Transcriptional profiles of individuals with KDM5A variants

KDM5A is an ASD gene and chromatin regulator. We identified a cohort of 22 individuals harboring monoallelic and biallelic KDM5A variants. We cultured lymphoblastoid cell lines from a subset of these individuals and performed RNAseq. Overall design: RNA was extracted from LCL pellets derived from patients, parents, and siblings, when available, using TRIzol reagent (Invitrogen), and purified with the RNeasy Mini Kit (Qiagen). Genomic DNA was removed using the RNase-free DNase kit (Qiagen). RNA quality was assessed using the Agilent TapeStation 4200, and all samples had a RIN score of = 8. RNA concentrations were measured using a Qubit fluorometer, and 1 µg of DNase-treated total RNA was used for library preparation with the TruSeq Stranded mRNA Library Prep Kit (Illumina). Poly-A RNA was purified and fragmented, and strand-specific libraries were amplified and purified using AmpureXP beads. Samples were sequenced on the Illumina NextSeq 500 using V2.5 reagents.