{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Kathryn Wolhuter"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15583"],"description":["The PHACTR1 gene to a range of vascular and neurological diseases, underscoring its pivotal role in biology. As part of a larger multi-omics study, we performed bulk RNA-seq on stable HT1080 cell lines with overexpression or knockdown of PHACTR1, comparing them to scrambled control cells, to understand how PHACTR1 expression affects the transcriptome.   Cell lines were generated by lentiviral transfection with viral particles produced in Lenti-X 293T cells. Stable cell lines were selected with puromycin and maintained in media containing the selection agent.  RNA was extracted from cells (n=6 per condition) and RNA libraries were prepared using RNA with RIN score >9.8 using the KAPA Total RNA Library Preparation kit (Roche). Barcoded libraries were subsequently analyzed using an Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit v1.5 (300 cycles, Illumina) with paired-end lengths of 150 base pairs with a depth of >40 million reads. Fastq files were mapped onto the human GENECODE 29 version using STAR 2.7.5. The average reads/sample was 57M. No samples were excluded from analysis after quality control."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Cells were washed once with ice-cold PBS and RNA was extracted from cells using RNeasy Mini Kit (QIAGEN, #74104), as per the manufacturer’s instructions.","Library Construction - RNA libraries were prepared using RNA with RIN score >9.8 using the KAPA Total RNA Library Preparation kit (Roche, #08098093702).","Sequencing - Barcoded libraries were subsequently analyzed using an Illumina NovaSeq 6000 (Kinghorn Centre for Clinical Genomics Sequencing Facility, Sydney, Australia) using NovaSeq 6000 S1 Reagent Kit v1.5 (300 cycles, Illumina, #20028317) with paired-end lengths of 150 base pairs with a depth of >40 million reads.","Sample Collection - All cell samples (n=6/cell line) were generated in parallel using the same passage cells, tissue culture reagents and culture conditions followed by concurrent harvesting. Cells were plated 24 hours prior to harvest at 2.2 x 105 cells/mL in DMEM with 10% FBS and 0.2 μg/mL puromycin for stable cell lines."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Fastq files were mapped onto the human GENECODE 29 version using STAR 2.7.5. The average reads/sample was 57M.","Data Transformation - Data quality control was performed using FASTQC. Differential gene expression between PHACTR1 overexpression or knockdown versus scramble was analyzed using R package limma-voom."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Multi-omic Analysis of PHACTR1 Signaling Networks in Human Cells"],"pubmed_authors":["Jason Kovacic","Kathryn Wolhuter, Lijiang Ma, Nicole S Bryce, Osvaldo Contreras, Natalie Mellett, Ling Zhong, Chris Thekkedam, Corey Giles, Richard P Harvey, Thomas Hennessy, Chris Fouracre, David Bradley, Peter J Meikle, Johan L M Björkegren, Jason C Kovacic","Kathryn Wolhuter"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of PHACTR1 knockdown and overexpression in HT1080 stable cell lines","description":"The PHACTR1 gene to a range of vascular and neurological diseases, underscoring its pivotal role in biology. As part of a larger multi-omics study, we performed bulk RNA-seq on stable HT1080 cell lines with overexpression or knockdown of PHACTR1, comparing them to scrambled control cells, to understand how PHACTR1 expression affects the transcriptome.   Cell lines were generated by lentiviral transfection with viral particles produced in Lenti-X 293T cells. Stable cell lines were selected with puromycin and maintained in media containing the selection agent.  RNA was extracted from cells (n=6 per condition) and RNA libraries were prepared using RNA with RIN score >9.8 using the KAPA Total RNA Library Preparation kit (Roche). Barcoded libraries were subsequently analyzed using an Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit v1.5 (300 cycles, Illumina) with paired-end lengths of 150 base pairs with a depth of >40 million reads. Fastq files were mapped onto the human GENECODE 29 version using STAR 2.7.5. The average reads/sample was 57M. No samples were excluded from analysis after quality control.","dates":{"release":"2025-12-22T00:00:00Z","modification":"2025-12-22T02:01:22.569Z","creation":"2025-09-12T12:10:02.052Z"},"accession":"E-MTAB-15583","cross_references":{"ENA":["ERP180015"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}