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Sample GSM1053064 Query DataSets for GSM1053064
Status Public on Jan 01, 2013
Title E14_AbaSeq_rep2
Sample type SRA
Source name embryonic stem cell (E14)
Organism Mus musculus
Characteristics cell line: E14
cell type: embryonic stem cell
passage: 12
Extracted molecule genomic DNA
Extraction protocol 100 ng E14 genomic DNA was glucosylated and then was digested by AbaSI.
biotinylated Ilumina's adapters were ligated onto the AbaSI digested DNA. Ligated DNA was then sonicated to a range around 300bp and captured by streptavidin beads. End-repair and A-tailing were done consecutively by using the NEBNext® End Repair Module (NEB: E6050S) and the NEBNext® dA-Tailing Module (NEB: E6053S) on the DNA-bound beads. The second Illumina's adapter was ligated onto the biotin-free end of dA-tailed DNA. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
Data processing Library strategy: Aba-Seq
CASAVA version 1.8.2 was used for basecalling
Aba-seq reads were mapped to the mouse reference (UCSC mm9) using the Bowtie aligner with parameters (-v 2 –m 1)
Neighboring sequences of the aligned AbaSI cleavage sites were interrogated in search of putative 5hmC sites at expected distance (-CN11-13 or +N9-11G).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file containing genomic position (bed-format) and sequencing depth of 5hmC sites
Submission date Dec 13, 2012
Last update date May 15, 2019
Contact name Yu Zheng
Organization name New England Biolabs
Street address 240 County Road
City Ipswich
ZIP/Postal code 01938
Country USA
Platform ID GPL13112
Series (1)
GSE42898 High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells
SRA SRX209784
BioSample SAMN01831113

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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