|
| Status |
Public on Dec 28, 2011 |
| Title |
Nanog-like_3.5hpf |
| Sample type |
SRA |
| |
|
| Source name |
3.5hpf zebrafish embryos
|
| Organism |
Danio rerio |
| Characteristics |
tissue: embryos
developmental stage: 3.5hpf
strain: TU
chip antibody: Myc
binding site: Nanog-like
|
| Growth protocol |
Embryos are grown in E3 fish water at 28 degree
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with Myc antibody (abcam, ab9132). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Nanog_ZV8Embryo3.5.ylf; genome build: zv8
Nanog_ZV8Embryo3.5.WIG.gz; genome build: zv8
Counts: Sequence reads were obtained and mapped to the zebrafish Zv8 genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows. Counts included.
|
| |
|
| Submission date |
Dec 22, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Cong Xu |
| E-mail(s) |
congxu@fas.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02134 |
| Country |
USA |
| |
|
| Platform ID |
GPL9319 |
| Series (2) |
| GSE34683 |
Genome-wide maps of binding sites of Nanog-like and Mxtx2 in blastula stage zebrafish embryos |
| GSE34684 |
Nanog-like Regulates Endoderm Formation through the Mxtx2-Nodal Pathway |
|
| Relations |
| SRA |
SRX113062 |
| BioSample |
SAMN00768221 |
