|
| Status |
Public on Mar 29, 2024 |
| Title |
M953_Input |
| Sample type |
SRA |
| |
|
| Source name |
Whole embryo
|
| Organism |
Xenopus laevis |
| Characteristics |
developmental stages: 14
tissue: Whole embryo
|
| Treatment protocol |
Embryos were injected in both blastomeres at two-cell stage with trace amounts of mRNA encoding Pax3-FLAG-HA (75 pg), Tfap2a-FLAG or Tfap2e-FLAG. Injected embryos were collected at mid-neurula stage 14 (Pax3 and Tfap2a, 100 embryos/condition) or at NC migratory stage 19 (Tfap2e, 100 embryos/condition)
|
| Growth protocol |
Xenopus laevis embryos were handled using standardized protocols (http://www.xenbase.org). Embryos were staged according to Nieuwkoop and Faber’s table (P. D. Nieuwkoop, J. Faber, Normal table of Xenopus laevis (Daudin): edited by P. D. Nieuwkoop and J. Faber Garland Publishing. Trends Genet. 11, 418 (1994)).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from Xenopus embryos by sonication, using a 3.2 mm tapered microtip for 13 mm horn (Branson 450 sonicator)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Bowtie2 alignment
MACS2 peaks calling
Target genes search with bedtools
Assembly: X.tropicalis v.10 , X.laevis v. 9.2
Supplementary files format and content: Three tables for pax3, tfap2a, and tfap2e targets in a csv format. Target genes was searched with 10kb window around the peaks called with MACS2.
|
| |
|
| Submission date |
Mar 12, 2022 |
| Last update date |
Mar 29, 2024 |
| Contact name |
Anne-Hélène Monsoro-Burq |
| E-mail(s) |
[email protected]
|
| Organization name |
Curie Institute
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| State/province |
Ile-de-France |
| ZIP/Postal code |
75248 |
| Country |
France |
| |
|
| Platform ID |
GPL18936 |
| Series (2) |
| GSE198492 |
From neural border epithelium to neural crest emigration: A comprehensive single cell roadmap of the timing and regulatory logic underlying cranial and vagal neural crest emergence [ChIPseq] |
| GSE198494 |
A time-resolved single-cell roadmap of the logic driving anterior neural crest diversification from neural border to migration stages |
|
| Relations |
| BioSample |
SAMN26631117 |
| SRA |
SRX14448849 |
