|
| Status |
Public on Jun 12, 2017 |
| Title |
Input_KD |
| Sample type |
SRA |
| |
|
| Source name |
Human colorectal cancer HCT116 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: Human colorectal cancer
chip antibody: none
|
| Treatment protocol |
siRNA treatment followed by Invitrogen RNAimax protocol
|
| Growth protocol |
DMEM with 10% FBS, 37 degree with 5% CO2 culture for 2 days in 10cm dish
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Ovation Ultralow DR Multiplex System )
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using bcl2qfastq, version2.17.1.14
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie
peaks were called using algorithm described previously (Ferrari R et al., Genome Res. 2012:1212-21). The statistical cutoff for significant peaks was P < 10−3 and with two neighboring windows of the same significance
Genome_build: hg19
Supplementary_files_format_and_content: wig files reports significant normalized tag counts. bed files reports the position of significant peaks.
|
| |
|
| Submission date |
Aug 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Cunyu Wang |
| E-mail(s) |
[email protected]
|
| Phone |
3108256317
|
| Organization name |
UCLA
|
| Department |
School of Dentistry
|
| Lab |
CHS 56-200
|
| Street address |
10833 Le Conte Ave
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE71885 |
ChIP-seq verifiy KDM3B recruitment on Wnt target gene promoters |
|
| Relations |
| SRA |
SRX1140480 |
| BioSample |
SAMN03980281 |
