Bursts were detected using the Inter-Spike Interval (ISI). Number of active electrodes and number of spikes were counted in a period of 2 min respectively. The weighted mean firing rate was calculated as the mean firing rate, averaged across only the active electrodes (minimum spike rate for active electrode was set to 5 spikes/min). For recordings, a Butterworth band-pass filter (with a high-pass cutoff of 200 Hz and a low-pass cutoff of 3000 Hz) was applied, along with an adaptive threshold spike detector set to detect any amplitude greater than or equal to a multiple of six standard deviation (6xSD) of the estimated noise on each channel. All recordings were conducted at 37 ☌, unless otherwise stated. Channels were sampled simultaneously with a sampling rate of 12.5 kHz/channel, voltage scale of 5.51E-08 V/sample, and digital high pass IIR-filter of 5 Hz. The resulting variant files were combined (GATK, v3.6, CombineVariants) and processed with KGGSeq (v1.0, 14/Apr./2017).ĭata were acquired using Axion BioSystems' Integrated Studio (AxIS, version 2.3.1.11) software, and 2 min raw data files were taken for each recording. Variants called by at least two programs were considered for further analysis. Three variant callers were applied for variant detection (GATKLite UnifiedGenotyper (variant version: 2.3-9-gdcdccbb), SAMtools (mpileup version: 0.1.19-44428cd), FreeBayes (version: 0.9.14-14-gb00b735)). Genome version hg19 was used for the alignment. ![]() Alignment and variant calling was performed with SeqMule (v1.2), (FastQC (version: 0.11.2), BWA-MEM (version: 0.7.8-r455), SAMtools (rmdup version: 0.1.19-44428cd), SAMtools (filter version: 0.1.19-44428cd), SAMtools (index version: 0.1.19-44428cd, and GATKLite (realign version: 2.3-9-gdcdccbb). Enrichment was done with an Illumina Enrichment Kit (Nextera Rapid Capture Exome v1.2) and the respective libraries were sequenced on a NextSeq500 sequencer (Illumina, San Diego, USA). Whole-exome Sequencing was performed with DNA from fibroblast cells. The Lancet Regional Health – Western Pacificįibroblasts of the patient suffering from SFN were cultured from a skin biopsy of the patient and two age matched controls (Ctrl1 and Ctrl2) after written informed consent (Review Board approvals Nr.The Lancet Regional Health – Southeast Asia.The Lancet Gastroenterology & Hepatology.
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