Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MED12

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
fresh frozn tissue
tissue
fresh frozn tissue
subject id
patient #965
tissue/cell type
LM
genotype
G44D
antibody
anti-MED12

Sequenced DNA Library

library_name
GSM6203193
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
0.2-0.5 g of frozen LM and matched MM tissues were used for ChIP-seq. Tissue was finely grounded with mortar and pestle in liquid nitrogen, followed by fixation in 1% paraformaldehyde for 15 min and quenching with 1X glycine for 5 minutes at room temperature. Chromatin was isolated using the SimpleChIP Enzymatic Chromatin IP Kit (Cat no: 9003S, Cell Signaling Technology, Danvers, MA) following the manufacturer's protocol. 15 µg of chromatin was incubated with 6 µg of each of the antibodies against PR, MED12, or ERα to immunoprecipitate the target protein-bound DNA, which was then purified for library preparation. The libraries were prepared using the KAPA Hyper Prep Kit (Cat no: KK8502, KAPA Biosystems) and KAPA Single-Indexed Adapter Kit (Cat no: KK8722, KAPA Biosystems). The libraries were sequenced as 75 bp single-end for 40 million reads per sample at Northwestern University's NUSeq Core using the NextSeq 500 system (Illumina, San Diego, CA).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
37716850
Reads aligned (%)
98.2
Duplicates removed (%)
7.1
Number of peaks
1352 (qval < 1E-05)

hg19

Number of total reads
37716850
Reads aligned (%)
97.3
Duplicates removed (%)
8.0
Number of peaks
1234 (qval < 1E-05)

Base call quality data from DBCLS SRA