{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["tanushree agarwal"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17121"],"description":["Total RNA-seq was performed on HeLa cells to investigate transcriptomic changes associated with physiological protein condensates. rRNA was depleted using NEBNext rRNA Depletion Kit. Strand-specific libraries were prepared using QIAseq FastSelect and NEBNext Ultra II Directional RNA Library Prep Kit. Sequencing was performed on Illumina NovaSeq X Plus with 2x150 paired-end configuration. Reads were trimmed with Trimmomatic, mapped to human reference genome (ENSEMBL) using STAR, and gene counts generated with featureCounts."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - HeLa cells were grown under standard conditions and harvested for RNA extraction.","Nucleic Acid Extraction - RNA extraction was performed using the RNeasy Micro Kit (Qiagen) following the manufacturer's instructions. RNA was quantified using Qubit 4.0 Fluorometer and integrity checked using RNA Kit on Agilent 5600 Fragment Analyzer.","Sequencing - Libraries were sequenced on Illumina NovaSeq X Plus with 2x150 paired-end configuration. Raw BCL files were converted to FASTQ using bcl2fastq v2.20 with one mismatch allowed for index identification.","Library Construction - rRNA was depleted using QIAseq FastSelect -rRNA HMR Kit and NEBNext rRNA Depletion Kit (Human/Mouse/Rat). Strand-specific libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Briefly, rRNA-depleted RNA was fragmented, first and second strand cDNA synthesised with dUTP incorporation, adenylated at 3' ends, ligated with indexed adapters, and amplified by limited cycle PCR. dUTP incorporation enabled second strand degradation to maintain strand specificity."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Reads were trimmed with Trimmomatic v0.36, mapped to Homo sapiens reference genome (ENSEMBL) using STAR v2.5.2b, and gene counts generated using featureCounts from Subread package v1.5.2."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"pubmed_abstract":["Biomolecular condensates are membraneless compartments, crucial for organising and regulating diverse cellular processes. Current approaches to study condensate biology either use simplified recombinant protein systems with limited physiological relevance, or complex live-cell models with restricted experimental control and scalability. Here, we present ExVivo PhaseScan, a droplet microfluidics platform that couples mammalian lysate-based reconstitution with scalable analysis to generate high-resolution phase diagrams of physiological protein condensates. We apply this approach to study two complex multicomponent condensate systems, stress granules and nucleoli, and dissect the physicochemical interactions that influence their stability. We further developed a machine learning pipeline to analyse condensate morphology which we use to reveal how mutations in the ALS-linked protein FUS remodels condensate phase landscapes. We identify liquid-to-solid transitions of mutant FUS within stress granules and nucleoli, and show that these transitions can be reversed by RNA aptamer-based interventions. Together, these findings establish ExVivo PhaseScan as a versatile tool for dissecting the physicochemical and pathological regulation of condensates, with potential to inform therapeutic strategies for diseases driven by aberrant phase transitions."],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Mapping high resolution, multidimensional phase diagrams of physiological protein condensates"],"pubmed_authors":["tanushree agarwal"],"additional_accession":[]},"is_claimable":false,"name":"Mapping high resolution, multidimensional phase diagrams of physiological protein condensates","description":"Total RNA-seq was performed on HeLa cells to investigate transcriptomic changes associated with physiological protein condensates. rRNA was depleted using NEBNext rRNA Depletion Kit. Strand-specific libraries were prepared using QIAseq FastSelect and NEBNext Ultra II Directional RNA Library Prep Kit. Sequencing was performed on Illumina NovaSeq X Plus with 2x150 paired-end configuration. Reads were trimmed with Trimmomatic, mapped to human reference genome (ENSEMBL) using STAR, and gene counts generated with featureCounts.","dates":{"release":"2026-06-13T00:00:00Z","modification":"2026-06-13T01:00:39.59Z","creation":"2026-06-05T17:05:41.632Z"},"accession":"E-MTAB-17121","cross_references":{"ENA":["ERP194549"],"doi":["10.1101/2025.11.24.690258"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0004184"]}}