Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Blood
Cell type
Hematopoietic progenitors
NA
NA

Attributes by original data submitter

Sample

ENA first public
2018-08-20
ENA last update
2017-03-10
ENA-CHECKLIST
ERC000011
External Id
SAMEA103906301
INSDC center alias
Friedrich Alexander University Erlangen-Nurnberg FAU Department Biology
INSDC center name
Friedrich Alexander University Erlangen-Nurnberg FAU Department Biology
INSDC first public
2018-08-20T17:02:52Z
INSDC last update
2017-03-10T14:51:49Z
INSDC status
public
Submitter Id
E-MTAB-5569:H2AUb_smpl2
broker name
ArrayExpress
cell line
Meer
cell type
hematopoietic precursor cell
common name
house mouse
genotype
Mll-ENL-ER
sample name
E-MTAB-5569:H2AUb_smpl2

Sequenced DNA Library

library_name
H2AUb_smpl2_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For generation of Meer cells primary hematopoietic precursor cells were isolated from the bone marrow of Meer mice that carry a knock-in of an ENL-ER (mutant estrogen receptor ligand binding domain) portion into the mouse Mll locus. (Lit: Takacova, S. et al. Cancer Cell 21, 517-31, 2012). CD117 (c-kit) positive cells were isolated by magnetic enrichment according to the instructions of the manufacturer (CD117 enrichment kit, Miltenyi Biotech, Bergisch-Gladbach, Germany) and initially plated in methocel (MethoCult M3234, StemCellTechnologies, Koln, Germany) to purge residual stroma cells that cannot grow in semisolid media. After two rounds of growth in methylcellulose cells were expanded in RPMI1640 supplemented with 10% FCS. All media contained 50ng/ml recombinant murine (rm) SCF, 10ng/ml of rm-IL3, IL6, GM-CSF (cytokines were bought from Miltenyi Biotech, Bergisch-Gladbach, Germany) and for activation of the estrogen receptor 100nM 4-hydroxytamoxifen (TAM, Sigma, Taufkirchen, Germany). ChIP was done exactly as described in (Milne, T.A., Zhao, K. & Hess, J.L. Chromatin immunoprecipitation (ChIP) for analysis of histone modifications and chromatin-associated proteins. Methods Mol Biol 538, 409-23 (2009) with the exception that protein G-coupled paramagnetic beads from CellSignalingTechnologies (CST/NEB, Frankfurt, Germany) were used as precipitating agent. Antibodies and concentrations used : anti-H2AUb, Cell Signaling Technologies (#8240) 10µl; anti-H2BUb, Cell Signaling Technologies (#5546) 5µl ChIP Seq library construction with Illumina Kit according to the instructions of the manufacturer

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
17832139
Reads aligned (%)
98.8
Duplicates removed (%)
3.7
Number of peaks
155 (qval < 1E-05)

mm9

Number of total reads
17832139
Reads aligned (%)
98.7
Duplicates removed (%)
3.8
Number of peaks
128 (qval < 1E-05)

Base call quality data from DBCLS SRA