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Sample GSM931354 Query DataSets for GSM931354
Status Public on May 16, 2012
Title Replication timing of 11-118 leukemic patient sample, replicate 1
Sample type genomic
 
Channel 1
Source name Early-replicating DNA of 11-118 leukemic patient sample
Organism Homo sapiens
Characteristics diagnosis: ALL (B), Pediatric
age (yrs): 5
gender: F
disease stage: Relapse
karyotype: 46,XY[20] including t(12;21)
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 11-118 leukemic patient sample
Organism Homo sapiens
Characteristics diagnosis: ALL (B), Pediatric
age (yrs): 5
gender: F
disease stage: Relapse
karyotype: 46,XY[20] including t(12;21)
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 2.5 kb across the human 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 5/12/12
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].
 
Submission date May 15, 2012
Last update date Apr 26, 2019
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 GPL15436
Series (1)
GSE37987 Abnormal Developmental Control of Replication Timing Domains in Pediatric Acute Lymphoblastic Leukemia
Relations
Reanalyzed by GSE130372

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

Data table
ID_REF VALUE
CHR01FS000032108 -0.038384929
CHR01FS000036566 -0.038384929
CHR01FS000037196 -0.038384929
CHR01FS000038109 0.795442076
CHR01FS000039532 0.792879876
CHR01FS000049283 0.775400603
CHR01FS000052308 0.77000595
CHR01FS000055650 0.764061416
CHR01FS000059489 0.757252949
CHR01FS000060884 0.75478426
CHR01FS000072260 0.734759599
CHR01FS000241735 0.460632423
CHR01FS000357503 0.236840233
CHR01FS000389471 0.201759294
CHR01FS000403676 0.175663156
CHR01FS000443361 0.113839417
CHR01FS000530358 0.122747817
CHR01FS000532718 0.124984841
CHR01FS000547649 0.144222571
CHR01FS000553694 0.154798913

Total number of rows: 719689

Table truncated, full table size 20635 Kbytes.




Supplementary file Size Download File type/resource
GSM931354_471075_2011-05-23_Cycle1_532.pair.gz 13.6 Mb (ftp)(http) PAIR
GSM931354_471075_2011-05-23_Cycle1_635.pair.gz 13.7 Mb (ftp)(http) PAIR
Processed data included within Sample table

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