Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CEBPB

Cell type

Cell type Class
Others
Cell type
Mesenchymal stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
hMSC
cell type
Human Mesenchymal Stem Cells
chip antibody
CEBPb, sc-150, Santa Cruz

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell pellets were prepared from 1.8x106 cells, crosslinked in 1 % formaldehyde for 15 minutes. A 5 minute quench was performed with 125mM glycine. Cells were harvested from 10 or 15cm dishes in DPBS using a cell scraper. To prepare ChIP extracts, nuclei were suspended SDS lysis buffer (50 mM HEPES/NaOH pH 7.5, 1% SDS, 10 mM EDTA, Complete protease inhibitor), incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency. ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
41704759
Reads aligned (%)
33.1
Duplicates removed (%)
58.6
Number of peaks
37858 (qval < 1E-05)

hg38

Number of total reads
41704759
Reads aligned (%)
34.6
Duplicates removed (%)
57.2
Number of peaks
38301 (qval < 1E-05)

Base call quality data from DBCLS SRA