|
| Status |
Public on Apr 22, 2016 |
| Title |
Gata.a ChIP-chip in Ciona intestinalis embryo (16-cell stage) Sample 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Whole Cell Extract (WCE) DNA
|
| Organism |
Ciona intestinalis |
| Characteristics |
Stage: 16-cell stage
tissue: whole embryo
|
| Treatment protocol |
Ciona intestinalis embryos were cultured until 16-cell stage without any specific treatment.
|
| Growth protocol |
Ciona intestinalis adults were obtained from the National BioResource Project Ciona intestinalis Organization and were maintained under constant light to induce oocyte maturation. Eggs and sperm were obtained surgically from the gonoduct. Following insemination, eggs were washed and maintained in seawater at 18˚C in Millipore-filtered seawater containing 50ug/ml streptomycin sulfate.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The embryo were fixed with 1% formaldehyde for 15 min. Chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for Gata.a, Tcf7 and Zic-r.a, respectively. After reversal of the fixation, the immunoprecipitated DNA were amplified by LM-PCR.
|
| Label |
Cy3
|
| Label protocol |
Amplified DNA was directly labeled by random-primed, Klenow-based extension protocol that is used with CGH Labeling kit (Invitrogen).
|
| |
|
| Channel 2 |
| Source name |
Gata.a ChIP in Ciona intestinalis embryo (16-cell stage)
|
| Organism |
Ciona intestinalis |
| Characteristics |
Stage: 16 cell stage
tissue: whole embryo
|
| Treatment protocol |
Ciona intestinalis embryos were cultured until 16-cell stage without any specific treatment.
|
| Growth protocol |
Ciona intestinalis adults were obtained from the National BioResource Project Ciona intestinalis Organization and were maintained under constant light to induce oocyte maturation. Eggs and sperm were obtained surgically from the gonoduct. Following insemination, eggs were washed and maintained in seawater at 18˚C in Millipore-filtered seawater containing 50ug/ml streptomycin sulfate.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The embryo were fixed with 1% formaldehyde for 15 min. Chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for Gata.a, Tcf7 and Zic-r.a, respectively. After reversal of the fixation, the immunoprecipitated DNA were amplified by LM-PCR.
|
| Label |
Cy5
|
| Label protocol |
Amplified DNA was directly labeled by random-primed, Klenow-based extension protocol that is used with CGH Labeling kit (Invitrogen).
|
| |
|
| |
| Hybridization protocol |
Hybridization and washing protocols were according to the manufacturer’s instructions (Agilent Technologies).
|
| Scan protocol |
The microarrays were scanned with an Agilent G2565BA Microarray Scanner (Agilent Technologies).
|
| Description |
Gata.a ChIP-chip sample 1. WT Ciona intestinalis embryo, untreated, harbested, immunoprecipitated by polyclonal anti-Gata.a antibody
|
| Data processing |
The resulting fluorescence intensity for each spot was quantified using Agilent Feature Extraction Software ver. 9.1 (Agilent Technologies).
|
| |
|
| Submission date |
Jul 14, 2015 |
| Last update date |
Apr 22, 2016 |
| Contact name |
Atsushi Kubo |
| Organization name |
Kyoto University
|
| Department |
Department of zoology, Graduate School of Science
|
| Street address |
Sakyo-ku
|
| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
606-8502 |
| Country |
Japan |
| |
|
| Platform ID |
GPL8993 |
| Series (1) |
| GSE70902 |
Gata.a, Tcf7 and Zic-r.a ChIP-chip analysis in Ciona intestinalis embryo (16-cell stage) |
|
