|
| Status |
Public on Feb 08, 2020 |
| Title |
Sample 127459: WTICD3 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Cricetulus griseus |
| Characteristics |
genotype: Beta1-ICD
tissue: lung
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Incubator; 37 degrees C and 5% CO2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiagen RNeasy Plus Mini Kit
stranded TruSeq mRNA (poly A selection).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-Seq was performed using Illumina NovaSeq-6000, paired-end 50 cycle
Base-calling software: Illumina Casava 1.8 software
Alignment was conducted using TopHat (version 2.0.13) and Bowtie (version 2.2.1), with default parameter settings, with exception of: "---b2-very-sensitive" for additional search of valid alignments
Expression quantitation was performed with HTSeq
Genome_build: CriGri_1.0
Supplementary_files_format_and_content: htseq raw counts
|
| |
|
| Submission date |
Sep 05, 2019 |
| Last update date |
Apr 06, 2020 |
| Contact name |
Bioinformatics Core |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Michigan
|
| Street address |
BRCF Bioinformatics Core, 2800 Plymouth Rd
|
| City |
Ann Arbor |
| State/province |
Mi |
| ZIP/Postal code |
48109-2800 |
| Country |
USA |
| |
|
| Platform ID |
GPL27425 |
| Series (1) |
| GSE136927 |
Voltage-gated sodium channel (VGSC) beta1 subunit-intracellular domain (Beta1-ICD) overexpression in Chinese hamster lung cells |
|
| Relations |
| BioSample |
SAMN12699082 |
| SRA |
SRX6805923 |
