
Series (2)
GSE229006 New strategies for the identification of intronic variants related to splicing events in pancreas cancer [iCELL8]
GSE229007 New strategies for the identification of intronic variants related to splicing events in pancreas cancer
Relations
BioSample SAMN34080784
SRA SRX19879600

Supplementary file Size Download File type/resource
GSM7147720_KFO-PDX_chip3_barcodes.csv.gz 2.9 Kb (ftp)(http) CSV
GSM7147720_KFO-PDX_chip3_genematrix.csv.gz 8.5 Mb (ftp)(http) CSV
GSM7147720_KFO-PDX_chip3_metadata.csv.gz 35.7 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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