|
| Status |
Public on Feb 01, 2012 |
| Title |
soc1-2_rep1 |
| Sample type |
genomic |
| |
|
| Source name |
SOC1 ChIP DNA from soc1-2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: soc1-2
tissue: 9-day-old whole seedlings
antibody: SOC1 rabbit polyclonal
ecotype: Col-0
|
| Growth protocol |
Arabidopsis thaliana plants of different genotypes (Col-0) were grown on soil under long days (16-hour light/8-hour dark) at 23°C ± 2°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP-chip experiments were performed in biological triplicates using the aerial part of 9-day-old whole seedlings of soc1-101D (Lee et al., 2000) or 35S:SVP (Li et al., 2008) against soc1-2 (Lee et al., 2000) or svp-41 (Hartmann et al., 2000) as a negative control, respectively. 9-day-old whole seedlings were fixed for 45 min in cold MC buffer (10 mM potassium phosphate, pH 7.0, 50 mM NaCl and 0.1 M sucrose) with 1% formaldehyde under vacuum. Fixed tissues were ground and homogenized. Chromatin was isolated and sonicated to produce DNA fragments below 500 bp. Endogenous SOC1 and SVP protein were immunoprecipitated by anti-SOC1 and anti-SVP antibody (Shen et al., 2011) bound to Protein A-agarose beads, respectively. Genomic DNA was purified after reverse cross-link the chromtain complex eluted from the beads.
|
| Label |
biotin
|
| Label protocol |
5 µg of DNA from each sample was fragmentated and terminally labelled with the GeneChip® WT (Whole Transcript) Double-Stranded DNA Terminal Labeling Kit following the manufacturer’s protocol
|
| |
|
| Hybridization protocol |
The hybridization cocktail was prepared for each fragmented and labeled DNA target according to Affymetrix® Chromatin Immunoprecipitation Assay Protocol. The sample solution was injected into the Affymetrix® Arabidopsis Tiling 1.0R Array and incubated in 45℃ hybridization oven at 60 rpm rotating overnight.
|
| Scan protocol |
After hybridization, washing and staining was performed using the fluidics protocol FS450_0001 on the GeneChip® Fluidics Station 450 controlled by GeneChip® Operating Software (GCOS). The probe array was then scanned by the GeneChip® Scanner 3000 7G.
|
| Description |
SOC1 ChIP from soc1-2 biological replicate 1 (negative control)
|
| Data processing |
The raw .CEL and .DAT files were exported by the Data Transfer Tool. The ChIP-on-chip tiling array data was analyzed using the CisGenome suite. All the probes were mapped to the TAIR 9 genome. Briefly, raw .CEL files were quantile normalized and probe intensity was computed by perfect match-mismatch (PM-MM). Peaks were called using TileMapv2. Only peaks detected at FDR < 0.05 were used for further analyses.
additional results files: At35b_MR_v04-2_TAIR9.bpmap
results file descriptionsL .BAR are generated by CisGenome software after quantile normalization
|
| |
|
| Submission date |
Oct 27, 2011 |
| Last update date |
Sep 04, 2019 |
| Contact name |
Zhen Tao |
| E-mail(s) |
dbstaoz@nus.edu.sg
|
| Organization name |
National University of Singapore
|
| Department |
Biological Sciences
|
| Lab |
Plant Functional Genomics
|
| Street address |
S1A 07-01, 14 Science Drive 4
|
| City |
Singapore |
| ZIP/Postal code |
117543 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL10977 |
| Series (1) |
| GSE33297 |
Genome-Wide binding sites of two MADS-domain transcription factors SOC1 and SVP in Arabidopsis during the floral transition |
|
| Relations |
| Reanalyzed by |
GSE136843 |
