Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Bisulfite-Seq
Antigen
Bisulfite-Seq

Cell type

Cell type Class
Others
Cell type
Olfactory epithelium
NA
NA

Attributes by original data submitter

Sample

source_name
Bisulfite_WT
strain background
B6.129P2(C)-Mecp2tm1.1Bird/J X C57BL/6J
genotype/variation
wild-type, MeCP2(+/y)
age
8 weeks
tissue
Olfactory epithelium

Sequenced DNA Library

library_strategy
Bisulfite-Seq
library_source
GENOMIC
library_selection
RANDOM
library_construction_protocol
500 nanograms (ngs) of DNA was isolated from two wild-type olfactory epithelia (OE) and bisulfite converted using the EZ DNA methylation-Lightning kit (Zymo Research, Irvine, CA). 100 ngs of bisulfite converted DNA from each OE was then used to make indexed, Illumina sequencing compatible libraries using the Epignome Methyl-Seq Kit (Epicentre, Madison WI) and Epignome Index PCR Primers (Epicentre). Each bisulfite converted OE sample had a separate sequencing index allowing for paired end sequencing of both samples in one lane. Whole genome bisulfite-treated DNA libraries were sequenced with 100 pb paired end reads by Beijing Research Institute (BGI), Sacramento, CA. We performed sequencing in two biological replicates obtaining 173M and 161M pair-end reads, respectively. library construction protocol

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
173223420
Reads aligned (%)
81.6
Coverage rate (×)
3.7
Number of hyper MRs
320580 (qval < 1E-05)

mm9

Number of total reads
173223420
Reads aligned (%)
81.6
Coverage rate (×)
3.8
Number of hyper MRs
320322 (qval < 1E-05)

Base call quality data from DBCLS SRA