|
| Status |
Public on Apr 10, 2014 |
| Title |
faireseq_cr25_treatment |
| Sample type |
SRA |
| |
|
| Source name |
Hepa-1_Cr25_FAIRE-seq
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Hepa-1c1c7 (Hepa-1)
cell type: mouse hepatoma cells
cell type: Hepa-1c1c7
treated with: Cr25 (25 µM CrK2O4)
|
| Treatment protocol |
Cells exposed acutely with high concentration Cr(VI) were treated with a final concentration of 25 µM CrK2O4 in their growth medium for 90 minutes. The medium of cells chronically exposed to low concentration Cr(VI) was supplemented with 0.5 μM CrK2O4 every 24 hours and the cells were grown for a total of 20 passages, approximately equivalent to 50 cell divisions. Control cells were passaged for the same number of passages in the absence of chromium.
|
| Growth protocol |
Hepa-1c1c7 (Hepa-1) mouse hepatoma cells from the American Tissue Culture Collection were maintained in α-minimum essential media (α-MEM, Gibco) with 5%(v/v) fetal bovine serum (Sigma) and 1% (v/v) antibiotic-antimycotic (Gibco) in a 5% CO2 humidified atmosphere at 37° C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
mRNA was extracted by TirReagent. Cell debris were removed by micro-centrifugation and free DNA was extracted from the collected supernatant by phenol/chloroform extraction. Under these conditions, DNA not crosslinked to proteins remains in the aqueous phase while the DNA crosslinked to proteins remains in the phenol phase.
Libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
processed data file: Cr25VsCtrl_peaks.bed
s_7
|
| 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 for RNA-Seq samples and bwa for FAIRE-Seq samples
For RNA-Seq samples, number of reads was calculated for each Entrez gene. Differential expression analysis was performed using Deseq.
For FAIRE-Seq samples, peaks were identified using MACS.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns for RNA-Seq samples. Bed files for FAIRE-Seq data.
|
| |
|
| Submission date |
Apr 09, 2014 |
| 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) |
| GSE56636 |
Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) Analysis Uncovers Broad Changes in Chromatin Structure Resulting from Hexavalent Chromium Exposure |
|
| Relations |
| BioSample |
SAMN02724746 |
| SRA |
SRX514232 |
