|
| Status |
Public on Dec 17, 2009 |
| Title |
H3K4me3 replicate1a |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3K4me3 ChIP DNA from Xenopus tropicalis embryos, Nieuwkoop-Faber stage 11-12
|
| Organism |
Xenopus tropicalis |
| Characteristics |
chip antibody: H3K4me3
developmental stage: Nieuwkoop-Faber stage 11-12
tissue: whole embryo
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Xenopus tropicalis embryos were obtained from a natural mating procedure after human chorion gonadotropin injection, dejellied in 2% cysteine and collected at stage 11-12. Chromatin (300 embryos) was fixed in 1% formaldehyde, sheared using a Branson sonifier, immunoprecipitated using 1-5 µg of antibody ( α-H3K4me3 (Abcam) or α-TBP (SL33)), washed, decrosslinked, DNA was purified and amplified using the T7 amplification protocol.
|
| Label |
Cy3
|
| Label protocol |
According to manufacturer's protocol (Roche Nimblegen)
|
| |
|
| Channel 2 |
| Source name |
Input DNA from Xenopus tropicalis embryos, Nieuwkoop-Faber stage 11-12
|
| Organism |
Xenopus tropicalis |
| Characteristics |
chip antibody: none, input DNA
developmental stage: Nieuwkoop-Faber stage 11-12
tissue: whole embryo
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Xenopus tropicalis embryos were obtained from a natural mating procedure after human chorion gonadotropin injection, dejellied in 2% cysteine and collected at stage 11-12. Chromatin (300 embryos) was fixed in 1% formaldehyde, sheared using a Branson sonifier, immunoprecipitated using 1-5 µg of antibody ( α-H3K4me3 (Abcam) or α-TBP (SL33)), washed, decrosslinked, DNA was purified and amplified using the T7 amplification protocol.
|
| Label |
Cy5
|
| Label protocol |
According to manufacturer's protocol (Roche Nimblegen)
|
| |
|
| |
| Hybridization protocol |
According to manufacturer's protocol (Roche Nimblegen)
|
| Scan protocol |
According to manufacturer's protocol (Roche Nimblegen)
|
| Description |
ChIP-chip of H3K4me3 in Xenopus tropicalis embryos
|
| Data processing |
ChIP/input log2 ratio, scaled using Tukey's biweight
|
| |
|
| Submission date |
Dec 10, 2009 |
| Last update date |
Dec 17, 2009 |
| Contact name |
Gert Jan Veenstra |
| E-mail(s) |
g.veenstra@science.ru.nl
|
| Phone |
+31 24 3610541
|
| Organization name |
Radboud University
|
| Department |
Molecular Developmental Biology
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL9778 |
| Series (1) |
| GSE19413 |
ChIP-chip Designs to Interrogate the Xenopus Embryo Genome for Transcription Factor Binding and Epigenetic Regulation |
|
