|
| Status |
Public on Dec 03, 2013 |
| Title |
ARRY-3:CCSP/TGFalpha mice on Doxycycline 8 weeks |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB/N
cell group: MAPK inhibitor
treatment: Treated
day: 8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
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 |
Hardie-29_TAGCTT_L005_R1_combined
|
| Data processing |
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm9 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited rpkm values with genes in rows and samples in columns
|
| |
|
| Submission date |
Dec 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Mario Medvedovic |
| Organization name |
University of Cincinnati
|
| Department |
Department of Environmental Health
|
| Lab |
Laboratory for Statistical Genomics and Systems Biology
|
| Street address |
3223 Eden Av. ML 56
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45267-0056 |
| Country |
USA |
| |
|
| Platform ID |
GPL15103 |
| Series (1) |
| GSE52854 |
Inhibition of MEK and PI3K alone or in combination alters the transcriptome of the lung during TGFα-induced pulmonary fibrosis |
|
| Relations |
| BioSample |
SAMN02428166 |
| SRA |
SRX385532 |
