|
| Status |
Public on Feb 02, 2015 |
| Title |
8-oxoG challenge - 60 min |
| Sample type |
SRA |
| |
|
| Source name |
Lung, 8-oxoG, 60min
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: Balb/cJ
genotype/variation: wild type
gender: female
age: 8 weeks
tissue: lung
treatment: 8-oxoguanine
time point: 60min
|
| Treatment protocol |
Mice (5 per group) were intranasally challenged with 8-oxoguanine (1 µM, 60 µl) for 30, 60 and 120 min. Control group mice were intranasally challenged with saline (60 µl).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy Mini Kit (Qiagen) followed by DNase I treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
Sample type: test
|
| Data processing |
Base call conversion to sequence reads was done with Casava-1.8.2 software (Illumina).
Sequence data were analyzed with the Bowtie 2.
Splice junction mapping was performed with TopHat.
Assembly and estimation of abundance was performed with GFOLD.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: *RPKM.txt: Tab-delimited text files that include abundance measurements (RPKM values) for each Sample.
Supplementary_files_format_and_content: All_samples_fold_change.txt: Tab-delimited text file that includes fold changes (test/control).
|
| |
|
| Submission date |
Sep 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Istvan Boldogh |
| Organization name |
UNIVERSITY OF TEXAS MEDICAL BRANCH
|
| Department |
Microbiology & Immunology
|
| Street address |
301 UNIVERSITY BLVD.
|
| City |
Galveston |
| State/province |
Texas |
| ZIP/Postal code |
77555 |
| Country |
USA |
| |
|
| Platform ID |
GPL15103 |
| Series (1) |
| GSE61095 |
OGG1-initiated DNA base excision repair is linked to inflammatory gene expression and lung inflammation |
|
| Relations |
| BioSample |
SAMN03018623 |
| SRA |
SRX694867 |
