GSM5346022: SM006; Homo sapiens; RNA-Seq
3 organoids per samples and dissociated using the papain dissociation protocol (Worthington Biochemicals) The 10x Genomics Chromium Single Cell 3' Solution The resulting pooled, 3'-end libraries are typically sequenced on a NovaSeq 6000 Ten forebrain organoids per line (i.e., 3 control-derived lines, 3 patient-derived lines) were collected at 8 weeks in vitro. Total RNA was isolated from hiPSC-derived cortical neurons using miRNeasy kit (Qiagen, USA) according to instructions of the manufacturer.A poly-A pull-down step was performed to enrich mRNAs from total RNA samples (200 ng to 1 µg per sample, RIN > 8 required) library preparation was done using Illumina TruSeq RNA prep kit Libraries were sequenced using Illumina HiSeq2000 at the Columbia Genome Center. Multiplex samples with unique barcodes were mixed in each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane. RTA software (Illumina) was used for base calling, and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. The reads were mapped to a reference human genome (hg19) using Tophat2.0 (version 2.0.4) with four mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
GEO Accession
GSM5346022