ChIP-Atlas: SRX8168421

Antigen

Cell type Class: Others
Cell type: Cochlea
MeSH Description: The part of the inner ear (LABYRINTH) that is concerned with hearing. It forms the anterior part of the labyrinth, as a snail-like structure that is situated almost horizontally anterior to the VESTIBULAR LABYRINTH.

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: Cells were collected by FACS purification into cold PBS, and centrifuged 500 xg for 15 min. Cell pellet were resuspended with 50 ul transposition buffer consisting of 10mM Tris-HCL pH8.0, 5 mM MgCl2, 10% DMF, 0.2% NP40, and home-made transposase Tn5. Transposition was performed at 37 degree for 20 min. DNA was collected immediately after transposition using Qiagen Mini-elute kit. Histone ChIP-seq protocol was developed by us based on μChIP-PCR protocol published previously (Stojanova et al., 2015) with additional Tn5 tagmentation step. Briefly, chromatin was cross-linked with 1% formaldehyde (Thermo Fisher) for 8 min, quenched with 125mM Glycine (Sigma) for 5 min at room temperature, sonicated using the microtip of a High Intensity Ultrasonic Processor (Sonics & Materials, Newtown, CT; amplitude 50, power 50) for 8 x 30 sec with 30 sec pause, tagmentated with Tn5 transposase for 30 min at 37°C, incubated with antibody complexed with Dynabeads Protein A (Thermo Fisher) overnight at 4°C, precipitated and washed three times on magnetic rack, and finally PCR amplified with primers matching Tn5 adapters.