NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5834177 Query DataSets for GSM5834177
Status Public on May 16, 2022
Title Hyperglycemic PDX repl-4
Sample type SRA
 
Source name Orthotopic tumor from KPC K8484 cells
Organism Mus musculus
Characteristics strain: C57BL/6
Treatment protocol Hyperglycemia was induced by allowing mice to drink high glucose content water (30% dextrose; abbreviated as D30)
Growth protocol Mice were maintained under pathogen-free conditions in the animal facility.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using PureLink RNA isolation (Life Technologies, 12183025) and treated with DNase (Life Technologies, AM2222).
Strandspecific RNA-seq library was prepared using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, Ipswich, MA) according to the manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Base calling and generation of FASTQ files were performed using standard CASAVA pipeline
RNA-seq quality was checked by running FastQC, and TrimGalore was used for adapter and quality trimming. RNA-seq reads were mapped against GRCm39 using STAR (v 2.7.0e) aligner with default parameters.
Differential gene expression analysis was performed using DESeq2.
Genome_build: GRCm39
Supplementary_files_format_and_content: Tab-delimited text files of normalized abundance measurements.
 
Submission date Jan 25, 2022
Last update date May 16, 2022
Contact name Ata Abbas
E-mail(s) ata.abbas@case.edu
Organization name Case Western Reserve University
Department Division of Hematology & Oncology
Street address 10900 Euclid Ave
City Cleveland
State/province OH
ZIP/Postal code 44106
Country USA
 
Platform ID GPL24247
Series (1)
GSE194369 Increased intra-tumoral glucose level is associated with enhanced chemotherapeutic response in pancreatic cancer
Relations
BioSample SAMN25243352
SRA SRX13898355

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap