Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me3

Cell type

Cell type Class
Neural
Cell type
Sciatic Nerve
MeSH Description
A nerve which originates in the lumbar and sacral spinal cord (L4 to S3) and supplies motor and sensory innervation to the lower extremity. The sciatic nerve, which is the main continuation of the sacral plexus, is the largest nerve in the body. It has two major branches, the TIBIAL NERVE and the PERONEAL NERVE.

Attributes by original data submitter

Sample

source_name
sciatic nerve
strain
C57BL/6
gender
male
age
8 weeks
antibody
H3K27me3
antibody vendor/catalog/lot
Millipore 07-449, Lot#2064519

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Freshly dissected mouse sciatic nerve was minced in 1% formaldehyde for 10min and then quenched for 10min with glycine to a final concentration of 0.125M. Samples were sequentially lysed in buffers LB1, LB2, and LB3 + 0.03% SDS (Schmidt et. al., 2009, PMCID: PMC4052679). DNA was fragmented to an average size of 0.5-2kb using 4x10min Bioruptor (Diagenode) cycles on the medium setting. Each aliquot of sonicated chromatin (300ug) was incubated overnight at 4°C with 5ug of H3K27me3 antibody (Millipore 07-449, Lot#2064519). A 10% aliquot was saved for input analysis. An 80ul aliquot of Protein G Dynabead (Invitrogen) slurry was added to each ChIP sample for 4hrs at 4°C. IPs were washed 5x in RIPA buffer than eluted at 65°C with reverse crosslinking buffer (50mM Tris, 10mM EDTA, 1% SDS). ChIP DNA was purified by phenol chloroform extraction and resuspended in 10mM Tris pH 8.0. Libraries were prepared from H3K27me3 ChIP sample, and corresponding input, using the Illumina TruSeq ChIP Sample Preparation Kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
40661961
Reads aligned (%)
87.7
Duplicates removed (%)
84.0
Number of peaks
280 (qval < 1E-05)

mm9

Number of total reads
40661961
Reads aligned (%)
87.6
Duplicates removed (%)
84.1
Number of peaks
240 (qval < 1E-05)

Base call quality data from DBCLS SRA