biostudies-arrayexpressConor TempletonHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15997HPV 31 positive cervical keratinocytes (CIN 612 cells) were transduced with lentiviruses to stably express either a scramble control sequence (Scrm CIN 612) or shRNAs targeting the RNA helicase, senataxin (SETX). RNA sequencing was performed on these cell lines to identify cellular genes whose expression was regulated by SETX expression. The experiment was done in biological duplicate, and two different shRNA sequences were used (shSETX1/13 and shSETX2/30).biostudies-arrayexpressLibrary Construction - RNA libraries for RNA-seq were prepared using the DNBseq Eukaryotic Strand-specific Transcriptome Resequencing; stranded mRNA library (HNO2D).Sample Collection - NIH-3T3 J2 cells were removed through treatment with versene for >5min. Primary cells were then scraped and harvested on ice.Sequencing - Sequenced using the DNBSEQ-G50 by BGI. Paired end reads were generated with a read length of 150.Nucleic Acid Extraction - RNA was extracted using the Qiagen RNeasy Mini Kit. At least 1ug of RNA was submitted per sample.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - RNA sequencing was performed using the DNBSEQ platform with a sequencing length of PE150. Raw data was filtered using the software, SOAPnuke (v1.5.2). Filtered reads were aligned to the reference genome using HISAT2 software (v2.0.4). Bowtie2 software was used to align the clean reads to the reference gene sequence, and RSEM was used to calculate gene expression levels. DESeq2 (v1.4.5) was used to identify the differentially expressed genes (DEGs). The resultant DEG table is included.UnknownTranscriptomicsGenomicsProteomicsDNBSEQ-G50RNA-seq of coding RNAHomo sapiensConor TempletonLaimonis LaiminsfalseRNA-sequencing of scrambled control CIN 612 cells and CIN 612 cells depleted of senataxin (SETX) through stable expression of shRNAsHPV 31 positive cervical keratinocytes (CIN 612 cells) were transduced with lentiviruses to stably express either a scramble control sequence (Scrm CIN 612) or shRNAs targeting the RNA helicase, senataxin (SETX). RNA sequencing was performed on these cell lines to identify cellular genes whose expression was regulated by SETX expression. The experiment was done in biological duplicate, and two different shRNA sequences were used (shSETX1/13 and shSETX2/30).2025-11-15T00:00:00Z2025-11-15T02:02:22.542Z2025-11-06T12:18:31.597ZE-MTAB-15997ERP183802EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184