Curated Sample Data


Genome
mm9
Antigen Class
Input control
Antigen
Input control
Cell type Class
Blood
Cell type
Hematopoietic Stem Cells

Cell type information


MeSH Description
Progenitor cells from which all blood cells derived. They are found primarily in the bone marrow and also in small numbers in the peripheral blood.

Attributes by Original Data Submitter


source_name
stem/progenitor from bone marrow
cell source
stem/progenitor from bone marrow
genotype
JMJD1B knockout
ChIP
Input

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP on native chromatin from hematopoitic stem/progenitor cells was performed following previously published protocols (M. Girardot et al., 2014. Nucleic acids research 42, 235-248) with the following modifications using ChIP-grade Magna protein A/G beads (Cat#: 16-663, EMB Millipore). The isolated nuclei were incubated for 15 min at 37°C with 4 units/uL of Micrococcal nuclease (M0247, New England Biolabs) to produce mono/di-nucleosomes as verified by agarose gel electrophoresis. Nucleosomes were precipitated with control IgG, ChIP-grade anti-H4R3me2s (Cat#: Ab5823, Abcam) or anti-H3K9me2s (Cat#: 39375, Active motif). ChIP or input DNA was purified with Ampure XP beads (Cat#: A63880, Beckman Coulter). ChIP libraries were repard according to standard Illumina protocols. Transcriptome libraries were constructed with TruSeq RNA Sample Preparation Kit V2 (Illumia) with minor modifications.

Platform Information


instrument_model
Illumina HiSeq 2500

External Database Query

Logs in read processing pipeline


Number of total reads
54501763
Reads aligned (%)
97.8
Duplicates removed (%)
8.4
Number of peaks
334 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA