*4.6. RNA-Sequencing and Data Analysis*

RNA sequencing was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), a member of the Vienna BioCenter (VBC), Austria. From the total RNA, we provided they conducted poly-A enrichment for mRNAs and prepared libraries using the Illumina TruSeq RNA kit. The six libraries (3 control oligo, 3 *LINC01133* knock-down) were multiplexed on a single lane and subjected to 125 bp paired-end sequencing on an Illumina HiSeq2500 machine. The facility provided de-multiplexed BAM files containing the raw reads, which we converted to fastq using Samtools (v1.10) for alignment with STAR using the parameters: –outFilterMultimapNmax 1 –outSAMstrandField intronMotif –outFilterIntronMotifs RemoveNoncanonical –outSAMtype BAM SortedBy-Coordinate –quantMode GeneCounts. On average 38M reads (94% of all reads) mapped uniquely to the human genome (Table S2B). Annotation files and genome sequences were downloaded from https://www.gencodegenes.org (accessed on 2 December 2020). Index for alignments was prepared using STAR (2.7.6a\_patch\_2020-11-17) [53] with FASTA files from the GRCh38.p13 assembly and Gencode (v36) gene annotation in GTF format.

Differential gene expression analysis was performed in the R statistical computing environment (v4.0.3) [54] using the DESeq2 package (v1.30.0) [55] with count tables produced by STAR during alignment (\*ReadsPerGene.out.tab files).
