|
| Status |
Public on Mar 01, 2016 |
| Title |
ChIP-4b_wild-input |
| Sample type |
SRA |
| |
|
| Source name |
Oral cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell: T3M-1 Cl-10
genotype: wild type
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
T3M-1 Cl-10 cells were infected with a mock retrovirus or virus generated from pMXS-ires-EGFP expressing FLAG-epitope–tagged ELF4 or ELF4(L211M). ChIP was conducted with anti-FLAG M2 antibody (Sigma-Aldrich). The precipitated DNA fragments were subjected to massively parallel sequencing with Genome Analyzer IIx (Illumina) for 51 bases from both ends of the fragments.
ChIP-seq libraries were prepared using Illumina NEBNext ChIP-Seq Library Prep Reagent Set following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
wild_qv30_E_0_peak.cod
|
| Data processing |
Basecalls performed using CASAVA version 1.6.0
Sequenced reads were selected for high-quality read (quality value >=30), and mapped to hg19 whole genome using bowtie v0.12.7 with parameters -q -n 0 -l 50 -p 30 --k 1 -X 500.
Mapped results were converted to ALN files by using bowtie2aln in CisGenome v2.0.
Peaks were calculated using CisGenome with the following setting: Read Extension Length E (0).
Motifs were calculated using CisGenome with the following setting: No.of Motifs (30), No. of MCMC iterations (1000).
Genome_build: hg19
Supplementary_files_format_and_content: Peaks (*.cod) were tab-delimited text files.
|
| |
|
| Submission date |
Dec 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Mizuo Ando |
| E-mail(s) |
ando.hnc@gmail.com
|
| Phone |
03-3815-5411
|
| Organization name |
The University of Tokyo
|
| Department |
Otolaryngology-Head and Neck Surgery
|
| Street address |
7-3-1 Hongo
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-0033 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE53357 |
Genome-wide screening for ELF4-binding sites. |
|
| Relations |
| BioSample |
SAMN02444804 |
| SRA |
SRX392688 |
