GSM8524673: Insoluble_fraction_vehicle_RNA_Ins1; Homo sapiens; RNA-Seq
RNA was extracted from cytosolic, nuclear, and insoluble fractions using the PureLink™ RNA Mini Kit (Invitrogen™ 12183018A), according to the manufacturer protocol, continue with on-column DNase treatment PureLink™ DNase Set (Invitrogen™ 12185010). RNAs were stored at -80. RNA integrity was quantified using Qubit and checked on an RNA 6000 Nano Agilent Lab-on-a-Chip kit with Bioanalyzer Systems before cDNA library preparation. The generation of cDNA for the RNA sequencing data was carried out as detailed in (Shademan et al., 2024), using the 1C library preparation protocol. The generation of cDNA for the RNA-seq data was carried out with the mcSCRB-seq protocol, with the following modifications to the workflow: instead of single cells, we used 1–100 ng isolated total RNA, 7.5% PEG8000 was replaced with 0.5% polyvinylpyrrolidone, and the oligo-dT primer was replaced with the SCIFI_LIG384_001 primer. All samples were barcoded during reverse transcription using a well barcode. Illumina paired-end sequencing of the library was done on a NovaSeq 6000 using paired-end 150-bp sequencing and v1.5 chemistry. After sequencing followed by filtering en clipping the reads on used adapter sequences, the first 8 bases with the qvalues of read2 were pasted at the beginning of read 1. 1C RNA-seq