ChIP-Atlas: SRX5248674

Antigen

Cell type Class: Neural
Cell type: Hippocampus
MeSH Description: A curved elevation of GRAY MATTER extending the entire length of the floor of the TEMPORAL HORN of the LATERAL VENTRICLE (see also TEMPORAL LOBE). The hippocampus proper, subiculum, and DENTATE GYRUS constitute the hippocampal formation. Sometimes authors include the ENTORHINAL CORTEX in the hippocampal formation.

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: Hippocampi were micro-dissected after cervical dislocation, washed in ice-cold PBS and pooled together, when fixation was needed 1% FA was used. TRAP immunoprecipitation followed the original protocol by (Heiman et al., 2014) with small changes. Nuclei were isolated using our improved FANS protocol for SUN1-GFP+ cells, in case NE condition nuclei were stained against FOS. Extensive description of protocols indicated in Supplemental Experimental Procedures. For riboRNA and nuRNA, extraction was re-suspended in RLT buffer for purification with RNeasy Micro kit (Qiagen 74004). Truseq libraries were prepared from ribo-depleted total RNA in the case of nuRNA-seq and from polyA-selected mRNA in the case of riboRNA-seq. ATAC-seq experiments were conducted as the original protocol (Buenrostro et al., 2013), libraries were purified with MinElute PCR purification kit (Qiagen 28004). ChIP-seq was conducted as previously described (Lopez-Atalaya et al., 2013) using the anti-H3K4me3 (Millipore 07-473), anti-CBP (sc583x) and anti-RNAPII (sc901x). In situ Hi-C were conducted as the original protocol (Rao et al., 2014), libraries were prepared with TruSeq.