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Sample GSM797458 Query DataSets for GSM797458
Status Public on Dec 01, 2012
Title RRBS HL60 rep1
Sample type SRA
 
Source name HL60 Cell lines
Organism Homo sapiens
Characteristics cell line: HL60
digestion: MspI
treatment: bisulfite
Treatment protocol Genomic DNA was isolated from the myeloid cell lines HL-60. DNA was digested with MspI (NEB), a methylation-insensitive enzyme that cuts C'CGG. Digested DNA was size selected on a 4% NuSieve 3:1 Agarose gel (Lonza). For each sample, two slices containing DNA fragments of 40-120 bp and 120-220 bp, respectively, were excised from the unstained preparative portion of the gel. These two size fractions were kept apart throughout the procedure including the final sequencing. Pre-annealed Illumina adaptors containing 5'-methyl-cytosine instead of cytosine were ligated to size-selected MspI fragments. Adapter-ligated fragments were bisulfite-treated using the EZ DNA Methylation kit (Zymo Research, Orange, CA). The products were PCR amplified, size selected, and sequenced on the Illumina GA IIxat a reading length of 36 bp.
Growth protocol HL-60 were grown in DMEM supplemented with 10%FBS, at 37 °C in a humidified atmosphere with 5% CO2
Extracted molecule genomic DNA
Extraction protocol DNA was digested with MspI (NEB), a methylation-insensitive enzyme that cuts C'CGG. Digested DNA was size selected on a 4% NuSieve 3:1 Agarose gel (Lonza). For each sample, two slices containing DNA fragments of 40-120 bp and 120-220 bp, respectively, were excised from the unstained preparative portion of the gel. These two size fractions were kept apart throughout the procedure including the final sequencing. Pre-annealed Illumina adaptors containing 5'-methyl-cytosine instead of cytosine were ligated to size-selected MspI fragments. Adapter-ligated fragments were bisulfite-treated using the EZ DNA Methylation kit (Zymo Research, Orange, CA). The products were PCR amplified, size selected before subjecting to sequencing.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina Genome Analyzer IIx
 
Description Reduced Representation Bisulfite Sequencing of HL60
Data processing Alignment: Sequencing reads were mapped to the reference genome hg19 using RRBSmap allowing 2 mismatches.
 
Submission date Sep 15, 2011
Last update date May 15, 2019
Contact name Touati Benoukraf
E-mail(s) tbenoukraf@mun.ca
Phone +1 (709) 864-6671
Organization name Memorial University of Newfoundland
Department Faculty of Medicine, Division of BioMedical Sciences
Street address Craig L. Dobbin Genetics Research Centre,
City St. John's
State/province NL
ZIP/Postal code A1B 3V6
Country Canada
 
Platform ID GPL10999
Series (2)
GSE32168 RRBS (Reduced Representation Bisulfite Sequencing) of HL60
GSE32260 Relationship between DNMT1-RNA interactions, DNA methylation and gene expression
Relations
SRA SRX103284
BioSample SAMN00744409

Supplementary file Size Download File type/resource
GSM797458_s_4_sequence.bsp.gz 721.6 Mb (ftp)(http) BSP
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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