|
| Status |
Public on Feb 25, 2011 |
| Title |
H3K4me1_ChIPSeq |
| 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: anti-H3K4me1
|
| Growth protocol |
Wild type zebrafish embryos at 24 hours post fertilization.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Histone-DNA complexes were isolated from sonicated chromatin 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 adaptors 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) genome using the Illumina Genome Analyzer Pipeline. All reads uniquely mapped with two or fewer mismatches were retained for subsequent peak detection. The alignment files are in bed format.
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. The peak files are in wig format.
|
| |
|
| Submission date |
Mar 10, 2010 |
| 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 |
SRX018125 |
| BioSample |
SAMN00010382 |
