Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TEAD4

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
cell line
placenta
Placenta
chip antibody
TEAD4 (Abcam, ab58310)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei were isolated from formaldehyde crosslinked HTS cells. Then Lysates were clarified from sonicated nuclei and chromatin fragments were immunoprecipitated with anti TEAD4 antibody. The ChIP-Seq was performed using the Illumina NovaSeq 6000 Sequencing System at the University of Kansas Medical Center – Genomics Core (Kansas City, KS). Fragmented input and immunoprecipitated chromatin (20ng) was used to initiate the TruSeq ChIP Sample Prep Kit library preparation protocol (Illumina cat#IP-202-1012). The fragmented chromatin underwent end repair and 3' adenylation prior to illumina indexed adapter ligation. Library sizing (target size – 320bp) was performed using the Sage Pippin Prep automated size selection system. PCR amplification of the sized library fraction was performed using Illumina adaptor specific priming with final library purification using KAPA Pure magnetic bead purification (KAPA cat#KK8002). Following Agilent TapeStation 4200 QC for sizing of the library preparation and library quantification using the Roche Lightcycler96 with Roche FastStart Essential Green Master qPCR kit (Roche cat#06402712001 ) and KAPA Library Quant (Illumina) DNA Standards (KAPA cat#KK4903), the CHiP-Seq libraries were adjusted to a 2.125nM concentration and pooled for multiplexed sequencing.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg19

Number of total reads
97207799
Reads aligned (%)
18.8
Duplicates removed (%)
89.9
Number of peaks
445 (qval < 1E-05)

hg38

Number of total reads
97207799
Reads aligned (%)
20.1
Duplicates removed (%)
89.2
Number of peaks
1173 (qval < 1E-05)

Base call quality data from DBCLS SRA