GSM4654696: NB_4ATAC_Retina; Mus musculus; ATAC-seq
Fresh retina and RPE tissues were harvested from photosensitive Abca4-/-Rdh8-/- mice according to published protocols. Under a dissecting microscope, spring scissors were used to puncture the eye and remove the cornea, iris, and lens. The remaining eyecup had 4 radial incisions made every 90 degrees, resulting in a flat and open eye cup. The retina was then gently removed using curved tweezers and placed in a 1.5 ml microcentrifuge tube containing RNAlater (Qiagen, Hilden, Germany). The RPE-containing eyecup was placed in a 1.5 ml microcentrifuge tube containing RNAprotect (Qiagen). The second eye was processed identically and pooled with the first eye from the same mouse. Total RNA from RPE cells was isolated using the simultaneous RPE cell isolation and RNA stabilization (SRIRS) method. Briefly, the tube containing RNAprotect with the 2 pooled RPE/choroid eyecups was agitated after 10 min and collected at 20 min at RT.  After the second agitation the eyecups (choroid) were removed, with dissociated RPE cells remaining in solution. Retina and RPE samples in RNAlater and RNAprotect, respectively, were stored at 4° C for up to one week.  Illumina TruSeq Stranded mRNA Library, ATAC-Seq library preparation, Illumina Nextera DNA library prep kit