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Series GSE91023 Query DataSets for GSE91023
Status Public on Jan 16, 2017
Title Tethered Oligonucleotide-Primed sequencing (TOP-seq): a high resolution economical approach for DNA epigenome profiling
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary We describe the development and thorough validation of a new approach for epigenome analysis (named TOP-seq) that is based on a novel concept – combination of selective covalent tagging and targeted genomic sequencing of the genome. The technique reports the modification status of each genomic CpG site by priming the DNA polymerase action from a tethered oligonucleotide probe that is selectively attached to the unmodified CpG sites.
Overall design DNA methylation analysis of 4 human tissues/cell lines (Prefrontal brain cortex - 4 replicates; IMR90 - 9 replicates; Neuroblastoma specific LA1-55n - 3 replicates; Non-neuronal progenitor LA1-5s - 3 replicates)

Please note that processed files created by merging data from multiple samples are linked as Series supplementary file and are indicated in the corresponding Sample description field.
Contributor(s) Staševskij Z, Gibas P, Gordevičius J, Kriukienė E, Klimašauskas S
Citation(s) 28111014
Submission date Dec 08, 2016
Last update date May 15, 2019
Contact name Saulius Klimašauskas
Organization name Vilnius University
Department Department of Biological DNA Modification, Institute of Biotechnology
Street address Sauletekio al. 7
City Vilnius
ZIP/Postal code LT-10257
Country Lithuania
Platforms (1)
GPL17303 Ion Torrent Proton (Homo sapiens)
Samples (19)
GSM2419856 Brain-1 R1
GSM2419857 Brain-1 R2
GSM2419858 Brain-2 R1
BioProject PRJNA356692
SRA SRP094749

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
GSE91023_RAW.tar 5.4 Gb (http)(custom) TAR (of BEDGRAPH)
GSE91023_mEstimate_IMR90_all.bedGraph.gz 359.2 Mb (ftp)(http) BEDGRAPH
GSE91023_mEstimate_IMR90_high1.bedGraph.gz 357.1 Mb (ftp)(http) BEDGRAPH
GSE91023_mEstimate_IMR90_high2.bedGraph.gz 356.9 Mb (ftp)(http) BEDGRAPH
GSE91023_uDensity_IMR90_3.bedGraph.gz 376.2 Mb (ftp)(http) BEDGRAPH
GSE91023_uDensity_IMR90_4.bedGraph.gz 376.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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