|
| Status |
Public on Dec 22, 2011 |
| Title |
H3K4me3 IP 24 hpf |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo at 24 hours post fertilization, H3K4me3 ChIP
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo
developmental stage: 24 hours post fertilization
genotype: wt
antibody: anti-H3K4me3
antibody manufacturer: Abcam
antibody catalog #: ab8580
|
| Treatment protocol |
Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS (137 mM NaCl, 2.7 mM KCl, 1.5 mM KH2PO4, 8 mM Na2HP04, pH 7.4) and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer, dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed, and pellets were rinsed twice with PBS, flash frozen in liquid nitrogen and stored at –80C.
|
| Growth protocol |
Zebrafish embryos or adults grown under standard condition
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-Seq was carried out as described in Guenther et al. 2010 (GSE22499)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
ChIP-Seq was carried out as described in Guenther et al. 2010 (GSE22499)
|
| Data processing |
Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie, allowing for up to one mismatch and up to 4 genomic matches. Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/), using the Input libraries to assess FDR
|
| |
|
| Submission date |
Oct 11, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Igor Ulitsky |
| Organization name |
Whitehead Institute for Biomedical Research
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02472 |
| Country |
USA |
| |
|
| Platform ID |
GPL9319 |
| Series (1) |
| GSE32880 |
Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution |
|
| Relations |
| SRA |
SRX100923 |
| BioSample |
SAMN00739134 |
