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Sample GSM500934 Query DataSets for GSM500934
Status Public on Mar 24, 2010
Title Replication timing of BG02 ESC, replicate 2
Sample type genomic
 
Channel 1
Source name Early-replicating DNA of BG02 ESC
Organism Homo sapiens
Characteristics cell line: BG02
cell type: ESC
Extracted molecule genomic DNA
Extraction protocol Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].
Label Cy5
Label protocol Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.
 
Channel 2
Source name Late-replicating DNA of BG02 ESC
Organism Homo sapiens
Characteristics cell line: BG02
cell type: ESC
Extracted molecule genomic DNA
Extraction protocol Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].
Label Cy3
Label protocol Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.
 
 
Hybridization protocol Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (34 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 1.1 kb across the human genome.
Scan protocol GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).
Description submitted as of 1/20/10
Data processing NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and averaged (limma package, R/Bioconductor).The mean early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].
 
Submission date Jan 25, 2010
Last update date Mar 24, 2010
Contact name Tyrone Ryba
Organization name Florida State University
Department Biological Science
Lab David Gilbert
Street address 319 Stadium Dr.
City Tallahassee
State/province FL
ZIP/Postal code 32306
Country USA
 
Platform ID GPL9973
Series (2)
GSE20027 Evolutionarily conserved replication timing profiles distinguish cell types and predict long range chromatin interaction
GSE51334 DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions

Data table header descriptions
ID_REF
VALUE Log2 transformed loess normalized early/late replication timing ratio

Data table
ID_REF VALUE
CHR01FS000017781 -0.224379704778926
CHR01FS000030659 -0.220745034181284
CHR01FS000031123 -0.22062270885016
CHR01FS000032108 -0.220365026772212
CHR01FS000036566 -0.219232750191142
CHR01FS000037196 -0.219077229623736
CHR01FS000038109 -0.218853824383188
CHR01FS000039532 -0.218510290870064
CHR01FS000040816 -0.218205195533792
CHR01FS000042256 -0.217868545610354
CHR01FS000042535 -0.217803994120638
CHR01FS000043737 -0.217528395216489
CHR01FS000045589 -0.217111724605213
CHR01FS000046716 -0.216862897562277
CHR01FS000047089 -0.216781332722092
CHR01FS000048466 -0.216483619540609
CHR01FS000049283 -0.216309510111391
CHR01FS000050787 -0.21599392444945
CHR01FS000052308 -0.215681272965696
CHR01FS000052784 -0.215584772068648

Total number of rows: 2161679

Table truncated, full table size 74216 Kbytes.




Supplementary file Size Download File type/resource
GSM500934_294988_BG02hESCp43_532.pair.gz 36.5 Mb (ftp)(http) PAIR
GSM500934_294988_BG02hESCp43_635.pair.gz 36.3 Mb (ftp)(http) PAIR
Processed data included within Sample table

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