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Sample GSM1099770 Query DataSets for GSM1099770
Status Public on Mar 18, 2013
Title Day_3
Sample type genomic
 
Channel 1
Source name reprogrammed somatic cells
Organism Mus musculus
Characteristics cell type: in vitro reprogrammed somatic cells
restriction enzyme: MspI
time point: day 3
Extracted molecule genomic DNA
Extraction protocol Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)
Label Cy3
Label protocol Random 9-mers pre-labeled with either Cy3 or Cy5
 
Channel 2
Source name reprogrammed somatic cells
Organism Mus musculus
Characteristics cell type: in vitro reprogrammed somatic cells
restriction enzyme: HpaII
time point: day 3
Extracted molecule genomic DNA
Extraction protocol Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)
Label Cy5
Label protocol Random 9-mers pre-labeled with either Cy3 or Cy5
 
 
Hybridization protocol See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details
Scan protocol Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.
Data processing Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII and MspI signals are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167). After intra-array normalization each channel was centered by subtracting background noise (2.5 median absolute deviations from the median of the random probes’ log2 signal for that channel) from its log2-transformed signal intensities. The HpaII/MspI (unmethylated/reference) ratio was then determined for each probe set on array.
 
Submission date Mar 18, 2013
Last update date Mar 18, 2013
Contact name Ben S. Wittner
E-mail(s) wittner.ben@mgh.harvard.edu
Organization name Massachusetts General Hospital
Department Center for Cancer Research
Lab Lawrence
Street address 149 13th Street
City Boston
State/province MA
ZIP/Postal code 02129
Country USA
 
Platform ID GPL10283
Series (2)
GSE42478 Defining a molecular roadmap of cellular reprogramming into iPS cells
GSE45248 Defining a molecular roadmap of cellular reprogramming into iPS Cells [DNA methylation]

Data table header descriptions
ID_REF
VALUE log2 Ratio (HpaII/MspI)

Data table
ID_REF VALUE
MM5MSPIS00000029 1.967899604
MM5MSPIS00000030 3.265393918
MM5MSPIS00000131 -1.499176758
MM5MSPIS00000132 -2.064850243
MM5MSPIS00000259 2.209051964
MM5MSPIS00000260 0.133282545
MM5MSPIS00000282 1.154556199
MM5MSPIS00000285 -0.084228052
MM5MSPIS00000335 0.917130775
MM5MSPIS00000336 -0.984060367
MM5MSPIS00000388 -0.693394838
MM5MSPIS00000438 -3.097472955
MM5MSPIS00000452 -3.119184965
MM5MSPIS00000453 -3.06500454
MM5MSPIS00000558 2.447583743
MM5MSPIS00000622 0.831274313
MM5MSPIS00000718 2.99705342
MM5MSPIS00000719 1.41849964
MM5MSPIS00000826 -1.121782611
MM5MSPIS00000939 0.199453645

Total number of rows: 25720

Table truncated, full table size 735 Kbytes.




Supplementary file Size Download File type/resource
GSM1099770_342271_635.pair.gz 6.1 Mb (ftp)(http) PAIR
GSM1099770_342271_MM5_532.pair.gz 6.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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