|
| Status |
Public on Apr 25, 2016 |
| Title |
ChIP-beta-catenin-2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole embryo
|
| Organism |
Xenopus laevis |
| Characteristics |
Stage: 11.5
replicate: 1
|
| Treatment protocol |
Embryos were injectedanimally with 500pg triple FLAG tagged beta-catenin into both blastomeres of a two-cell staged embryo.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromtin was crosslinked using formaldehyde and embryos were frozen at -80 until processing. Pools of 100 embryos were sonicated and chromatin bound by flag-tagged beta-catenin was immunoprecipitated using FLAG anitbody (Sigma F3165).
Illumina TruSeq ChIP prep kit was used for library preperation
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
fastq_illumina_filter, with settings -v -N -o
Reads were aligned to Xenopus laevis genome version 9.1 using bowtie2 and default settings.
Samtools was used to remove PCR duplicates
Peaks were called with both MACS peak caller and Homer peak caller using input chromatin libraries as control.
Common-peaks.txt was generated using bedtools intersect.
Genome_build: X.laevis v9.1
Supplementary_files_format_and_content: bed files with peak locations called by either MACS or Homer.
|
| |
|
| Submission date |
Jan 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard Harland |
| Organization name |
University of California, Berkeley
|
| Street address |
Life Sciences Addition #3200
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL17682 |
| Series (2) |
| GSE77363 |
Genome-wide binding pattern of β-catenin during Xenopus gastrulation |
| GSE77365 |
Wnt/β-catenin in Xenopus laevis gastrulation |
|
| Relations |
| BioSample |
SAMN04447687 |
| SRA |
SRX1552576 |
