Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
INTS12

Cell type

Cell type Class
Lung
Cell type
Bronchial epithelial cells
NA
NA

Attributes by original data submitter

Sample

source_name
INTS12_ChIPseq_D7F3158
donor
7F3158
cell type
Human bronchial epithelial cells HBECs
passage
3
source
Lonza
chip antibody
INTS12 (Sigma cat. num. HPA03577)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNAseq: Total RNA was extracted using a mammalian total RNA prep kit with on-column DNaseI digestion ChIP-seq: Unprecipitated genomic DNA (i.e. input control) was prepared from a pool of equal aliquots of the two donor samples. Genomic DNA regions of interest were isolated using 4 µg of antibody against INTS12 (Sigma cat. num. HPA03577) following manufacturer’s specifications (Active Motif). RNA-seq: The sequencing libraries were prepared with Illumina TruSeq RNA Sample Prep Kit v2. mRNA was poly-A selected by capturing total RNA samples with oligo-dT coated magnetic beads. The mRNA was then fragmented and randomly primed. cDNA was synthesised using random primers. Finally a ready-for-sequencing library was prepared by end-repair, phosphorylation, A-tailing, adapter ligation and PCR amplification. Paired-end sequencing was performed on the HiSeq2000 platform (Illumina) using TruSeq v3 chemistry over 100 cycles yielding ~40 million reads per sample. ChIP-seq: Libraries (Illumina) were prepared from the both ChIP and input DNAs and the resulting libraries were sequenced yielding ~40 million reads per two ChIP samples from each donor cells and one input control of both donors. DNA libraries obtained from single donor were sequenced on NextSeq 500 sequencing machine

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
47776470
Reads aligned (%)
78.2
Duplicates removed (%)
15.4
Number of peaks
8982 (qval < 1E-05)

hg38

Number of total reads
47776470
Reads aligned (%)
80.0
Duplicates removed (%)
14.3
Number of peaks
9263 (qval < 1E-05)

Base call quality data from DBCLS SRA