biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsMonika Drobna-ŚledzińskaIllumina NovaSeq XRNA-seq of coding RNAHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16358We performed mRNA sequencing upon the lentiviral shRNA knockdown of circN4BP2L2 in JURKAT T-ALL cell line compared to non-targeting shRNA transduced cells to characterize the effect of this circRNA on gene expression profile. The cells were collected for RNA isolation 5 days after lentiviral transduction. Libraries were prepared using the TruSeq Stranded mRNA kit (fragmentation at 90 °C for 2 minutes [doi:10.1016/j.ygeno.2021.10.018]). Sequencing was carried out on an Illumina NovaSeqX platform (2×150 bp paired-end, ~150 million read pairs per sample). This work has been supported by National Science Centre, Poland (OPUS 2022/47/B/NZ5/00663).biostudies-arrayexpressSequencing - The libraries were sequenced on an Illumina NovaSeqX platform, using the following settings: 2x150 PE (paired end sequencing with 150 nt reads), read depth of coverage: 150 million read pairs/sample.Sample Collection - 3 x 10^6 cells were collected from culture for RNA isolation 5 days after lentiviral transduction with miRZip pGreenPuro shRNA encoding vector.Growth Protocol - Cells were cultured under standard conditions in RPMI-1640 medium (Thermo Fisher Scientific, Waltham, MA, USA) with 10% of fetal bovine serum (Thermo Fisher Scientific).Library Construction - Libraries were constructed from isolated RNA, using TruSeq Stranded mRNA protocol. Fragmentation was performed at 90′C for 2 minutes, as described previously [https://doi.org/10.1016/j.ygeno.2021.10.018].Sample Treatment - For transduction of Jurkat T-ALL cell line, cells were seeded and then filtered medium containing lentiviral particles was added to each well. Polibrene Reagent (Sigma Aldrich) was added to each well at a final concentration of 8 μg/ml. Cells were spinfected for 90 min (at 1500 rpm and 32°C). Antibiotic selection of transduced cells was started 3–4 days post-transduction. For selection, puromycin dihydrochloride (Gibco, Thermo Fisher Scientific) was used at a concentration of 10 μg/ml for 4 days. The effectiveness of transduction was assessed with the use of the CytoFlex S flow cytometer (Beckman Coulter) with GFP as a marker.Nucleic Acid Extraction - RNA was isolated directly using the Quick-RNA MicroKit (Zymo Research, Irvine, CA, USA). RNA concentration was measured with Quantus Fluorometer (Promega, Madison, WI, USA) using Qubit HS RNA Assay Kit (Thermo Fisher Scientific). RNA integrity was determined with 4200 Tapestation using High Sensitivity RNA ScreenTape (Agilent Technologies, Santa Clara, CA, USA).OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMonika Drobna-ŚledzińskafalsemRNA-seq in JURKAT T-ALL cell line upon shRNA knockdown of circN4BP2L2We performed mRNA sequencing upon the lentiviral shRNA knockdown of circN4BP2L2 in JURKAT T-ALL cell line compared to non-targeting shRNA transduced cells to characterize the effect of this circRNA on gene expression profile. The cells were collected for RNA isolation 5 days after lentiviral transduction. Libraries were prepared using the TruSeq Stranded mRNA kit (fragmentation at 90 °C for 2 minutes [doi:10.1016/j.ygeno.2021.10.018]). Sequencing was carried out on an Illumina NovaSeqX platform (2×150 bp paired-end, ~150 million read pairs per sample). This work has been supported by National Science Centre, Poland (OPUS 2022/47/B/NZ5/00663).2026-01-01T00:00:00Z2026-01-02T02:03:15.16Z2025-12-02T18:36:50.428ZE-MTAB-16358E-MTAB-16337EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003738EFO_0004184EFO_0003969