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Sample GSM450288 Query DataSets for GSM450288
Status Public on Nov 25, 2009
Title Replication timing of partially-reprogrammed iPSC, 1A2
Sample type genomic
 
Channel 1
Source name Early-replicating DNA of partially-reprogrammed iPSC, 1A2
Organism Mus musculus
Characteristics cell line: piPSC, 1A2
developmental stage: partially reprogrammed iPSC (induced pluripotent stem cells), female
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 partially-reprogrammed iPSC, 1A2
Organism Mus musculus
Characteristics cell line: piPSC, 1A2
developmental stage: partially reprogrammed iPSC (induced pluripotent stem cells), female
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 (6 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 5.8 kb across the mouse genome (Nimblegen, 2006-07-26_MM8_WG_CGH).
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 none
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 Sep 04, 2009
Last update date Apr 16, 2013
Contact name David M. Gilbert
E-mail(s) gilbert@bio.fsu.edu
Phone 8506457583
Organization name Florida State University
Street address 319 Stadium Drive
City Tallahassee
State/province Florida
ZIP/Postal code 32306-4295
Country USA
 
Platform ID GPL9156
Series (3)
GSE17983 Replication Timing Reveal An Epigenetic Commitment To Differentiation Prior To Germ Layer Specification (WG_CGH, RT)
GSE18019 Genome-Wide Dynamics of Replication Timing Revealed by In Vitro Models of Mouse Embryogenesis
GSE51334 DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions

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

Data table
ID_REF VALUE
CHR01FS003001832 -0.608965849
CHR01FS003018759 -0.631920332
CHR01FS003036253 -0.658724297
CHR01FS003041992 -0.66820196
CHR01FS003053606 -0.68841958
CHR01FS003065156 -0.709906754
CHR01FS003076536 -0.732428529
CHR01FS003087994 -0.756463297
CHR01FS003093673 -0.769088452
CHR01FS003105423 -0.79712226
CHR01FS003110919 -0.810837506
CHR01FS003116559 -0.825124607
CHR01FS003122452 -0.840132152
CHR01FS003134224 -0.869725225
CHR01FS003156928 -0.921239232
CHR01FS003162762 -0.932940996
CHR01FS003174487 -0.955940207
CHR01FS003180251 -0.966658764
CHR01FS003185980 -0.976711182
CHR01FS003191525 -0.98571882

Total number of rows: 384849

Table truncated, full table size 11046 Kbytes.




Supplementary file Size Download File type/resource
GSM450288_319048-3piPS1A2_532.pair.gz 6.3 Mb (ftp)(http) PAIR
GSM450288_319048-3piPS1A2_635.pair.gz 6.3 Mb (ftp)(http) PAIR
Processed data included within Sample table

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