ChIP-Atlas: SRX1744309

Antigen

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)

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: For ChIP, cells were fixed with 1% formaldehyde. Extracted nuclei were sonicated and subjected to pull down with respective antibodies. The libraries were constructed with the Kapa Hyper Prep Kit from Kapa Biosystems (Kapa Biosystems, MA). Briefly, DNAs (10ng) were blunt-ended, 3’-end A-tailed and ligated to indexed adaptors with 6nt barcodes. Adaptored DNA were amplified by PCR to selectively enrich for those fragments that have adapters on both ends. Amplification was carried out for 10 cycles with the Kapa HiFi polymerase (Kapa Biosystems, Woburn, MA) to reduce the likeliness of multiple identical reads due to preferential amplification. The final libraries were run on Agilent bioanalyzer DNA high-sensitivity chip (Agilent, Santa Clara, CA) to determine the average fragment size and to confirm the presence of DNA of the expected size range. They were also quantitated by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA) prior to pooling and sequencing.