Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Neural
Cell type
Dorsal root ganglia
NA
NA

Attributes by original data submitter

Sample

source_name
DRG
treatment
spinal cord dorsal column axotomy (DCA) + MS275
strain
C57BL/6
tissue
L4-L6 Dorsal Root Ganglia
age
6-8 weeks old
chip antibody
none

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
RNAseq: RNA was extracted using RNeasy kit (Qiagen), according to manufacturer's guidelines. Residual DNA contamination was removed by treating the spin column with 40 units of RNase-free DNase I (Qiagen) for 15 min at room temperature prior to RNA elution. RNA concentrations and purity were verified for each sample following elution with Agilent 2100 Bioanalyzer (Agilent). RNA with RIN factor above 8.0 was used for library preparation. RNA-Seq: Libraries were generated using the NEBNext poly(A) mRNA magnetic isolation module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the recommended manufacturer protocol. Ligation and library integrity was verified using a Tapestation and Glowmax station. The NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) adapter sequences were ligated to each sample in each group to allow for sequencing multiplexing. Sample libraries ligated with unique adapter sequences, were multiplexed, and sequencing was performed in an Illumina HiSeq4000, generating 75bp pair-ended reads. ATACseq: ATAC-seq was performed according to a previously published protocol (Buenrostro, 2015; Buenrostro, 2013). Briefly, sciatic L4-L6 DRGs (1 mouse/sample) were extracted 24 hours after surgery and crushed using an automatic pestle in Lysis buffer containing 0.1% Igepal (Sigma). 50000 nuclei were used for the transposition reaction with Nextera Tn5 Transposase (Illumina, FC-121-1030). The product was purified using the minElute PCR purification kit (Qiagen). ATACseq: Transposase-accessible purified DNA was amplified by 11 cycle PCR using barcoded primers. Libraries were run on an Agilent Bioanalyser for size and quality control checking, quantified using Qbit (ThermoFisher), and multiplexed. Sequencing was performed in an Illumina HiSeq4000, generating 75bp pair-ended reads.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
113273601
Reads aligned (%)
76.3
Duplicates removed (%)
30.0
Number of peaks
1107 (qval < 1E-05)

mm9

Number of total reads
113273601
Reads aligned (%)
76.2
Duplicates removed (%)
30.1
Number of peaks
1150 (qval < 1E-05)

Base call quality data from DBCLS SRA