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Series GSE229006 Query DataSets for GSE229006
Status Public on May 10, 2024
Title New strategies for the identification of intronic variants related to splicing events in pancreas cancer [iCELL8]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Most clinical diagnostic settings and genomic research focus almost exclusively on coding regions and essential splice sites, mostly ignoring non-coding variants. Indeed, the investigation of intronic mis-splicing variants interpreting mechanisms to disease-associated splicing events requires both genomic and transcriptomic data. Unfortunately, there are not many datasets where both are available, leading to the understanding of intronic variants in diseases full of gaps. In this study, we present for the first time a full-length single nuclei RNA-sequencing (snRNA-Seq) approach improving the proper investigation of pathogenic mis-splicing intronic variants in pancreatic cancer showing its contribution to abnormal splicing changes and their transcriptional effects. Finally, we discuss the demands of further machine learning-based methods to process the growing number of single cell data and to enhance the precision and recall.
 
Overall design Bulk RNA Seq from PDAC compared to single nuclei RNA Seq
 
Contributor(s) Salinas G, Sitte M, Taylan Duman E, Hessmann E
Citation(s) 38800828
Submission date Apr 05, 2023
Last update date Jun 12, 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
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (10)
GSM7147714 KFO-Organoid_chip1
GSM7147715 KFO-Organoid_chip2
GSM7147716 KFO-Organoid_chip3
This SubSeries is part of SuperSeries:
GSE229007 New strategies for the identification of intronic variants related to splicing events in pancreas cancer
Relations
BioProject PRJNA952549

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE229006_Gene_info.csv.gz 1.0 Mb (ftp)(http) CSV
GSE229006_RAW.tar 126.2 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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