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Sample GSM428254 Query DataSets for GSM428254
Status Public on Mar 04, 2010
Title rad27- rep1
Sample type genomic
 
Channel 1
Source name G1-phase cells
Organism Saccharomyces cerevisiae
Characteristics strain: BY4741
Treatment protocol G1- and S- phase cells were sorted by FACS
Growth protocol Cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) at 30º to log phase and fixated.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using the MasterPure Yeast DNA purification kit (Epicentre)
Label cy3
Label protocol DNA was digested with DpnII and amplified by four ronds of random-octamer-primed Exo-Klenow DNA synthesis (Invitrogen BioPrime ArrayCGH amplification kit) with amino-allyl modified nucleotides and subsequently labeled with Cy dyes
 
Channel 2
Source name S-phase cells
Organism Saccharomyces cerevisiae
Characteristics strain: BY4741
Treatment protocol G1- and S- phase cells were sorted by FACS
Growth protocol Cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) at 30º to log phase and fixated.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using the MasterPure Yeast DNA purification kit (Epicentre)
Label cy5
Label protocol DNA was digested with DpnII and amplified by four ronds of random-octamer-primed Exo-Klenow DNA synthesis (Invitrogen BioPrime ArrayCGH amplification kit) with amino-allyl modified nucleotides and subsequently labeled with Cy dyes
 
 
Hybridization protocol Agilent
Scan protocol Agilent, 5micron, 100%PMT
Description raw data column: Strains8 (block3)
S vs G1 Replication timing
Data processing Images were analyzed with SpotReader (Niles Scientific). Weak (<2std above control probe mean) and saturated probe reads were removed from further analysis. Data was LOWESS-normalized.
 
Submission date Jul 15, 2009
Last update date Mar 04, 2010
Contact name Amnon Koren
E-mail(s) [email protected]
Organization name Harvard Medical School
Department Genetics
Street address 77 Avenue Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL4131
Series (1)
GSE17120 MRC1-Dependent Scaling of the Budding Yeast DNA Replication Timing Program

Data table header descriptions
ID_REF
VALUE Log2 (S/G1)

Data table
ID_REF VALUE
12
13
14 0.015719712
15 -0.097920662
16 0.389882783
17 -0.175488257
18 -0.459933099
19 0.360799364
20 -0.334438202
21 -0.089619215
22 -0.520751728
23 0.141775595
24 -0.326455944
25 -0.273669897
26 -0.3063501
27
28 0.92505618
29 -0.421493897
30 1.237557203
31 -0.287786511

Total number of rows: 41480

Table truncated, full table size 703 Kbytes.




Supplementary file Size Download File type/resource
GSM428254.srr.gz 23.6 Mb (ftp)(http) SRR
Processed data included within Sample table
Processed data are available on Series record

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