|
| Status |
Public on Jun 19, 2018 |
| Title |
RNAP_Etoposide |
| Sample type |
SRA |
| |
|
| Source name |
IMR90 fetal lung fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
treatment: etoposide (100uM, 6hrs)
passages: Passage # 30-35
antibody: RNAP
|
| Treatment protocol |
Proliferating IMR90 fibroblasts were treated with etoposide
|
| Growth protocol |
IMR90 fibroblasts were grown in DMEM with 10% FBS at 3% oxygen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, cells were crosslinked with formaldehyde (1% final) for 10min at room temperature, and harvested for sonication. Nuclei were extracted and chromatin was sheared to an average size of 200bp using a Diagenode Bioruptor. For RNA-seq, cells were harvested and PolyA+ RNA was isolated using the NEBNext Ultra RNA-seq Isolation Module. For ATAC-seq, cells were harvested, nuclei were prepped,and transposase was added for 30 minutes at 30C.
Sequencing libraries for ChIP-seq were constructed using the NEBNext Ultra kit as per manufacturer's recommended instructions.
Sequencing libraries for ATAC-seq were constructed using custom Nextera-compatible primers, from Nextera-adapted DNA fragments
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw FastQ files were aligned to the hg19/ncbi37 genome assembly using bowtie2.
Regions of significant enrichment were called using MACSv2 with sonicated DNA input controls
Genome_build: ncbi37/hg19
|
| |
|
| Submission date |
Jun 18, 2018 |
| Last update date |
Jun 19, 2018 |
| Contact name |
Morgan A Sammons |
| E-mail(s) |
masammons@albany.edu
|
| Organization name |
University at Albany - SUNY
|
| Department |
Biological Sciences
|
| Lab |
Sammons
|
| Street address |
1400 Washington Ave, Life Sciences 2075
|
| City |
Albany |
| State/province |
NY |
| ZIP/Postal code |
12222 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE115940 |
p53 binding and chromatin dynamics after etoposide treatment of primary lung fibroblast |
|
| Relations |
| BioSample |
SAMN09439833 |
| SRA |
SRX4230308 |
