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Sample GSM853236 Query DataSets for GSM853236
Status Public on Dec 28, 2011
Title Mxtx2_4.5hpf
Sample type SRA
 
Source name 4.5hpf zebrafish embryos
Organism Danio rerio
Characteristics tissue: embryos
developmental stage: 4.5hpf
strain: TU
chip antibody: Myc
binding site: Mxtx2
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 Mxtx_ZV8Embryo4.5.ylf; genome build: zv8
Mxtx_ZV8Embryo4.5.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 SRX113064
BioSample SAMN00768223

Supplementary file Size Download File type/resource
GSM853236.ylf.gz 24.7 Mb (ftp)(http) YLF
GSM853236_Mxtx_ZV8Embryo4.5.WIG.gz 1.9 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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