Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GTF3C2

Cell type

Cell type Class
Lung
Cell type
IMR-90
Primary Tissue
Lung
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
IMR90
cell line
IMR90
media
EMEM with 10% FBS
serum
non-serum starved
chip-antibody
in house anti-GTF3C2 rabbit polyclonal

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
20666577
Reads aligned (%)
36.4
Duplicates removed (%)
56.6
Number of peaks
805 (qval < 1E-05)

hg38

Number of total reads
20666577
Reads aligned (%)
37.9
Duplicates removed (%)
55.2
Number of peaks
776 (qval < 1E-05)

Base call quality data from DBCLS SRA