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Sample GSM1112425 Query DataSets for GSM1112425
Status Public on Apr 16, 2013
Title Replication timing of L1210 cell line, replicate 1
Sample type genomic
 
Channel 1
Source name Early-replicating DNA of L1210 cell line
Organism Mus musculus
Characteristics strain: DBA/2
Sex: F
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] and Ryba et al [Nature Protocols (2011) 6: 870–895]
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 L1210 cell line
Organism Mus musculus
Characteristics strain: DBA/2
Sex: F
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] and Ryba et al [Nature Protocols (2011) 6: 870–895]
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 2.5 kb (MEL, CH12; GPL10989) or 5.8 kb (L1210; GPL9156) across the mouse genome.
Scan protocol NimbleGen MS200 microarray scanner (Roche NimbleGen, Inc.) and MS200 data collection software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).
Description Submitted as of 3-28-13
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 differentially labeled were loess-normalized to remove signal intensity-dependent bias, then scaled to a reference data set to have the same median absolute deviation (limma package, R/Bioconductor). The 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 the loess function 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] and Ryba et al [Nature Protocols (2011) 6: 870–895]
 
Submission date Apr 02, 2013
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 GPL11620
Series (4)
GSE18019 Genome-Wide Dynamics of Replication Timing Revealed by In Vitro Models of Mouse Embryogenesis
GSE45716 Replication timing profiling by Repli-chip in Mus musculus
GSE49847 A comparative encyclopedia of DNA elements in the mouse genome

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

Data table
ID_REF VALUE
CHR01FS126000000 -0.528778842223345
CHR01FS100004408 -0.864583869419079
CHR01FS100010073 -0.86442045197808
CHR01FS100015976 -0.862552909815231
CHR01FS100021356 -0.859787939253634
CHR01FS100027497 -0.855927319978984
CHR01FS100038863 -0.848774217954018
CHR01FS100050174 -0.844849432885109
CHR01FS010005395 1.29555307916398
CHR01FS100055776 -0.844402607357627
CHR01FS100061990 -0.84411225740982
CHR01FS100079227 -0.844514954376424
CHR01FS100084923 -0.845063686503795
CHR01FS100096500 -0.846861071143368
CHR01FS100102033 -0.848057339105453
CHR01FS100107861 -0.84956333193449
CHR01FS010011200 1.28171586328147
CHR01FS100113515 -0.851272832946982
CHR01FS100130640 -0.856435181271403
CHR01FS100136582 -0.858017890214074

Total number of rows: 384849

Table truncated, full table size 13209 Kbytes.




Supplementary file Size Download File type/resource
GSM1112425_L1210LymphoblastR1_532.pair.gz 6.5 Mb (ftp)(http) PAIR
GSM1112425_L1210LymphoblastR1_635.pair.gz 6.5 Mb (ftp)(http) PAIR
Processed data included within Sample table

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