|
| Status |
Public on Jan 01, 2013 |
| Title |
E14_AbaSeq_rep1 |
| 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 |
| E-mail(s) |
zhengy@neb.com
|
| 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 |
|
| Relations |
| SRA |
SRX209783 |
| BioSample |
SAMN01831112 |
