Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MEN1

Cell type

Cell type Class
Bone
Cell type
HT-1080
Primary Tissue
Bone
Tissue Diagnosis
Fibrosarcoma

Attributes by original data submitter

Sample

source_name
Human fibrosarcoma HT1080 cells
cell line
HT1080
cell type
Human fibrosarcoma cells
chip antibody
Menin antibody (Bethyl lab, A300-105A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
As to RNA-seq, total RNA was extracted using TRIZOL Reagent (Life technologies) following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100.Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. The ChIP was performed with an EZ-ChIP kit (Millipuro) following the manufacture's instruction. In this experiment, the DNA fragments were sonicated between 100bp to 500bp. For H3K4me3 ChIP, 2 X 107 cells were used. For MYC, Menin, RNA Pol II, 8X 107 cells were used. RNA-sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. ChIP-sequencing libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
27077532
Reads aligned (%)
97.2
Duplicates removed (%)
21.0
Number of peaks
911 (qval < 1E-05)

hg38

Number of total reads
27077532
Reads aligned (%)
98.1
Duplicates removed (%)
19.8
Number of peaks
762 (qval < 1E-05)

Base call quality data from DBCLS SRA