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Sample GSM2175341 Query DataSets for GSM2175341
Status Public on Jan 30, 2017
Title HeLa_S3 (WGSBS).
Sample type SRA
Source name HeLa_S3
Organism Homo sapiens
Characteristics cell line: HeLa
passage: 4
Growth protocol Cell were cultured in Dulbecco's Modified Eagle medium supplemented with 4.5 g/L glucose, 10% FBS and 2 nM glutamine in humidified incubator at 37 deg. C with 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated using the DNeasy Blood & Tissue Kit (QIAGEN)
Library construction was performed using the EpiGnome/TruSeq DNA Methylation Kit. Briefly, genomic DNA (50-100 ng) was denatured and bisulfite converted in a reaction containing 0.5 ng of unmethylated lambda DNA (Promega) as a control. Following purification, the BS converted DNA was hybridized with oligonucleotides consisting of random hexamers linked to Illumina P5 adapter sequences and strand replicated using EpiGnome polymerase. Adapter-ligated DNA molecules were enriched by 10 cycles of PCR.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina Genome Analyzer
Data processing Illumina Genome Analyzer was used for basecalling
The WGSBS fastq data were aligned in Novoalign bisulfite mode using the following parameters: -oSAM -rRandom -t240 -h120 -b2
sam alignments were sorted with the Picard SortSam.jar script and all duplicates removed using the Picard MarkDuplicates.jar script for WGSBS datasets. The results were converted into .bam files and indexed using Samtools
Peak calling was performed with the USeq NovoalignBisulfiteParser to parse the alignments into four binary PointData sets containing the number of observed converted Cyt and non-converted Cyt at each reference Cyt site sequenced in the genome for both the plus and minus strands
Genome_build: hg19
Supplementary_files_format_and_content: read coverage tracks files were built with Useq
Submission date May 23, 2016
Last update date May 15, 2019
Contact name Bethany Buck-Koehntop
Organization name University of Utah
Department Chemistry
Street address 315 S 1400 E, rm 2020
City Salt Lake City
State/province Utah
ZIP/Postal code 84112
Country USA
Platform ID GPL9052
Series (2)
GSE81779 ZBTB33 (Kaiso) Differentially Regulates Cell Cycle Through cyclin D1 and cyclin E1 in a Cell Specific Manner [BiSulfite-seq]
GSE81784 ZBTB33 (Kaiso) Differentially Regulates Cell Cycle Through cyclin D1 and cyclin E1 in a Cell Specific Manner
BioSample SAMN05163696
SRA SRX1793681

Supplementary file Size Download File type/resource
GSM2175341_BaseFractionNonConverted.wig.gz 76.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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