|
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 |