|
| Status |
Public on May 16, 2022 |
| Title |
Normoglycemic PDX repl-2 |
| 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 |
SAMN25243359 |
| SRA |
SRX13898348 |
