Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PSIP1

Cell type

Cell type Class
Muscle
Cell type
Myotube
NA
NA

Attributes by original data submitter

Sample

source_name
Myotube
genotype
Wild type
tissue
Myotube
chip antibody
LEDGF, Proteintech, #25504-1-AP

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, nuclei was isolated from cells fixed with 1% Formaldehyde. Next, chromatin was fragmented into ~250bp. Chromatin immunoprecipitation was performed with the indicated antibodies. For RNA-seq, total RNA was isolated with RNAeasy (Qiagen) and reverse transcribed using Superscript III and random hexamers (Life Technologies) to synthesize the 1st strand. Second strand was synthesized with dUTP to generate strand asymmetry using DNA Pol I (NEB, M0209L) and the E. coli ligase (Enzymatics, L6090L). For ChIP-seq and RNA-seq, libraries were prepared by standard protocol. First, fragments are repaired to generate blunt 5' P ends using 'EndIT DNA End Repair kit' (Epicentre). Second, 3' A overhang was generated using 'Klenow Fragment (3´→ 5´ exo-)' (NEB). Third, Illumina barcodes were ligated using 'Rapid T4 DNA Ligase' (Enzymatics). Lastly, libraries were size selected using 'Ampure beads' (Beckman Coulter), then amplified, quantified and pooled.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
54749333
Reads aligned (%)
80.0
Duplicates removed (%)
10.5
Number of peaks
1009 (qval < 1E-05)

hg38

Number of total reads
54749333
Reads aligned (%)
81.5
Duplicates removed (%)
9.3
Number of peaks
820 (qval < 1E-05)

Base call quality data from DBCLS SRA