|
| Status |
Public on Oct 07, 2016 |
| Title |
siControl_anti-H2ApT120 |
| Sample type |
SRA |
| |
|
| Source name |
fibrosarcoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HT1080
chip antibody: anti-H2ApT120
sirna: siControl
|
| Treatment protocol |
Transfection was performed by siRNAs targeting human VRK1 or non-targeting siRNA (stealth RNAi, Thermo Fisher Scinetific) using Lipofectamine® RNAiMAX transfection reagent and opti-MEM serum-free medium ( Thermo Fisher Scinetific)
|
| Growth protocol |
HT1080 cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10 µg/ml gentamicin and 10% fetal calf serum (Thermo Fisher Scinetific).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates derived from fixed and sonicated nuclei was immunoprecipitated by anti-H2ApT120, anti-H2AubK119 and anti-VRK1 antibody.
To add single adenosine, DNA was treated with klewnow exo- (3’ and 5’ exo minus; Illumina). Illumina adaptors were added and subjected to 20 cycles of PCR amplification according to manufacturer's instructions. Purified DNA was subjected to cluster generation and 36 cycles of sequencing on the Illumina cluster station and Genome Analyzer following the manufacturer’s instractions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Basecalls performed using CASAVA-1.8.2
ChIP-Seq reads were aligned to the human hg19 genome assembly using Bowtie version 0.12.8 with parameters -a --best --strata -m 1 -v 2.
peaks were called using Partek Genomic suite version 6.6 with the following setting: Maximum average fragment size 200 no reference window size 100 within a gap distance 100 FDR 0.1 Entire region.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files
|
| |
|
| Submission date |
Jul 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
TAKEYA NAKAGAWA |
| E-mail(s) |
[email protected]
|
| Organization name |
Nagasaki unversity
|
| Department |
Biochemistry
|
| Street address |
1-12-4 sakamoto
|
| City |
Nagasaki |
| ZIP/Postal code |
852-8523 |
| Country |
Japan |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE84583 |
Histone H2A T120 phophorylation promotes oncogenic transformation via upregulation of cyclin D1 [ChIP-seq] |
| GSE84968 |
Histone H2A T120 phophorylation promotes oncogenic transformation via upregulation of cyclin D1y |
|
| Relations |
| BioSample |
SAMN05417663 |
| SRA |
SRX1961294 |
