GSM7573901: HSC3 cells, Untreated Sample 4; Homo sapiens; RNA-Seq
Total RNA was isolated using miRNeasy Mini Kit (Qiagen, #1038703) for RNASeq and RNeasy mini kit (Qiagen, #74106). A NanoDrop spectrophotometer (Thermo Scientific, #13400519) was used to measure the 260/280 The Illumina sequencing run produced 774,131,516 raw paired-end reads from 12 samples (54,874,503-71,100,845 reads). Quality control of raw sequencing reads was performed using FastQC (v0.11.5).Low-quality reads, sequencing adapters and overrepresented K-mers were removed using Trimmomatic (v0.32) resulting a total of 708,579,673 trimmed reads (46,791,160-66,701,914). The reads were aligned to the Human reference genome (Ensembl release 84-GRCh38) using the STAR aligner (v2.5.2a) and default alignment parameters to produce BAM files. HTSeq-Count (v0.6.1p1) was then used to generate read counts per gene based on the 84-GRCh38 GTF considering that the RNASeq library is stranded. The counts generated were then filtered to remove unexpressed or very lowly expressed genes to retain only genes with a minimum of 5 reads in 50% of samples in at least one of the three conditions investigated. The Illumina sequencing run produced 774,131,516 raw paired-end reads from 12 samples (54,874,503-71,100,845 reads). Quality control of raw sequencing reads was performed using FastQC (v0.11.5).Low-quality reads, sequencing adapters and overrepresented K-mers were removed using Trimmomatic (v0.32) resulting a total of 708,579,673 trimmed reads (46,791,160-66,701,914). The reads were aligned to the Human reference genome (Ensembl release 84-GRCh38) using the STAR aligner (v2.5.2a) and default alignment parameters to produce BAM files. HTSeq-Count (v0.6.1p1) was then used to generate read counts per gene based on the 84-GRCh38 GTF considering that the RNASeq library is stranded. The counts generated were then filtered to remove unexpressed or very lowly expressed genes to retain only genes with a minimum of 5 reads in 50% of samples in at least one of the three conditions investigated.