biostudies-arrayexpressMichal MalewiczHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15067In this project we use RNA obtained from HEK293 cells to investigate the expression profile of the following lines: wild type (control cell line), LYAR knockout cell line (CRISPR-generated) and LYAR-rescued (LYAR KO cell line transfected with plasmid encoding wild type FLAG-LYAR protein) by RNA-seq.biostudies-arrayexpressSample Collection - Cells were plated on 10 cm plates and grown for 48 hours. Subsequently, the cells were pelleted, washed twice with PBS, and stored at -80°C.Sequencing - This step was performed by Novogene Europe. Samples were sequenced using Illumina NovaSeq PE150, Q30≥85%.Nucleic Acid Extraction - Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.The concentration of isolated RNA was measured by NanoDrop.Library Construction - This step was performed by Novogene Europe. Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesizedusing random hexamer primers, followed by the second strand cDNAsynthesis using either dUTP for directional library or dTTP for non-directional library.For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantificationand bioanalyzer for size distribution detection. Quantified libraries were and sequenced on Illumina platforms, according to effective library concentration and data amount.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - This step was performed by Novogene Europe. Raw data (raw reads) in fastq format was firstly processed through in-house perl scripts. In this step, clean data (clean reads) was obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content were calculated. All the downstream analyses were based on the clean data with high quality.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensMichal MalewiczMalgorzata SzatkiewiczfalseThe role of Lyar in the regulation of cell cycle checkpointsIn this project we use RNA obtained from HEK293 cells to investigate the expression profile of the following lines: wild type (control cell line), LYAR knockout cell line (CRISPR-generated) and LYAR-rescued (LYAR KO cell line transfected with plasmid encoding wild type FLAG-LYAR protein) by RNA-seq.2026-04-30T00:00:00Z2026-06-01T15:05:58.441Z2025-04-23T13:07:12.074ZE-MTAB-15067ERP171891EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184