Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BDP1

Cell type

Cell type Class
Breast
Cell type
MCF 10A
Primary Tissue
Breast
Tissue Diagnosis
Fibrocystic Disease

Attributes by original data submitter

Sample

source_name
MC10A
cell line
MC10A
media
DMEM/F12 supplied with 20 ng/ml epidermal growth factor, 0.5 ug/ml hydrocortisone, 10 ug/ml insulin, and 5% horse serum (with the addition of 100 ng/ml cholera toxin), then subjected to serum starvation (0% serum) for 16h
serum
serum-starved
chip-antibody
in house anti-BDP1 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
NextSeq 500

hg19

Number of total reads
28481
Reads aligned (%)
73.7
Duplicates removed (%)
17.4
Number of peaks
0 (qval < 1E-05)

hg38

Number of total reads
28481
Reads aligned (%)
74.6
Duplicates removed (%)
17.1
Number of peaks
0 (qval < 1E-05)

Base call quality data from DBCLS SRA