Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Muscle
Cell type
RD
Primary Tissue
Skelatal Muscle
Tissue Diagnosis
Rhabdomyosarcoma

Attributes by original data submitter

Sample

source_name
Rhabdomyosarcoma
cell line
RD cells
passages
p10-p15
knockdown
siRNA_LSD1
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Genomic DNA was extracted by manual lysis with a douncer for nuclear extraction followed by sonification (Covaris, M220). DNA-Histone-complexed were precipated with antibody against H3K4me2. ChIPSeq library was prepared according to the standard protocol with Illumina TrueSeq Library Preparation Kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
26422078
Reads aligned (%)
99.2
Duplicates removed (%)
4.1
Number of peaks
812 (qval < 1E-05)

hg19

Number of total reads
26422078
Reads aligned (%)
98.6
Duplicates removed (%)
5.3
Number of peaks
1022 (qval < 1E-05)

Base call quality data from DBCLS SRA