|
| Status |
Public on Apr 06, 2011 |
| Title |
H3K4me1_ChIPSeq rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo at 24 hours post fertilization, H3K4me1 ChIP
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo
developmental stage: 24 hours post fertilization
genotype: wild type
antibody: H3K4me1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Histone-DNA complexes were isolated from sonicated chromtin using antibodies against H3K4me1 or H3K4me3. DNA was isolated and ends were polished using the END-IT DNA Repair Kit (Epicentre). Blunt ends were treated with exo-minus Klenow and dATP to add a protruding 3' adenosine. Standard Illumina adpators were ligated and the resulting library was PCR amplified with Illumina primers for 15 cycles followed by gel purification of approximately 250 bp library fragments. Cluster generation and subsequent sequencing was performed on a Genome Analyzer according to manufacturer's specifications.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against H3K4me1
|
| Data processing |
Alignments: Sequence reads were obtained and mapped to the zebrafish (Zv7) genomes using the Illumina Genome Analyzer Pipeline. All reads uniquely mapped with two or fewer mismatches were retained for subsequent peak detection.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS 1.3.6) algorithm (http://liulab.dfci.harvard.edu/MACS/) with default setting except for these parameters --shiftsize=150 --oldfdr --gsize=1700000000 --tsize=36 --bw=150 --mfold=10
|
| |
|
| Submission date |
Mar 07, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Lihua Julie Zhu |
| Organization name |
Umass Medial School
|
| Department |
Program in Gene Function and Expression
|
| Street address |
364 Plantation St
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL10164 |
| Series (1) |
| GSE20600 |
Genome-wide identification of putative cis-regulatory elements through epigenetic profiling in zebrafish |
|
| Relations |
| SRA |
SRX046998 |
| BioSample |
SAMN00217185 |
