title: Sample 4
organism: Homo sapiens
description: Protocols: 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)
attributes.tag: ENA first public
attributes.value: 2025-12-10
attributes.tag: INSDC center name
attributes.value: National Centre for Biological Sciences-TIFR, Bengaluru
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-16227:Sample 4
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell line
attributes.value: iPSC derived cell line
attributes.tag: cell type
attributes.value: neuronal stem cell
attributes.tag: collection date
attributes.value: not collected
attributes.tag: common name
attributes.value: human
attributes.tag: disease
attributes.value: Oculocerebrorenal syndrome
attributes.tag: genetic modification
attributes.value: CRISPR-Cas9 OCRL Ko
attributes.tag: genotype
attributes.value: germline genotype
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: brain
attributes.tag: sample name
attributes.value: E-MTAB-16227:Sample 4
attributes.tag: scientific_name
attributes.value: Homo sapiens