|
| Status |
Public on Sep 01, 2010 |
| Title |
H3K4me2_HeLa_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa cells
antibody: H3K4me2
antibody catalog: ab7766
antibody manufacturer: Abcam
|
| Treatment protocol |
HeLa cells were either unsynchronized or synchronized by double thymidine block protocol to obtain G1 and G1/S phases cells or by colcemid to obtain M phase cells
|
| Growth protocol |
HeLa cells were cultured in DMEM medium with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
the libraries were constructed following Illumina's Chip-Seq. Sample prep kit. Briefly, Chip DNA was end-blunted and added with an "A" base so the adaptors from Illumina with a âTâ can ligate on the ends. Then 200-400 bp fragments are gel isolated and then purified. 18 cycles of PCR was done to amplify the library.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
ChIP against H3K4me2
|
| Data processing |
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline. The sequencing reads were aligned to the human genome UCSC build hg18 by using BOWTIE alignment. Both uniquely aligned reads and the sequencing reads that align to repetitive regions were kept for downstream analysis (if a read aligns to multiple genome locations, only one location is arbitrarily chosen).
|
| |
|
| Submission date |
Jun 21, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Rosenfeld |
| E-mail(s) |
mrosenfeld@ucsd.edu
|
| Phone |
8585345858
|
| Fax |
8585348180
|
| URL |
http://rosenfeldlab.ucsd.edu/
|
| Organization name |
HHMI/UCSD
|
| Department |
School of Medicine
|
| Lab |
Michael G Rosenfeld
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE22400 |
PHF8 mediates histone demethylation events in cell cycle progression |
| GSE22478 |
PHF8 mediates histone demethylation events in cell cycle progression [ChIP-Seq] |
|
| Relations |
| SRA |
SRX022431 |
| BioSample |
SAMN00016466 |
| Named Annotation |
GSM558468_H3K4me2.bed.gz |
