{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Manoj Valluru"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14624"],"description":["Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most common hereditary cause of kidney failure, resulting from germline mutations in PKD1 and PKD2 in over 90% of cases. Polycystin-1 (PC-1), a cell surface receptor linked to focal adhesion proteins, plays a critical role in regulating cell-matrix and cell-cell interactions. This study explores the hypothesis that the disrupted actin phenotype observed in ADPKD may be influenced by F-actin binding and the translational regulation of actin-associated proteins mediated by a PC1-BICC1 complex. We examined whether actin-associated pathways are deregulated in UCL93 kidney epithelial cells and CRISPR-Cas9 knockout models for PKD1 and BICC1. Total RNA was extracted for gene expression analysis using total RNA-Seq, and the data were util"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was extracted from the cells (n=3/ cell line) using a Trizol reagent and stored at -80°C. The RNA concentration and quality were determined using a Thermo Scientific™ NanoDrop™ spectrophotometer and Agilent 2100.","Library Construction - After rRNA removal at Novogene, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.","Sequencing - The qualified libraries are fed into the Illumina HiSeq sequencer and sequenced (Paired-end 150 bp) at the Novogene facility.","Sample Collection - UCL93 and KO cells were plated at 5x10^5 cells/mL in 10 cm2 plates and incubated at 33°C under 70% confluency was reached. Total RNA was extracted from the cells (n=3/ cell line)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Data was processed in ShARC (Sheffield Advanced Research Computer at the University of Sheffield). Quality control checks on raw sequence data were done using the bioconda package fastqc-0.11.8-1. The adapter trimming was performed using cutadapt-1.18, and reads were aligned to the human genome (human genome GRCh38 and annotations gencode.v29) using star=2.6.1 and Transcriptome.out.bam was realigned and quantified using rsem=1.2.28.","Data Transformation - Expected counts and TPM values were extracted from gene-level expression estimates files for further analysis. The expected counts were subjected to DESeq2 normalisation and two-group differential expression analysis in R."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Agilent 2100","Illumina HiSeq 2500","ShARC"],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_title":["An Integrin Beta-1 anchored Bicaudal C1-Polycystin-1 protein complex essential for cyst formation through regulating F-actin organization and focal adhesion function"],"pubmed_authors":["Manoj Valluru","Andrew J Streets, Manoj K Valluru, Devon Smith, Natalia Bulgakova, Iddo Ben-Dov, Stuart Wilson, Chris Toseland, Lisa Chang, Albert CM Ong"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptome Profiling of UCL93 Kidney Epithelial Cells and CRISPR-Cas9 Knockouts for PKD1 and BICC1 Using Total RNA-Seq","description":"Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most common hereditary cause of kidney failure, resulting from germline mutations in PKD1 and PKD2 in over 90% of cases. Polycystin-1 (PC-1), a cell surface receptor linked to focal adhesion proteins, plays a critical role in regulating cell-matrix and cell-cell interactions. This study explores the hypothesis that the disrupted actin phenotype observed in ADPKD may be influenced by F-actin binding and the translational regulation of actin-associated proteins mediated by a PC1-BICC1 complex. We examined whether actin-associated pathways are deregulated in UCL93 kidney epithelial cells and CRISPR-Cas9 knockout models for PKD1 and BICC1. Total RNA was extracted for gene expression analysis using total RNA-Seq, and the data were util","dates":{"release":"2026-07-27T00:00:00Z","modification":"2026-07-27T15:03:39.039Z","creation":"2024-11-21T23:34:44.345Z"},"accession":"E-MTAB-14624","cross_references":{"ENA":["ERP166425"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}