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Sample GSM3530767 Query DataSets for GSM3530767
Status Public on Dec 27, 2018
Title genomic_changes_due_to_re-replication_at_ChrIV 567 kb_3
Sample type genomic
 
Channel 1
Source name negative control MC2A strain in G2/M
Organism Saccharomyces cerevisiae
Characteristics yjl number: YJL8427
gal induction: n/a
Extracted molecule genomic DNA
Extraction protocol DNA was purified by organic extraction and ethanol precipitation. This re-replicating genomic DNA was prepared by Method 1 as described in a previous publication from Joachim Li's lab: Finn and Li JJ PloS Genetics 2013.
Label Cy3
Label protocol amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.
 
Channel 2
Source name YJL11111_a MC2A strain with ars317-567 kb lys2InsEA14-CAN1- 637 kb in G2/M induced in galactose for 3 h
Organism Saccharomyces cerevisiae
Characteristics yjl number: YJL11111
galactose induction: re-replication at ChrIV 567 kb
Extracted molecule genomic DNA
Extraction protocol DNA was purified by organic extraction and ethanol precipitation. This re-replicating genomic DNA was prepared by Method 1 as described in a previous publication from Joachim Li's lab: Finn and Li JJ PloS Genetics 2013.
Label Cy5
Label protocol amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.
 
 
Hybridization protocol 90% of the re-replicating DNA preparation and 1 µg of the reference DNA were labeled, respectively, with Cy3 and Cy5 fluorescent dye (Fisher Scientific 45-001-270). The Cy3 and Cy5 labeled DNA were isolated, combined and applied to an in-house printed microarray. Hybridization was performed in 3X SSC, 25mM HEPES pH7.0, 0.25% SDS at 63oC for 18 to 24 hours.
Scan protocol Arrays were then scanned using an Axon Scanner 4B. GenePix Pro6.0 and BatchReplicationAnalyzer4.2 were then used to generate copy number information across the genome.
Description Supp. Figure 1
Data processing Data were filtered in GenePix to flag as bad features that had (1) obvious defects, (2) saturated pixels, (3) regression r^2 values less than 0.5 or (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to 1.
 
Submission date Dec 26, 2018
Last update date Dec 28, 2018
Contact name duyen Bui
E-mail(s) duyenthanh.bui@ucsf.edu
Phone 6073793347
Organization name UCSF
Lab Joachim Li
Street address 600 16th street
City San Francisco
State/province CALIFORNIA
ZIP/Postal code 94107
Country USA
 
Platform ID GPL3412
Series (1)
GSE124382 DNA re-replication is susceptible to nucleotide level mutagenesis

Data table header descriptions
ID_REF
VALUE Value is the normalized median ratio of Cy5 to Cy3

Data table
ID_REF VALUE
15S_rRNA_2 6.850096546
15S_rRNA1
15S_rRNA2
21S_rRNA_3
21S_rRNA_4
21S_rRNA0
21S_rRNA1 5.31087343
21S_rRNA2
9S_rRNA 5.069470092
9S_rRNA_5 5.437111872
CEN1 1.508217183
CEN10
CEN11
CEN12
CEN13 1.94008554
CEN14 1.979950311
CEN15
CEN16
CEN2 1.601234983
CEN3

Total number of rows: 14062

Table truncated, full table size 251 Kbytes.




Supplementary file Size Download File type/resource
GSM3530767_DBE02-09_JLi_UP17_122_YJL11111_PMT650590.gpr.gz 1.4 Mb (ftp)(http) GPR
Processed data included within Sample table

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