title: Mitochondria structure and function in OCRL depleted cells
design: Mitochondria structure and function in OCRL depleted cells
library_construction_protocol: Cells were cultured and maintained until ~75% confluency after which they were dissociated and pelleted.  humidified atmosphere with 5% CO2 at 37 C. NCRM5 and OCRL Knockout NSCs were maintained in Neural Expansion Media under similar incubator conditions. NCRM5 and OCRL Knockout NSCs were differentiated to 30 day old neurons in Neural differentiation media under similar incubator conditions.  Both control and OCRL Knockout cells were maintained in similar media conditions until RNA extraction. FastQC version 0.11.7 was run for all samples 1-12. For samples 1-6, adapter trimming was done using Cutadapt version 5.0 hisat2(2.2.1) was used to map trimmed reads to GrCH38   Trizol was added to the cell pellet. RNA was then extracted from the trizol samples using the chloroform extraction method.  rRNA depletion was performed on the isolated RNA using the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads (Catalog no-E7405L) following which RNA libraries for RNA-seq were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalog no-E7765L)