|
| Status |
Public on Mar 15, 2017 |
| Title |
ChIP-seq analysis of H3K36ac in Huh7 cells ( control ) |
| Sample type |
SRA |
| |
|
| Source name |
HuH7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: none
antibody: H3K36ac (Diagenode, C154 10307)
|
| Treatment protocol |
For the infection cells were incubated with DMEM containing the virus at a multiplicity of infection (MOI) of 1. The cells were further incubated at 33°C for 24h with either the CoV-229E or with the heat-inactivated virus. Control cells were left untreated, but were also incubated at 33°C. As positive control another sample of cells was treated with IL-1 (10 ng/ml) for 1h at 33°C .
|
| Growth protocol |
Approximately 10*10^6 Cells were seeded in culture vessels in Dulbecco’s Modified Eagle Medium (DMEM) with 10% Fetal calf serum and 2 mmol/l L-glutamine, 1 mmol/l sodium pyruvate, 100 U/ml penicillin, 100 μg/ml streptomycin GibcoBRL. Afterwards cells were infected with the human coronavirus 229E at 33°C, 5%CO2 - incubation for 24h.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris pH 8.1, 1mM PMSF, Roche protease inhibitor mix), followed by IP and purification of DNA
Sequencing libraries were prepared from 10 ng of immunoprecipitated DNA with the Illumina ChIPSeq DNA Sample Prep Kit according to Illuminas’ instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP-seq
|
| Data processing |
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse hg19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
MACS 1.4 was used to call peaks at default settings using ChIP sample as treatment file and input as control.
Enhancers were identified by calculating the union of H3K4me1 and H3K27ac peaks across all experimental conditions (supplementary files: enhancers.bed).
Genome_build: hg19
Supplementary_files_format_and_content: coverage Wiggle files were generated with Mscs1.4 at 10 bp resolution. Wig files were converted to bigwig using the wigToBigWig utility (UCSC)
|
| |
|
| Submission date |
Oct 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Marek Bartkuhn |
| E-mail(s) |
marek.bartkuhn@gen.bio.uni-giessen.de
|
| Organization name |
Justus-Liebig-University Giessen
|
| Department |
Biomedical Informatics and Systems Medicine
|
| Street address |
Aulweg 132
|
| City |
Giessen |
| State/province |
Hessen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE89212 |
ChIP-seq analysis of coronavirus-infected human cells |
|
| Relations |
| BioSample |
SAMN05944025 |
| SRA |
SRX2270110 |
