Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Atf4

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
M0_ATF4_ChIP
strain background
C57/BL6
genotype/variation
wild type
treatment
m-CSF
chip antibody
ATF4 antibody (D4B8, Cell Signaling Technology Cat. #11815)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin-IP was performed according to Cell Signaling ChIP kit # 9003 protocol Libraries were prepared according to NEBNext® Ultra™ II DNA Library Prep Kit for Illumina kit instructions (NEB #E7103). Briefly, DNA was end-repaired, using NEBNext Ultrea II end prep Enzyme mix. The blunt, phosphorylated ends were treated with fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were size selected using Ampure AMPure XP. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina HiSeq/NextSeq.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
73712560
Reads aligned (%)
95.1
Duplicates removed (%)
17.8
Number of peaks
236 (qval < 1E-05)

mm9

Number of total reads
73712560
Reads aligned (%)
94.9
Duplicates removed (%)
17.7
Number of peaks
259 (qval < 1E-05)

Base call quality data from DBCLS SRA