Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PRMT3

Cell type

Cell type Class
Others
Cell type
Mesenchymal stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
mesenchymal stem cell
cell type
mesenchymal stem cell
chip antibody
PRMT3 (Abcam, Cambridge, UK)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, cells were cross-linked with 1% formaldehyde, resuspended in lysis buffer (1% SDS, 10 mM EDTA, and 50 mM Tris-HCl [pH 8.0]) on ice for 3 min, and fragmented by sonication in RIPA ChIP buffer (0.5 mM EGTA, 140 mM NaCl, 10 mM Tris-HCl, pH 7.5, 1% TritonX-100, 0.01% SDS, 1 mM EDTA and protease inhibitor). The samples were then incubated overnight with Protein A/G-beads bound with antibodies [PRMT3 (Abcam, Cambridge, UK), H4R3me2a (Active Motif, Carlsbad, CA), H3 (Cell Signaling)]. After the crosslinking was reversed, immune complexes containing DNA were purified and eluted. The precipitated DNA for sequencing, including H4R3me2a and PRMT3, were constructed into libraries with NEBNext DNA Library Prep Reagent Set for Illumina (NEB) as described by the manufacturer.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
9483242
Reads aligned (%)
147.4
Duplicates removed (%)
22.6
Number of peaks
184 (qval < 1E-05)

hg38

Number of total reads
9483242
Reads aligned (%)
149.8
Duplicates removed (%)
22.3
Number of peaks
347 (qval < 1E-05)

Base call quality data from DBCLS SRA