|
| Status |
Public on Sep 17, 2014 |
| Title |
Tropicalis_Smad2/3_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: Smad2/3 (FL-425) (Santa Cruz Biotechnology, sc-8332)
|
| 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.
Libraries 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 II or HiSeq following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
ChIP-Seq reads are mapped to xenTro2 genome using the bowtie tool using the following settings: bowtie --best --strata -m 1 –chunkmbs 200. 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 |
GPL13741 |
| Series (1) |
| GSE56000 |
Enhancer chromatin signatures predict Smad2/3 binding in Xenopus |
|
| Relations |
| BioSample |
SAMN02691857 |
| SRA |
SRX495643 |
