NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2595606 Query DataSets for GSM2595606
Status Public on May 31, 2018
Title rad3∆_Replicate3_dye2
Sample type genomic
 
Channel 1
Source name cdc25-22 rad3∆
Organism Schizosaccharomyces pombe
Characteristics strain: cdc25-22 rad3∆; unreplicated DNA
Treatment protocol Cells were treated with 6mM HU 5 minutes after release from restrictive temperature. Unreplicated DNA samples were taken at this time.
Growth protocol S. pombe cells were grown in EMM6S to exponential phase at 25˚C and synchronized using a temperature shift (blocked 4h at 36.5˚C and shifted at 25˚C for release).
Extracted molecule genomic DNA
Extraction protocol Genomic DNA extraction was performed as in Hoffman and Winston, Gene, 1987, and samples were purified using the Qiagen Genomic Tip-20.
Label Alexa 647
Label protocol Genomic DNA samples were labeled using the BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen) with either Alexa 555/Alexa 647 dyes or Cy3/Cy5 dyes (Amersham CyDye Post-Labelling Reactive Dye pack).
 
Channel 2
Source name cdc25-22 rad3∆
Organism Schizosaccharomyces pombe
Characteristics strain: cdc25-22 rad3∆; S phase DNA
Treatment protocol Cells were treated with 6mM HU 5 minutes after release from restrictive temperature. S phase DNA samples were taken after a time when cells would normally have completed S phase in the absence of HU.
Growth protocol S. pombe cells were grown in EMM6S to exponential phase at 25˚C and synchronized using a temperature shift (blocked 4h at 36.5˚C and shifted at 25˚C for release).
Extracted molecule genomic DNA
Extraction protocol Genomic DNA extraction was performed as in Hoffman and Winston, Gene, 1987, and samples were purified using the Qiagen Genomic Tip-20.
Label Alexa 555
Label protocol Genomic DNA samples were labeled using the BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen) with either Alexa 555/Alexa 647 dyes or Cy3/Cy5 dyes (Amersham CyDye Post-Labelling Reactive Dye pack).
 
 
Hybridization protocol Labeled samples from before and after S phase entry were quantified and added to hybridization buffer (50 mM MES pH 6.7, 500 mM NaCl, 6 mM EDTA, 0.5% Sarcosine, 30% Formamide, 1.5 ng/µl herring sperm DNA, 0.8 µg/µl yeast tRNA, 0.05µg/µl Cot1 DNA). Samples were incubated in an Agilent hybridization oven at 42ºC for 18 to 20 hours, and washes were performed for 5 min at room temperature (2X wash 1: 6xSSPE, 0.005% N-Lauroylsarcosine, 1X wash 2: 0.06x SSPE).
Scan protocol Scanned on an Agilent G2505C scanner.
Data processing Agilent Feature Extraction Software (v 10.7.3.1)
1) pre-Value column: the ratios of S phase vs. unreplicated DNA, 2) Value column: pre-Value is baseline corrected as part of the protocol for origin identification described in the paper.
BASELINE CORRECTION:To obtain origin efficiencies, the lowest ratios, which represent non-replicated DNA, were adjusted to be centered on a value of 1. This resulted in a correction of 0.25 for all datasets
 
Submission date May 02, 2017
Last update date May 31, 2018
Contact name Pei-Yun Jenny Wu
E-mail(s) pei-yun.wu@ibgc.cnrs.fr
Organization name Institute of Biochemistry and Cellular Genetics
Lab CNRS UMR 5095
Street address 1 Rue Camille Saint Saens
City Bordeaux
ZIP/Postal code 33077
Country France
 
Platform ID GPL16235
Series (2)
GSE98444 Replication origin mapping in cdc25-22 and cdc25-22 rad3∆ in S. pombe
GSE98462 Genome-wide profiles of replication initiation, single-stranded DNA accumulation, and Rad52 binding in cells exposed to replication stress

Data table header descriptions
ID_REF
VALUE baseline corrected ratios of S phase vs. unreplicated DNA
SAMPLE12 (G/R) pre-VALUE

Data table
ID_REF VALUE SAMPLE12 (G/R) pre-VALUE
A_93_P00000019 0.972940235 0.722940235
A_93_P00000063 0.914465861 0.664465861
A_93_P00000146 0.900241901 0.650241901
A_93_P00000170 0.924118986 0.674118986
A_93_P00000206 0.859300879 0.609300879
A_93_P00000224 0.672202055 0.422202055
A_93_P00000283 0.853549541 0.603549541
A_93_P00000312 0.962061679 0.712061679
A_93_P00000350 0.959148419 0.709148419
A_93_P00000373 0.966645748 0.716645748
A_93_P00000405 0.891592251 0.641592251
A_93_P00000427 0.9274133 0.6774133
A_93_P00000467 0.899504786 0.649504786
A_93_P00000482 0.994741533 0.744741533
A_93_P00000506 1.016855572 0.766855572
A_93_P00000540 0.952215735 0.702215735
A_93_P00000572 1.14370429 0.89370429
A_93_P00000610 1.114085811 0.864085811
A_93_P00000633 1.012755946 0.762755946
A_93_P00000664 1.155312099 0.905312099

Total number of rows: 42641

Table truncated, full table size 1614 Kbytes.




Supplementary file Size Download File type/resource
GSM2595606_12.txt.gz 4.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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