|
| Status |
Public on Apr 29, 2022 |
| Title |
Vegt stage 10 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Whole embryos
|
| Organism |
Xenopus tropicalis |
| Characteristics |
tissue type: whole embryos at N&F stage 10
strain: Nigerian strain
|
| Growth protocol |
Xenopus tropicalis females were injected with 10 units of Chorulon (Merck and Co.) 1-3 nights before embryo collection and 100 units of Chorulon on the day of embryo collection. Eggs were collected in a dish coated with 0.1% BSA in 1/9x MMR. The eggs are in vitro fertilized with sperm suspension in 0.1% BSA in 1/9x MMR. The embryos are dejellied with 3% cysteine in 1/9x MMR, pH 7.8, 10 minutes after fertilization and are then ready for manipulation. Embryos were staged using the Nieukwoop-Faber developmental table.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin for ChIP-seq was obtained after formaldehyde fixation of embryos and sonication as previously described (Chiu et al., 2014) using custom rabbit peptide anti-Vegt. ChIP-seq libraries were generated using Bioo Scientific Nextflex ChIP-seq library preparation kit (Catalog #NOVA-5143-01) and Nextflex barcodes (Catalog #51410).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
ChIP-seq peak calling and IDR: Reads were aligned to the X. tropicalis genome v9.0 (Mitros et al., 2019; Karimi et al., 2018) using Bowtie v2.2.7 (Langmead and Salzberg 2012) with default options and peaks were called using Macs v2.0.10 (Zhang et al., 2008) with default options.
Assembly: Xenopus tropicalis v9.0
Supplementary files format and content: Peak calls
|
| |
|
| Submission date |
Apr 29, 2022 |
| Last update date |
Nov 29, 2022 |
| Contact name |
Kitt D. Paraiso |
| E-mail(s) |
kparaiso@uci.edu
|
| Phone |
949-824-7950
|
| Organization name |
University of California, Irvine
|
| Department |
Department of Developmental and Cell Biology
|
| Lab |
Ken W.Y. Cho
|
| Street address |
4410 Nat Sci II, University of California, Irvine
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL24898 |
| Series (1) |
| GSE161600 |
Uncovering the mesendoderm gene regulatory network through multi-omic data integration |
|
| Relations |
| BioSample |
SAMN27968810 |
| SRA |
SRX15047002 |
