|
| Status |
Public on Apr 21, 2009 |
| Title |
SEP3_replicate 1_Input |
| Sample type |
genomic |
| |
|
| Source name |
wildtype inflorescences
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
sheared input chromatin
|
| 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) 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)
|
| Label |
biotin
|
| Label protocol |
Labelling of sheared amplified ChIP material and unamplified input DNA was performed as described in Katou et al. 2006 (PMID: 16793414)
|
| |
|
| Hybridization protocol |
The samples are delivered in 60µl. The hybridization mixture is made according to the Affymetrix Genechip Whole Transcript Double-stranded Target Assay protocol. The Arabidopsis Tiling arrays are hybridized at 45°C for 16 hours
|
| Scan protocol |
The Command Console software form Affymetrix is used of the whole process of washing, staining, scanning of the chips and primary data extraction. The Genechip Scanner 3000 7G was used
|
| Description |
sheared input chromatin (replicate 1)
|
| Data processing |
The data were analyzed with Tiling Analysis Software version 1.1 (TAS 1.1) using Affymetrix default analysis settings except the bandwidth parameter set to 250
|
| |
|
| Submission date |
Jan 29, 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 |
GPL10977 |
| Series (2) |
| GSE14635 |
Target genes of the MADS transcription factor SEPALLATA3, ChIP-chip |
| GSE14636 |
Target genes of the MADS transcription factor SEPALLATA3 |
|
| Relations |
| Reanalyzed by |
GSE136843 |
