NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1350516 Query DataSets for GSM1350516
Status Public on Sep 17, 2014
Title Tropicalis_H3K27Ac_stage10.5
Sample type SRA
 
Source name ChIP DNA
Organism Xenopus tropicalis
Characteristics tissue: whole embryo
genotype/variation: wild type
developmental stage: 10.5
chip antibody: H3K27ac (Abcam, ab4729)
multiplex adapters: TTAGGC
Growth protocol X. tropicalis embryos were generated by in vitro fertilization and were staged according to Nieuwkoop and Faber morphological criteria.
Extracted molecule genomic DNA
Extraction protocol Chromatin immunoprecipitation from whole embryo lysates was performed using pools of 250 embryos. ChIP DNA was used for library construction.
Illumina multiplex adopter were used for these samples and libaries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). 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 (3' to 5' 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 200~400 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 IIx or HiSeq2000 following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Multiplex-6-9pool
Data processing ChIP-Seq reads are mapped to xenTro2 genome using the bwa-sw tool. Aligned ChIP-Seq files are used to call peaks with the MACS2.08 software at a stringent q value of 0.00001.
Called peaks are annotated using HOMER software to the closest gene
Genome_build: UCSC xenTro2
Supplementary_files_format_and_content: ChIP-seq homer-output as a .txt file contains annotated peaks for Samples
 
Submission date Mar 19, 2014
Last update date May 15, 2019
Contact name Julie C Baker
Organization name Stanford University
Department Genetics
Lab Baker Lab
Street address 300 Pastuer Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL15472
Series (1)
GSE56000 Enhancer chromatin signatures predict Smad2/3 binding in Xenopus
Relations
BioSample SAMN02691867
SRA SRX495652

Supplementary file Size Download File type/resource
GSM1350516_Tropicalis_H3K27Ac_stage10.5_broad_peaks.homer.txt.gz 1.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap