|
| Status |
Public on Apr 21, 2009 |
| Title |
SEP3_ChIPSeq_ag_3 |
| Sample type |
SRA |
| |
|
| Source name |
Primary and secondary inflorescences of 5-7 weeks old plants
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
variable: Mutant:ag
|
| Treatment protocol |
Inflorescences were harvested and fixed using FAA following a protocol published in Gomez-Mena et al. 2005 (PMID: 15634696) with modifications in de Folter et al. 2007 (PMID: 17868439)
|
| Growth protocol |
Arabidopsis thaliana, wild-type (Col-0), sep3-1 (Col-0) and ag-1 (Ler) mutant plants were grown under standard greenhouse conditions (20°C, long day light regime: 16 h light, 8 hours dark cycle). Flower material was harvested from primary and secondary inflorescences of 5-7 weeks old plants
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were performed as described in Gomez-Mena et al. 2005 (PMID: 15634696) with modifications in de Folter et al. 2007 (PMID: 17868439)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against SEP3
|
| Data processing |
Reads were mapped to the unmasked Arabidopsis reference genome (ATH1.1con.01222004; ftp://ftp.arabidopsis.org/) using the SOAP software.Only uniquely mapped reads were retained. Reads were extended directionally to 300 nt. For each nucleotide position enrichment was tested using a Poisson model.
|
| |
|
| Submission date |
Jan 27, 2009 |
| Last update date |
Sep 04, 2019 |
| Contact name |
Gerco Angenent |
| E-mail(s) |
gerco.angenent@wur.nl
|
| Organization name |
Plant Research International
|
| Street address |
Bornsesteeg 65
|
| City |
Wageningen |
| ZIP/Postal code |
6708 PD |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL9062 |
| Series (2) |
| GSE14600 |
Target genes of the MADS transcription factor SEPALLATA3, ChIP-seq |
| GSE14636 |
Target genes of the MADS transcription factor SEPALLATA3 |
|
| Relations |
| Reanalyzed by |
GSE136843 |
| SRA |
SRX004994 |
| BioSample |
SAMN02195456 |
