Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Others
Cell type
Mesenchymal stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
MSC
cell type
MSC
treatment
vehicle
passages
p5
chip antibody
IgG

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Total RNA was extracted with Trizol reagent. To obtain the genomic DNA fragments of interest, the cells were crosslinked and lysed, and then the chromatin was sheared into fragments using sonication. Then samples were incubated with anti-H3K4me3 antibody(Abcam, ab8580) or anti-FLAG(Sigma, F1804) antibody overnight. The DNA was de-crosslinked and extracted on the next day. 1.5 μg of total RNA was used to construct RNA sequencing libraries by TruSeq RNA Sample Preparation Kit (Illumina) following the manufacturer’s recommended protocol. After the DNA was de-crosslinked and extracted, the ChIP-sequencing library was constructed by TruSeq DNA Sample Preparation Kit (Illumina) or NEBNext® DNA Library Prep Reagent Set (NEB) according to the manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
8471511
Reads aligned (%)
53.9
Duplicates removed (%)
5.4
Number of peaks
105 (qval < 1E-05)

hg19

Number of total reads
8471511
Reads aligned (%)
53.3
Duplicates removed (%)
5.6
Number of peaks
75 (qval < 1E-05)

Base call quality data from DBCLS SRA