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Sample GSM1673687 Query DataSets for GSM1673687
Status Public on Mar 11, 2016
Title Rrm3-Flag WT
Sample type genomic
 
Channel 1
Source name Rrm3-Flag ChIP DNA from WRBb-9B, asynchronous culture
Organism Saccharomyces cerevisiae
Characteristics strain: WRBb-9B+ pRS413-GAL::YRA1
genotype: MATa ade2-1 can1-100 trp1-1 his3-11,15 leu2-3,112 ura3::URA3/GPD-Tk(7x) Rrm3::FLAG + pRS413-GAL::YRA1
cell cycle stage: asynchronous
Growth protocol Yeast cells were grown in minimal medium + Glucose 2% to mid-log phase at 30°C. In samples with Rrm3-Flag ChIP, yeast cells were grown minimal medium + Galactose 2%
Extracted molecule genomic DNA
Extraction protocol ChIP was carried out as previously described (Katou et al. 2003, 2006): We disrupted 1.5 × 107 cells by Multi-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-HA polyclonal antibody (Abcam) was used for ChIP. Anti-FLAG M2 monoclonal (Sigma-Aldrich)
Label biotin
Label protocol Chromatin-immunprecipitated DNA was purified and amplified by random priming as described (Katou et al. 2003): A total of 5 μg of amplified DNA was digested with DNaseI to a mean size of 100 bp and purified, and the fragments were end-labeled with biotin-N6-ddATP.
 
Channel 2
Source name Input DNA from WRBb-9B
Organism Saccharomyces cerevisiae
Characteristics strain: WRBb-9B+ pRS413-GAL::YRA1
genotype: MATa ade2-1 can1-100 trp1-1 his3-11,15 leu2-3,112 ura3::URA3/GPD-Tk(7x) Rrm3::FLAG + pRS413-GAL::YRA1
cell cycle stage: asynchronous
Growth protocol Yeast cells were grown in minimal medium + Glucose 2% to mid-log phase at 30°C. In samples with Rrm3-Flag ChIP, yeast cells were grown minimal medium + Galactose 2%
Extracted molecule genomic DNA
Extraction protocol ChIP was carried out as previously described (Katou et al. 2003, 2006): We disrupted 1.5 × 107 cells by Multi-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-HA polyclonal antibody (Abcam) was used for ChIP. Anti-FLAG M2 monoclonal (Sigma-Aldrich)
Label biotin
Label protocol Chromatin-immunprecipitated DNA was purified and amplified by random priming as described (Katou et al. 2003): A total of 5 μg of amplified DNA was digested with DNaseI to a mean size of 100 bp and purified, and the fragments were end-labeled with biotin-N6-ddATP.
 
 
Hybridization protocol Approximately 5 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. The arrays were hybridized for 16 hours at 45° at 60 rpm using an Affymetrix hybridization oven. The probe was removed from these arrays and reused to hybridize the remaining three arrays.
Scan protocol Arrays were scanned on an Affymetrix Scanner 3000 7G
Description GAL::YRA1 Rrm3 exp1 and exp2
Data processing Primary data analyses were carried out using the Affymetrix TAS 1.1.02 software to obtain hybridization intensity, signal log2 ratio value and change P-value for each locus. For the discrimination of positive and negative signals for the binding, we compared the chromatin-immunprecipitated fraction with the supernatant fraction by using two criteria. First, the reliability of binding ratio was judged by change P-value (P ≤ 0.01). Second, clusters consisting of at least twenty-five contiguous probe-sets (positive signal, max. gap 250bp, min run. 100bp) that filled the above criteria were selected.
Locus identification, raw signal intensity, detection signal log ratio, and change p-value was obtained using the Affymetrix TAS 1.1.02 software.
 
Submission date May 04, 2015
Last update date Mar 12, 2016
Contact name Andrés Aguilera
Organization name CABIMER, Universidad de Sevilla
Department Genome BIology
Lab Genome Instability & Cancer
Street address Av. Américo Vespucio 24
City Seville
ZIP/Postal code 41092
Country Spain
 
Platform ID GPL7250
Series (2)
GSE68486 ChIP-chip data of HA-Yra1 and Rrm3-Flag in wild-type and cells overexpressing YRA1
GSE68488 YRA1 overexpression microarray and ChIP-chip

Supplementary file Size Download File type/resource
GSM1673687_R3_YRA_ip_Assay01.CEL.gz 23.5 Mb (ftp)(http) CEL
GSM1673687_R3_YRA_ip_Assay02.CEL.gz 26.9 Mb (ftp)(http) CEL
GSM1673687_R3_YRA_pvalue07.bar.gz 13.2 Mb (ftp)(http) BAR
GSM1673687_R3_YRA_pvalue07.bed.gz 8.9 Kb (ftp)(http) BED
GSM1673687_R3_YRA_signal07.bar.gz 15.8 Mb (ftp)(http) BAR
GSM1673687_R3_YRA_sup_Assay01.CEL.gz 31.2 Mb (ftp)(http) CEL
GSM1673687_R3_YRA_sup_Assay02.CEL.gz 30.3 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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