|
| Status |
Public on Jun 11, 2017 |
| Title |
Mixl1_Input |
| Sample type |
SRA |
| |
|
| Source name |
whole zebrafish embryos
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB
Stage: 30-50% epiboly
|
| Treatment protocol |
Embryos fixed in 1.85% formaldehyde for 15 mins prior to chromatin extraction
|
| Growth protocol |
Embryos grown in E3 embryo medium at 28.5 degrees celcius and heat-shocket for one hour at 37 degrees celcius prior to fixation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sequential cytoplasmic and nuclear lysis, followed by sonication and centrifugal clarification was used to obtain chromatin of appropriate fragment size. Desired protein-DNA complexes were isolated using antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Sample Prep Kit (Part# FC-121-2001) with the exception that Illumina adapters were diluted 1:100 prior to use.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Reads were mapped to the Zv9 version of the genome with Bowtie using the following parameters: -y -m2 -k2 --best.
Peaks were called for each Mixl1 ChIP sample relative to this input sample using MACS with the following parameters: --gsize 1.3e+9 and –mfold 10 -pval 1e-5
Peak coordinates common to both ChIP replicates were identified for further analysis using custom Perl scripts
Genome_build: Zv9
Supplementary_files_format_and_content: Wig files for track visualization of ChIP and input data.
|
| |
|
| Submission date |
Jul 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew Christopher Nelson |
| E-mail(s) |
a.nelson.1@warwick.ac.uk
|
| Organization name |
University of Warwick
|
| Department |
School of Life Sciences
|
| Street address |
Gibbet Hill Campus
|
| City |
Coventry |
| ZIP/Postal code |
CV4 7AL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16509 |
| Series (2) |
| GSE84612 |
Genome-wide profiling of Ta, Tbx16 and Mixl1 binding in early zebrafish embryos |
| GSE84619 |
Microarray and ChIP-seq identification of Ta and Tbx16 target genes in zebrafish gastrulas and Mixl1 targets in blastulas |
|
| Relations |
| BioSample |
SAMN05420281 |
| SRA |
SRX1961790 |
