|
| Status |
Public on Aug 01, 2014 |
| Title |
Ctrl_Smad2_Lib1 |
| Sample type |
SRA |
| |
|
| Source name |
Control embryos
|
| Organism |
Xenopus tropicalis |
| Characteristics |
embryonic stage: Stage 10.5
chip characteristics: antibody: Smad2/3
barcode: none
|
| Growth protocol |
Embryos were raised in 1/9 MR to stage 10.5 (Nieuwkoop and Faber staging criteria)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
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.
Embryos were fixed for 1hr in 1% formaldehyde, glycine treated and frozen. Embryos were then homogenized, sonicated, and centrifuged to remove yolk and cytoplasm. Nuclei were complexed with antibody.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| 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
ChIP-seq homer-output as an excel file contains annotated peaks for Samples
Genome_build: UCSC XenTro2
|
| |
|
| Submission date |
Mar 25, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrea E. Wills |
| Organization name |
Stanford School of Medicine
|
| Department |
Genetics
|
| Lab |
Julie Baker
|
| Street address |
300 Pasteur Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL9320 |
| Series (1) |
| GSE56169 |
E2a is necessary for Smad2/3 dependent transcription and the direct repression of lefty |
|
| Relations |
| BioSample |
SAMN02699943 |
| SRA |
SRX500916 |
