GSM3562123: ATAC TPL2h Sal rep1; Mus musculus; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Neural
Cell type
Hippocampal neurons
NA
NA
Attributes by original data submitter
Sample
source_name
Hippocampal excitatory neurons
strain
C57BL/6J
tissue
Adult Forebrain (hippocampus)
age
3-6 month
gender
male
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
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.