Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CBX4

Cell type

Cell type Class
Others
Cell type
Mesenchymal stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
CBX4-/- hMSC induced with lentiviruses expressing Flag-CBX4, sample incubated with Flag antibody
cell type
MSC
passages
p8
chip antibody
Flag

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Total RNA was extracted with the RNeasy Mini Kit (Qiagen). To obtain the genomic DNA fragments of interest for ChIP-seq, 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, ab8050, lot#GR3190162-1) or anti-FLAG 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 NEB Next Ultra RNA Library Prep Kit (NEB) for Illumina following the manufacturer's recommended protocol. The ChIP-sequencing library and copy number variation analysis sequencing library were constructed by NEB Next Ultra DNA Library Prep Kit (NEB) for Illumina according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
6606716
Reads aligned (%)
34.2
Duplicates removed (%)
28.3
Number of peaks
1502 (qval < 1E-05)

hg38

Number of total reads
6606716
Reads aligned (%)
34.6
Duplicates removed (%)
28.1
Number of peaks
1488 (qval < 1E-05)

Base call quality data from DBCLS SRA