Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Cardiovascular
Cell type
Vascular smooth muscle cells
NA
NA

Attributes by original data submitter

Sample

source_name
VSMC_Input
strain
C57BL/6
cell type
primary vascular smooth muscle cell
passages
4-8
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
[RNA-Seq] Total RNA was extracted from cells using the GeneJet RNA Purification Kit (Thermo Scientific) 4 days after infection. One µg of RNA was used for generation of sequencing library using the TruSeq RNA Library Prep Kit V2 (Illumina) according to the manufacturer's instructions. [ChIP-Seq] Mouse VSMCs were fixed using 1% formaldehyde for 10 min, and 0.125 M glycine was added to stop fixation. Cells were harvested, and DNA was fragmented to 300–500 bp by sonication with Covaris S220 sonicator. Immunoprecipitation was performed with antibodies conjugated to Dynabeads Protein G beads (Life Technology). ChIP DNA was eluted, reverse cross-linked, extracted by phenol/chloroform, and precipitated. [RIP-Seq] RNA immunoprecipitation (RIP) was carried out using the Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore) according to manufacturer's instructions. Eluted RNA was precipitated, quantified, and subjected to RT-qPCR or library generation for sequencing. RNA sequencing libraries were prepared with the TruSeqTM RNA Sample Preparation Kit (Illumina).

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
24758117
Reads aligned (%)
95.0
Duplicates removed (%)
9.7
Number of peaks
223 (qval < 1E-05)

mm9

Number of total reads
24758117
Reads aligned (%)
94.9
Duplicates removed (%)
10.0
Number of peaks
214 (qval < 1E-05)

Base call quality data from DBCLS SRA