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Sample GSM2595605 Query DataSets for GSM2595605
Status Public on May 31, 2018
Title rad3∆_Replicate3_dye1
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 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).
 
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 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).
 
 
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
SAMPLE 11 (R/G) pre-value

Data table
ID_REF VALUE SAMPLE 11 (R/G) pre-value
A_93_P00000019 1.188459815 0.938459815
A_93_P00000063 1.203046735 0.953046735
A_93_P00000146 1.063850339 0.813850339
A_93_P00000170 1.304241707 1.054241707
A_93_P00000206 1.248426177 0.998426177
A_93_P00000224 1.359196287 1.109196287
A_93_P00000283 1.374203679 1.124203679
A_93_P00000312 1.270935282 1.020935282
A_93_P00000350 1.222478949 0.972478949
A_93_P00000373 1.218835903 0.968835903
A_93_P00000405 1.479692463 1.229692463
A_93_P00000427 1.263818774 1.013818774
A_93_P00000467 1.229202667 0.979202667
A_93_P00000482 1.223458639 0.973458639
A_93_P00000506 1.297652245 1.047652245
A_93_P00000540 1.210291561 0.960291561
A_93_P00000572 1.229308303 0.979308303
A_93_P00000610 1.185078421 0.935078421
A_93_P00000633 1.198980335 0.948980335
A_93_P00000664 1.055688242 0.805688242

Total number of rows: 42641

Table truncated, full table size 1614 Kbytes.




Supplementary file Size Download File type/resource
GSM2595605_11.txt.gz 4.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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