biostudies-arrayexpressJan KubovčiakHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-10750We have identified differentially expressed genes and defects in processing of UsnRNAs in BRAT1-deficient and BRAT1-mutated patient cells by RNA-sequencing and BRAT1 as a structural and functional component of Integrator, linking defects in this critical endonuclease complex with hereditary neurodegenerative disease. Due to the sensitive nature of the data, raw data files have not been uploaded.biostudies-arrayexpressSample Collection - Cells were harvested from respective cell cultures.Nucleic Acid Extraction - Total RNA was isolated from 1×106 cells by miRNeasy Micro Kit (Qiagen) with an additional DNase I treatment, according to the manufacturer’s instructions.Sequencing - Libraries were sequenced on the Illumina NextSeq® 500 instrument using 76 bp single-end configuration.Growth Protocol - Human fibroblasts were cultured in Minimum Essential Medium Eagle (MEM; Gibco) supplemented with 15 % fetal bovine serum (FBS; Gibco), 2 mM L-glutamine (Gibco), and the antibiotics penicillin (100 units/ml) and streptomycin (100 μg/ml) (Pen/Strep; Gibco) at 37°C. Human wild type osteosarcoma cells (U2OS) were cultured in Dulbecco’s Modified Eagle’s Medium-high glucose (DMEM-high glucose; Sigma) supplemented with 10 % FBS and the antibiotics Pen/Strep at 37°C.Library Construction - Sequencing ibraries were prepared with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian user manual (Takara Bio USA, Inc).Sample Treatment - BRAT1 KO gene edited U2OS cell lines were prepared using Cas9 and guide sequences designed in CRISPR direct (https://crispr.dbcls.jp).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Fastq files were processed using nf-core/rnaseq pipeline 1.4.2. Reads were trimmed using TrimGalore! v0.6.4 and aligned to GRCh38 assembly (Ensembl annotation v98) using Salmon v0.14.1.Data Transformation - Expression was quantified using Salmon v0.14.1. Resulting per sample gene counts and TPM values are attached as processed data.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500RNA-seq of coding RNAHomo sapiensZuzana CihlarovaJan KubovčiakHana HanzlikovafalseBRAT1 Links Integrator and Defective RNA Processing with NeurodegenerationWe have identified differentially expressed genes and defects in processing of UsnRNAs in BRAT1-deficient and BRAT1-mutated patient cells by RNA-sequencing and BRAT1 as a structural and functional component of Integrator, linking defects in this critical endonuclease complex with hereditary neurodegenerative disease. Due to the sensitive nature of the data, raw data files have not been uploaded.2023-01-02T00:00:00Z2025-05-12T14:36:18.091Z2025-05-12T14:36:18.091ZE-MTAB-10750EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969