Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Placenta
Cell type
Trophoblast giant cells
NA
NA

Attributes by original data submitter

Sample

source_name
Trophoblast giant cells - cultured
strain
129/Sv
chip antibody
H3K4me1 (Abcam, ab8895, lot 962583)
cell type
cultured trophoblast giant cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were trypsinized for 4 minutes and prepared using the ChIP kit (Millipore). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
3266690
Reads aligned (%)
92.9
Duplicates removed (%)
27.1
Number of peaks
74 (qval < 1E-05)

mm9

Number of total reads
3266690
Reads aligned (%)
92.6
Duplicates removed (%)
28.0
Number of peaks
91 (qval < 1E-05)

Base call quality data from DBCLS SRA