|
| Status |
Public on Jul 26, 2018 |
| Title |
6h_IFNa_MNase-Seq |
| Sample type |
SRA |
| |
|
| Source name |
cervix
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HeLa cell line
treatment: 6 hr interferon alpha
|
| Treatment protocol |
Mock or 1000 units/ml interferon alpha
|
| Growth protocol |
HeLa cells were cultured in DMEM media supplemented with 10% cosmic calf serum and 1% pen-strep on adherent plates in 37C incubator with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq: Lysates were clarified sonicated nuclei and STAT1, STAT2, and IRF9 was immunoprecipitated with the corresponding antibody. For Direct selection MNase-seq: Mononucleosomes were isolated following MNase digestion and direct selection via bacterial artificial chromosome hybridization isolation.
Libraries were prepared using the 5500 Series SOLiD Systems Fragment Library Preparation protocol using the ABI library preparation kit or NEBNext kit. The fragmented DNA was blunt-ended, size selected for 100-250 bp using Agencourt AMPure XP reagent, and then adding a dA tail for ligation with SOLiD adaptors. The adaptor-ligated DNA was purified using Agencourt AMPure XP reagent and PCR-amplified for 13-15 cycles. The quantity and size was verified using the Bioanalyzer .
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
ChIP-seq reads were aligned to the hg19 genome assembly using BioScope v1.3.1
ChIP-seq peaks were called with MACS software and a p-value cutoff at 1E-5.
Direct selection MNase-seq reads were aligned to the hg19 genome assembly using Bowtie-0.12.7
Direct selection MNase-seq nucleosome peaks and statistical analysis on differential nucleosome occupancy with a p-value cutoff 1E-5 was generated with the DANPOS software.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated by MACS software and represent unique peaks enriched compared to INPUT. ChIP-seq bigwig alignment files were generated using a Northwestern University Sequencing Core internal script and bedTools. Direct selection MNase-seq bigwig files were converted with Galaxy from wig files generated from the DANPOS software normalized relative to the Mock MNase-seq sample.
|
| |
|
| Submission date |
Feb 02, 2018 |
| Last update date |
Jul 27, 2018 |
| Contact name |
Nancy Au-Yeung |
| E-mail(s) |
wauyeung@u.northwestern.edu
|
| Phone |
7202315977
|
| Organization name |
Northwestern University
|
| Street address |
2200 Campus Dr
|
| City |
Evanston |
| State/province |
IL |
| ZIP/Postal code |
60208 |
| Country |
USA |
| |
|
| Platform ID |
GPL16288 |
| Series (1) |
| GSE110067 |
Genome-wide maps of STAT1, STAT2 and IRF9 in conjunction with nucleosome occupancy maps at 20 interferon-stimulated gene regions during steady state and after type I interferon stimulation. |
|
| Relations |
| BioSample |
SAMN08457506 |
| SRA |
SRX3643717 |
