NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM823562 Query DataSets for GSM823562
Status Public on Feb 01, 2012
Title svp-41_rep1
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 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

Supplementary file Size Download File type/resource
GSM823562.BAR.gz 17.9 Mb (ftp)(http) BAR
GSM823562.CEL.gz 23.6 Mb (ftp)(http) CEL
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap