Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Bone
Cell type
Osteosarcoma
MeSH Description
A sarcoma originating in bone-forming cells, affecting the ends of long bones. It is the most common and most malignant of sarcomas of the bones, and occurs chiefly among 10- to 25-year-old youths. (From Stedman, 25th ed)

Attributes by original data submitter

Sample

source_name
primary osteosarcoma tumor
tissue
primary osteosarcoma tumor
chip antibody
rabbit anti-H3K4me1 (Abcam #8895)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
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 (Part# 0801-0303). 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 (32 to 52 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 ~250 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 2500 following the manufacturer's protocols. ChIP-Seq: 36bp single end reads (MG63 and MG63.3), 50bp single end reads (all other samples); RNA-seq: 100bp paired-end reads

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
43366555
Reads aligned (%)
95.5
Duplicates removed (%)
1.4
Number of peaks
17482 (qval < 1E-05)

hg19

Number of total reads
43366555
Reads aligned (%)
95.1
Duplicates removed (%)
1.4
Number of peaks
17426 (qval < 1E-05)

Base call quality data from DBCLS SRA