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Sample GSM2595608 Query DataSets for GSM2595608
Status Public on May 31, 2018
Title nda3-km311_Replicate1_Dye2
Sample type genomic
 
Channel 1
Source name nda3-km311
Organism Schizosaccharomyces pombe
Characteristics strain: nda3-km311
time: 0 (unreplicated)
Treatment protocol Cells were treated with 6mM HU after the 6 h block
Growth protocol S. pombe cells were grown in EMM6S to exponential phase at 32˚C and synchronized using a temperature shift (blocked 6h at 18˚C and shifted at 32˚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 nda3-km311
Organism Schizosaccharomyces pombe
Characteristics strain: nda3-km311
time: 80 (S phase)
Treatment protocol Cells were treated with 6mM HU after the 6 h block
Growth protocol S. pombe cells were grown in EMM6S to exponential phase at 32˚C and synchronized using a temperature shift (blocked 6h at 18˚C and shifted at 32˚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)
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
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.
 
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)
GSE98445 Replication origin mapping in nda3-km311 and nda3-km311 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 Ratio of time 80 (S phase) to time 0 (G2/M block)
SAMPLE 14 (G/R) pre-value

Data table
ID_REF VALUE SAMPLE 14 (G/R) pre-value
A_93_P00000019 0.956543 0.706543
A_93_P00000063 0.935799 0.685799
A_93_P00000146 1.026564 0.776564
A_93_P00000170 0.889180 0.639180
A_93_P00000206 0.888638 0.638638
A_93_P00000224 0.837452 0.587452
A_93_P00000283 0.921882 0.671882
A_93_P00000312 0.969383 0.719383
A_93_P00000350 1.038959 0.788959
A_93_P00000373 1.023462 0.773462
A_93_P00000405 0.855723 0.605723
A_93_P00000427 0.955818 0.705818
A_93_P00000467 0.991069 0.741069
A_93_P00000482 1.026656 0.776656
A_93_P00000506 0.966229 0.716229
A_93_P00000540 0.964416 0.714416
A_93_P00000572 1.039364 0.789364
A_93_P00000610 0.971274 0.721274
A_93_P00000633 0.887220 0.637220
A_93_P00000664 1.062210 0.812210

Total number of rows: 42641

Table truncated, full table size 1374 Kbytes.




Supplementary file Size Download File type/resource
GSM2595608_14.txt.gz 4.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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