|
| Status |
Public on Feb 13, 2018 |
| Title |
DNA hydroxymethylation in iAsT cells |
| Sample type |
SRA |
| |
|
| Source name |
Lung Epithelial
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Sodium Arsenite
|
| 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.
RRHP
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| 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 bowtie1
Alignment files were analyzed and the count of reads with CCGG was calculated, this data is provided in bigbed files
Genome_build: hg19
Supplementary_files_format_and_content: bigbed, browser tracks that contain CCGG read counts
|
| |
|
| Submission date |
Sep 08, 2017 |
| 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) |
| GSE103626 |
Genome-wide profiling of DNA hydroxymethylation patterns in iAs-transformed cells |
|
| Relations |
| BioSample |
SAMN07622492 |
| SRA |
SRX3171009 |
