ChIP-Atlas: SRX6657807

Antigen

Cell type Class: Neural
Cell type: Retina
MeSH Description: The ten-layered nervous tissue membrane of the eye. It is continuous with the OPTIC NERVE and receives images of external objects and transmits visual impulses to the brain. Its outer surface is in contact with the CHOROID and the inner surface with the VITREOUS BODY. The outer-most layer is pigmented, whereas the inner nine layers are transparent.

library_strategy: ATAC-seq
library_source: GENOMIC
library_selection: other
library_construction_protocol: RNA was extracted from both GFP-positive and GFP-negative cell fractions using miRNAeasy Mini Kit (#217004, Qiagen). Ribosomal RNA was depleted, and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo-ZeroTM Gold (# 15032619, Illumina). For tagmentation, cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler (Illumnia Nextera DNA library prep kit, #FC1211030). DNA was cleaned up using MinElute PCR purification kit (#28006, Qiagen) and eluted in 10UL of EB buffer. Flow-sorted RNA samples were sent to the Deep Sequencing and Microarray Core (Johns Hopkins University) for library preparation and sequencing. Around 8-10 libraries were pooled and sequenced for paired-end 75 cycles using the NextSeq 500 system with ~400-500 million reads per run, resulting in ~45-55 million reads per library. Sorted cells (~50k-75k) from GFP-positive samples were used for ATAC library preparation. Completed ATAC-Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired-end 75 cycles using the NextSeq 500 system with ~400-500 million reads per run.