ChIP-Atlas: SRX8020471

Antigen

Cell type Class: Neural
Cell type: Brain
MeSH Description: The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.

source_name: Primary brain samples acquired post-mortem, Superior Temporal Gyri
tissue: brain
brain region: Superior Temporal Gyri

library_strategy: ATAC-seq
library_source: GENOMIC
library_selection: other
library_construction_protocol: Nuclei were isolated from frozen tissue in accordance with protocol dx.doi.org/10.17504/protocols.io.6t8herw. After isolation, nuclei were cryopreserved in BAM Banker (Wako Chemicals) and stored at -80°C for use in other assays such as scATAC-seq and HiChIP. Transposed fragments were purified and amplified as described previously (Buenrostro et al., Nature Methods 2015) with slight modification. Briefly, transposed fragments were pre-amplified for 3 cycles. Concentration of pre-amplified fragments was determined by qPCR and this concentration was used to estimate the total number of cycles required to obtain 160 femtomoles of fragments. A second PCR was performed to amplify the pre-amplified fragments for the desired number of cycles. Final libraries were again purified. Prior to sequencing, libraries were pooled and run on a 6% PAGE gel and excess primers and primer dimers below 125 bp were removed. Nuclei were isolated from frozen tissue in accordance with protocol dx.doi.org/10.17504/protocols.io.6t8herw. After isolation, nuclei were cryopreserved in BAM Banker (Wako Chemicals) and stored at -80°C for use in other assays such as scATAC-seq and HiChIP.