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Sample GSM500932 Query DataSets for GSM500932
Status Public on Mar 24, 2010
Title Replication timing of BG01 ESC
Sample type genomic
 
Channel 1
Source name Early-replicating DNA of BG01 ESC
Organism Homo sapiens
Characteristics cell line: BG01
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.
 
Channel 2
Source name Late-replicating DNA of BG01 ESC
Organism Homo sapiens
Characteristics cell line: BG01
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.
 
 
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 0.322585365586569
CHR01FS000030659 0.29981780874584
CHR01FS000031123 0.299015013514468
CHR01FS000032108 0.297314846279763
CHR01FS000036566 0.289688811878118
CHR01FS000037196 0.288620189124809
CHR01FS000038109 0.287075525487486
CHR01FS000039532 0.284677434040876
CHR01FS000040816 0.282523438999697
CHR01FS000042256 0.280118858844571
CHR01FS000042535 0.279654330535213
CHR01FS000043737 0.277658074235665
CHR01FS000045589 0.274598341298516
CHR01FS000046716 0.272745913651361
CHR01FS000047089 0.272134406791595
CHR01FS000048466 0.269883744281888
CHR01FS000049283 0.268553465086885
CHR01FS000050787 0.266114474979931
CHR01FS000052308 0.26366096067896
CHR01FS000052784 0.262895823542334

Total number of rows: 2161679

Table truncated, full table size 73991 Kbytes.




Supplementary file Size Download File type/resource
GSM500932_15473002_spatial_532.pair.gz 38.1 Mb (ftp)(http) PAIR
GSM500932_15473002_spatial_635.pair.gz 38.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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