|
| Status |
Public on Dec 16, 2014 |
| Title |
ChIP-seq analysis of H3K27Ac in KB cells (H3K27Ac IL1 5Z) |
| Sample type |
SRA |
| |
|
| Source name |
KB cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment_1: 10ng/ml IL-1alpha for 1 h
treatment_2: 1µM 5Z-7-oxozeaenol for 1 h
antibody: Anti-H3K27Ac (Diagenode, catalog# 174-050, Lot #A7071-001P)
|
| Treatment protocol |
IL-1 alpha and inhibitors PHA-408 and 5Z-oxozeaenol were added directly to the cell culture medium
|
| Growth protocol |
cells were cultured in DMEM, 10% FCS, to subconfluency
|
| 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
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 |
Dec 16, 2014 |
| 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 (2) |
| GSE64223 |
The activation of IL-1 induced enhancers depends on TAK1 kinase activity and NF-KB p65 [ChIP-Seq] |
| GSE64224 |
The activation of IL-1 induced enhancers depends on TAK1 kinase activity and NF-KB p65 |
|
| Relations |
| BioSample |
SAMN03266464 |
| SRA |
SRX811386 |
| Named Annotation |
GSM1566560_H3K27Ac_TAKIL1_hg19.bw |
