GSM9266087: Donor 3, NS-Y, rep2; Homo sapiens; RNA-Seq
120uL sample in lysis buffer was added to 50uL AMPure XP Reagent (Beckman Coulter, A63881) in a 96-well PCR plate and incubated for 20 minutes to allow RNA binding to the beads. The beads were pulled down using a DynaMag™-96 Side Skirted Magnet (Invitrogen, 12027) and washed 3x using 70% EtOH (100% EtOH (VWR, 20.816) mixed with ultrapure water). RNA was eluted by resuspending the beads in nuclease free water (Ambion, AM9937) and samples were stored at -80ᵒC until further use. Sequence reads were trimmed to remove possible adapter sequences and filtered on low-quality bases using fastp v0.23.2. Presumed adapter sequences were removed from the read when the bases matched a sequence in the adapter sequence set (TruSeq adapters). To remove noise introduced by sequencing errors, the reads were filtered based on the base quality score. Reads of which more than 40% of the bases had an average phred score below Q15 or which had more than 5 unknown bases (N) were removed. If the resulting reads were shorter than 15 bp, they were removed altogether (both pairs in paired-end reads). For each sample, the trimmed reads were mapped to the human GRCh38.p13 (Homo_sapiens.GRCh38.dna.primary_assembly.fa).
GEO
GSM9266087_r1