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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
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
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

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