|
| Status |
Public on Mar 08, 2017 |
| Title |
DNA methylation in iAsT cells |
| Sample type |
SRA |
| |
|
| Source name |
Lung Epithelial
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iAs-transformed lung epithelial cells
|
| Treatment protocol |
Cells were treated with 0.5 uM Sodium Arsenite for 36 days until transformation
|
| Growth protocol |
Cell cultures were incubated at 37 degree with humidified air and 5% CO2. Cells were harvested after each treatment. Cells were grown ensuring that 95% of the cells were viable. Harvested cells were centrifuged for five minutes at 200 X g.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using Qiagen Dneasykit according to manusfacturers instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw data files had their adapters removed using trim_galore, quality trimming was also done, reads shorter than 20 bp were discarded
Pre-processed fastq files were aligned to human hg19 using bismark
Methylation calling was done on the bamfiles to create browser tracks for CpG, CHG, and CHH sites for each sample, these are in bigbed format
Genome_build: hg19
Supplementary_files_format_and_content: bigbed, browser tracks that contain methylation count and total count of reads per site
|
| |
|
| Submission date |
Jul 30, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yvonne Nsokika Fondufe-Mittendorf |
| E-mail(s) |
y.fondufe-mittendorf@uky.edu
|
| Phone |
8593230091
|
| Organization name |
University of Kentucky
|
| Department |
Biochemistry
|
| Lab |
Mittendorf
|
| Street address |
741 South Limestone dr.
|
| City |
Lexington |
| State/province |
KY |
| ZIP/Postal code |
40536-0509 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE85012 |
Genome-wide profiling of DNA methylation patterns in iAs-transformed cells |
|
| Relations |
| BioSample |
SAMN05466466 |
| SRA |
SRX1990938 |
