Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FANCD2

Cell type

Cell type Class
Bone
Cell type
U2OS
Tissue
bone
Lineage
mesoderm
Description
osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590)

Attributes by original data submitter

Sample

source_name
U2OS cells expressing FANCD2-3xFLAG
treatment
DMSO control
antibody
FLAG Ab-IPed

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and FANCD2-DNA complexes were isolated with antibody. After franmentation to 200 bp using covaris, DNA libraries were prepared using the NEBNext ChIP-Seq library prep reagent set for Illumina (NEB #E6200) and the NEBNext multiplex oligos for Illumina (NEB #E7335 and #E7500) according to the instructions. Adapter ligated DNA was PCR amplified for 15 cycles. Libraries were sequenced on the Illumina Genome Analyzer IIx following the manufacturer's protocols (75 bp paried-end run).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
33115719
Reads aligned (%)
78.1
Duplicates removed (%)
22.7
Number of peaks
461 (qval < 1E-05)

hg38

Number of total reads
33115719
Reads aligned (%)
78.9
Duplicates removed (%)
22.0
Number of peaks
1080 (qval < 1E-05)

Base call quality data from DBCLS SRA