|
| Status |
Public on Aug 07, 2013 |
| Title |
cr_20_27_dmso-1 |
| Sample type |
SRA |
| |
|
| Source name |
Hepa-1 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Hepa-1
treatment: Grown for 20 passages with 0.5mM Cr(VI) followed by 5 without Cr(VI) and then treated for 8 hours with DMSO
passage: 25
|
| Treatment protocol |
Cells were grown in the presence of 0.5 mM Cr(VI) or grown normally for 20 or 25 passages. After Cr(VI) growth treatment cells were treated with 5 mM B[a]P
|
| Growth protocol |
Cells were grown in a-MEM with 5% FBS. Cells were passaged every 3 days.
|
| 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 |
Sample name: PJ-13
|
| 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 reads 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 |
Aug 06, 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) |
| GSE49571 |
Long-term exposure to low-concentrations of Cr(VI) induce DNA damage and disrupt the transcriptional response to benzo[a]pyrene |
|
| Relations |
| BioSample |
SAMN02303382 |
| SRA |
SRX331870 |
