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Series GSE51680 Query DataSets for GSE51680
Status Public on Sep 10, 2015
Title Genome-wide DNA methylation analyses by the HELP assay
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary The HELP tagging assay was performed on purified genomic DNAs. The protocol was modified for NEBNext Multiplex Oligos for Illumina (NEB) from the original protocol4 ( Briefly, genomic DNA was digested by HpaII or MspI, the former only cutting at CCGG sequences where the central CG dinucleotide is unmethylated. AS and AE adapters were prepared by annealing two oligo DNAs separately. The first Illumina AE adapter was ligated to the compatible cohesive end created, juxtaposing an EcoP15I site beside the HpaII/MspI digestion site and allowing EcoP15I to digest within the flanking genomic DNA sequence. An A-overhang was created, allowing the ligation of the second Illumina AS adapter. This created both AE-insert-AS products and AS-insert-AS molecules. By performing a T7 polymerase-mediated in vitro transcription from a promoter sequence located on the AE adapter, we selectively enriched for the AE-insert-AS product. PCR amplification by NEBNext Multiplex Oligos was performed to generate a single-sized amplicons for Illumina sequencing.
Overall design DNA methylation in Zscan4 positive and negative cells
Contributor(s) Oda M, Sakota M, Pian Y, Sharov A, Qian Y
Citation(s) 26324425
Submission date Oct 24, 2013
Last update date May 15, 2019
Contact name Minoru S.H. Ko
Phone 410-558-8359
Organization name NIH
Department National Institute on Aging
Lab Lab of Genetics
Street address 251 Bayview Blvd, Suite 100, 10C
City Baltimore
State/province MD
ZIP/Postal code 21224
Country USA
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (4)
GSM1250437 MC1-ZE7 cells (Em+ high fraction) Hpa II
GSM1250438 MC1-ZE7 cells (Em+ high fraction) Msp I
GSM1250439 MC1-ZE7 cells (Em-) Hpa II
This SubSeries is part of SuperSeries:
GSE51682 Zscan4 mediates transient remodeling and transcriptional burst of heterochromatin in mouse embryonic stem cells
BioProject PRJNA224549
SRA SRP031896

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE51680_RAW.tar 47.5 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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