{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["wenting xu"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16073"],"description":["We used three siRNAs to silence HSPA8 in MDA-MB-468 cells, and then used RNA-seq to compare HSPA8 knockdown cells with the controls."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - 48-hours post-transfection, total RNA was extracted using TRIzol reagent (Ambion).","Sample Collection - Cells transfected with siRNAs with Lipofectamin as the transfection reagent. Cells were cultured at 37°C in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 100 IU/mL penicillin-streptomycin solution under 5% CO2.","Sequencing - DNBSEQ-T7 system was used for 150 nt paired-end sequencing.","Library Construction - VAHTS Universal V8 RNA-seq Library Prep Kit (Vazyme) was used to prepare strand-specific RNA-seq libraries."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).  In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 .","Data Transformation - Uniquely mapped reads were used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["DNBSEQ-T7"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["wenting xu"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of HSPA8 knockdown in MDA-MB-468 cells","description":"We used three siRNAs to silence HSPA8 in MDA-MB-468 cells, and then used RNA-seq to compare HSPA8 knockdown cells with the controls.","dates":{"release":"2025-11-13T00:00:00Z","modification":"2026-05-30T17:00:18.4Z","creation":"2025-11-06T13:02:38.963Z"},"accession":"E-MTAB-16073","cross_references":{"ENA":["ERP183681"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}