NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1394668 Query DataSets for GSM1394668
Status Public on Sep 30, 2014
Title 552454A02
Sample type genomic
 
Channel 1
Source name HBEC3 DNMT1, MspI
Organism Homo sapiens
Characteristics cell line: HBEC3
genotype/variation: DNMT1
Growth protocol normal HBEC3 culture condition
Extracted molecule genomic DNA
Extraction protocol Representation of the genome generated by digestion with either HpaII or MspI and amplification by ligation-mediated PCR according to the HELP protocol
Label Cy3
Label protocol Labeling was done according to Roche-NimbleGen, Inc. protocol. The array is 720K Roche NimbleGen custom array for HpII tiny fragment Enriched by Ligation-mediated PCR (HELP) assay designname 100128_HG19_MKF_HELP_ChIP
 
Channel 2
Source name HBEC3 DNMT1, HpaII
Organism Homo sapiens
Characteristics cell line: HBEC3
genotype/variation: DNMT1
Growth protocol normal HBEC3 culture condition
Extracted molecule genomic DNA
Extraction protocol Representation of the genome generated by digestion with either HpaII or MspI and amplification by ligation-mediated PCR according to the HELP protocol
Label Cy5
Label protocol Labeling was done according to Roche-NimbleGen, Inc. protocol. The array is 720K Roche NimbleGen custom array for HpII tiny fragment Enriched by Ligation-mediated PCR (HELP) assay designname 100128_HG19_MKF_HELP_ChIP
 
 
Hybridization protocol Hybridization were done according to Roche-NimbleGen, Inc. protocol. The array is 720K Roche NimbleGen custom array for HpII tiny fragment Enriched by Ligation-mediated PCR (HELP) assay designname 100128_HG19_MKF_HELP_ChIP
Scan protocol Standard NimbleGen protocol.
Description DNA methylation
Data processing HELP package in R from Bioconductor
 
Submission date May 20, 2014
Last update date Sep 30, 2014
Contact name Duojia Pan
E-mail(s) [email protected]
Organization name UT Southwestern Medical Center
Department Physiology
Street address 6001 Forest Park
City Dallas
State/province Texas
ZIP/Postal code 75235
Country USA
 
Platform ID GPL18711
Series (1)
GSE57829 RFTS-deleted DNMT1 enhances tumorigenicity with focal hypermethylation and global hypomethylation

Data table header descriptions
ID_REF
VALUE scaled, log2 (HapII/MspI) ratio

Data table
ID_REF VALUE
RANDOM_GC50_DUAL -0.708312935
chr10:100026989-100027328 -0.167768336
chr10:100027478-100027738 1.484326554
chr10:100028159-100028367 -0.761414275
chr10:100028466-100028927 2.323617764
chr10:100028927-100029595 0.163282633
chr10:100029595-100029886 2.492106241
chr10:100173325-100174571 -3.324613163
chr10:100174837-100176441 -1.964841894
chr10:100176441-100177356 -1.986648813
chr10:100177369-100177626 -1.270168327
chr10:100177862-100178077 2.423520345
chr10:100178219-100178529 0.345719958
chr10:100205525-100205828 2.115795041
chr10:100205828-100206062 2.067013555
chr10:100206062-100206276 2.749092336
chr10:100206276-100206490 -0.415624983
chr10:100206923-100208207 -0.098429107
chr10:100208207-100209984 -1.464858794
chr10:100993595-100994000 0.803498309

Total number of rows: 117522

Table truncated, full table size 4183 Kbytes.




Supplementary file Size Download File type/resource
GSM1394668_552454A02_HG19HX3_532.pair.gz 13.4 Mb (ftp)(http) PAIR
GSM1394668_552454A02_HG19HX3_635.pair.gz 13.2 Mb (ftp)(http) PAIR
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap