Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Others
Cell type
Olfactory epithelium
NA
NA

Attributes by original data submitter

Sample

source_name
Input_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
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq was done based on methods established previously (Li, Y et al. 2014). Two independent chromatin immunoprecipitation assays were performed using MAGnify chromatin immunoprecipitation kit (Life Technologies, Grand Island, NY). Specifically, main olfactory neuroepithelia (MOE) were dissected from the nasal cavity and dissociated mechanically via trituration in phosphate buffer saline (PBS). Equal number of cells was used for subsequent steps. Protein-DNA complexes were cross linked by incubating dissociated MOE cells with 1% formaldehyde for 5 minutes on a rocker at room temperature. The cross-linking was quenched by adding Glycine. After washing off the media, MOE cells were lysed briefly in SDS containing buffer followed by sonication for 15 minutes with 30 second intervals to shear genomic DNA using a BioruptorTM 300 (Diagenode, Denville, NJ). Sheared DNA was evaluated by 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and selected for sizes ranging between 200 bp and 300 bp. Each sheared genomic DNA preparation was split into two equal portions and incubated with MeCP2 antibody (Diagenode, pAb-052-050) or Rabbit IgG (Millipore, Cat# 12-370) for the negative control. MeCP2-genomic DNA complexes were pulled down and reverse cross-linked by DNase-free Proteinase K and subsequently purified. MeCP2 ChIP-seq and input DNA library were prepared according to manufacturer’s instruction (Bioo Scientific, Austin, TX) using 5143-01 NEXTflex ChIP-Seq kit and 514120 NEXTflex ChIP-Seq Barcodes-6. ChIP and Input DNAs were PCR amplified, cleaned up and sequenced on Illumina Hi-Seq 2000 at QB3 Vincent J. Coates Genomics Sequencing Laboratory in the UC Berkeley. library construction protocol

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
119900968
Reads aligned (%)
83.6
Duplicates removed (%)
20.0
Number of peaks
926 (qval < 1E-05)

mm9

Number of total reads
119900968
Reads aligned (%)
83.3
Duplicates removed (%)
19.8
Number of peaks
1108 (qval < 1E-05)

Base call quality data from DBCLS SRA