Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SETX

Cell type

Cell type Class
Lung
Cell type
A549
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
A549 cells
cell line
A549
chip antibody
SETX
infection
Influenza PR8ΔNS1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Previously described protocols (see PMID: 17512414 and PMID: 17406303) with minor modifications were used: (i) Sonication: A refrigerated Bioruptor (Diagenode) was used . Sonication conditions were optimized to generate DNA fragments of approximately 200-500 bp. (ii) Antibodies (Ab) were coupled with Invitrogen Dynabeads anti-mouse M-280 #112-02, or Dynabeads anti-rabbit M-280 #112-04 for 6hours. Ab-beads and chromatin were then immunoprecipitated overnight. (iii) After the wash steps, reverse crosslinking was carried out at 65°C for 2 hours in a thermomixer programmed for mixing at 700 rpm 2 min on/ min off. ChIP DNA was then isolated, after RNase digestion and proteinase K digestion, using QIAGEN MinElute kit (28004). For library preparation, 30 ul of ChIP DNA was used to generate blunt-ended DNA using the Epicenter DNA ENDRepair kit (Epicenter Biotechnologies, cat# ER0720), and purified end-repaired DNA using the QIAGEN PCR purification kit (28104). DNA END Repair was done using Klenow Fragment (NEB M0212L), and purified DNA was collected with QIAGEN MinElute kit. Ligation of Illlumina/Solexa adapters (#FC-102-1003) to DNA fragments overnight was achieved using T4 DNA ligase (NEB M0202L). Adaptor-ligated DNA fragments were purified with the QIAGEN MinElute kit. 18 cycles of PCR was performed with the Illumina/Solexa primers 1.0 and 2.0, and an aliquot of material was used to check the fragment size on agarose gel. The remaining DNA was column purified and bio-analyzed before sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
296924252
Reads aligned (%)
28.8
Duplicates removed (%)
4.1
Number of peaks
2278 (qval < 1E-05)

hg38

Number of total reads
296924252
Reads aligned (%)
29.4
Duplicates removed (%)
3.0
Number of peaks
3080 (qval < 1E-05)

Base call quality data from DBCLS SRA