|
Status |
Public on Feb 01, 2012 |
Title |
svp-41_rep3 |
Sample type |
genomic |
|
|
Source name |
SVP ChIP DNA from svp-41
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype/variation: svp-41 tissue: 9-day-old whole seedlings antibody: SVP 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 |
SVP ChIP from svp-41 biological replicate 3 (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 |