|
| Status |
Public on Mar 07, 2015 |
| Title |
CCSP/- mice on Doxycycline 3 weeks_2 |
| Sample type |
SRA |
| |
|
| Source name |
Lung_control
|
| Organism |
Mus musculus |
| Characteristics |
genotype: CCSP/-
tissue: lung
|
| 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 |
SKM2
|
| Data processing |
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns
|
| |
|
| Submission date |
Mar 06, 2015 |
| 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) |
| GSE66634 |
Alteration in the transcriptome of the lung during TGFα-induced pulmonary fibrosis |
|
| Relations |
| BioSample |
SAMN03393365 |
| SRA |
SRX907007 |
