ChIP-Atlas: SRX2737330

Antigen

Cell type Class: Neural
Cell type: Cerebellum
MeSH Description: The part of brain that lies behind the BRAIN STEM in the posterior base of skull (CRANIAL FOSSA, POSTERIOR). It is also known as the "little brain" with convolutions similar to those of CEREBRAL CORTEX, inner white matter, and deep cerebellar nuclei. Its function is to coordinate voluntary movements, maintain balance, and learn motor skills.

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: All tissues were snap frozen and stored at -80°C. Tissues were pulverized in liquid nitrogen followed by chromatin fixation with 1% formaldehyde final concentration. Washed chromatin (PBS) was homogenized using a dounce tissue grinder in Farnham's lysis buffer and followed by chromatin fragmentation through sonication. Fragmentation efficiency in the range of 200 bp - 500 bp was controlled by gel electrophoresis and ChIP was performed using Dynabeads Protein A (Invitrogen) and the following antibodies: CTCF (Abcam ab70303 / Millipore 07-729) and H3K27ac (Abcam ab4729). Indexed libraries were produced using the NEBNext Ultra II DNA Library Prep Kit and NEBNext Index Primer Set for Illumina according to the manufacturer's protocol. Fragments between 200 bp and 500 bp were selected by gel electrophoresis and 50 bp single-end sequencing was performed on an Illumina HiSeq 2500. Libraries for sequencing were prepared using standard Illumina protocols.