|
| Status |
Public on Mar 01, 2017 |
| Title |
H3K27me3 t0_2 |
| Sample type |
SRA |
| |
|
| Source name |
T cell leukaemia
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat
treatment: none
time of treatment: 0 hrs
chip antibody: H3K27me3 (Millipore, 07-499, lot: 2194165)
|
| Treatment protocol |
For ELF-MF exposure experiments, cells were seeded at a density of 10e5 cells/mL and grown for the indicated time without addition of fresh medium. The leukaemic cell line was sinusoidal ELF-MF (50 Hz, 1 mT, 5’ on/10’ off) or sham exposed (50 Hz, 7 µT, 5’ on/10’ off) for approximately 3.5 cell cycles (72 h). As positive control, cells were treated with 10 nM trichostatin A (TSA).
|
| Growth protocol |
Jurkat cells (acute T cell leukaemia) were cultured in RPMI-1640 medium supplemented with 2 mM L-glutamine, 1 mM Na-pyruvate, 10% FCS and 0.6x penicillin/streptomycin (Sigma-Aldrich) at 37°C in a humidified atmosphere with 5% CO2. Fresh medium was supplied every 48 h.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell lysates of crosslinked cells were sonicated, clarified and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols for HiSeq platform
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-seq rads were aligned to hg19 using SMALT (v 0.6.2)
High quality alignments were extracted using samtools filter-mapQuality ">30"
domains were defined based on increased densities of center positions of ChIPped fragments using chipseq (http://ccg.vital-it.ch/chipseq/ )
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig
|
| |
|
| Submission date |
Aug 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Primo Schaer |
| E-mail(s) |
primo.schaer@unibas.ch
|
| Organization name |
University of Basel
|
| Department |
Department of Biomedicine
|
| Lab |
Genome Plasticity Laboratory
|
| Street address |
Mattenstrasse 28
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE85601 |
Genome-wide analysis of histone modifications in Jurkat cells upon ELF-MF exposure |
|
| Relations |
| BioSample |
SAMN05574603 |
| SRA |
SRX2022913 |
