{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jurjun Velde"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16601"],"description":["Deep RNA sequencing was performed to investigate the transcriptomic effects of siRNA-mediated knockdown of SRSF7 or SMNDC1 in the triple-negative breast cancer cell line MDA-MB-231. A total of 30 million cells MDA-MB-231 cells were seeded in 6-well plates. The following day, cells were transfected with siKinasePool siRNAs targeting SRSF7, SMNDC1, or a mock control. Samples from three biological replicates were collected 72 hours after transfection. Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). Stranded PolyA-selected libraries were prepared and sequenced on the DNBseq platform, generating 150-bp paired-end reads on a DNBSEQ-G400 sequencer (BGI Europe)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was isolated using the RNeasy plus mini kit (Qiagen). Samples from 3 biological replicates were used. RNA quality and quantity were measured on an Agilent-4200 Bioanalyzer.","Library Construction - Stranded PolyA-selected libraries were prepared using the DNBseq platform.","Sample Collection - A total of 30 million cells MDA-MB-231 cells were seeded in 6-well plates. The following day, cells were transfected with siKinasePool siRNAs targeting SRSF7, SMNDC1, or a mock control. Samples from three biological replicates were collected 72 hours after transfection.","Sequencing - 100 M 150-bp paired-end reads were sequenced on a DNBSEQ-G400 sequencer by BGI Europe."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Reads were aligned against the human GRCH38 reference genome (gencode version 45) using the STAR aligner (version 2.7.11b).","Data Transformation - Gene expression quantification was performed concurrently during mapping with the STAR --quantMode option set to GeneCounts."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["DNBSEQ-G400"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Bob Water","Sylvia Dévédec","Jurjun Velde"],"additional_accession":[]},"is_claimable":false,"name":"RNA seq of human breast cancer cell line MDAMB231 with knockdown of splicing factors SRSF7 and SMNDC1","description":"Deep RNA sequencing was performed to investigate the transcriptomic effects of siRNA-mediated knockdown of SRSF7 or SMNDC1 in the triple-negative breast cancer cell line MDA-MB-231. A total of 30 million cells MDA-MB-231 cells were seeded in 6-well plates. The following day, cells were transfected with siKinasePool siRNAs targeting SRSF7, SMNDC1, or a mock control. Samples from three biological replicates were collected 72 hours after transfection. Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). Stranded PolyA-selected libraries were prepared and sequenced on the DNBseq platform, generating 150-bp paired-end reads on a DNBSEQ-G400 sequencer (BGI Europe).","dates":{"release":"2026-06-01T00:00:00Z","modification":"2026-06-01T01:01:02.085Z","creation":"2026-01-29T11:22:13.327Z"},"accession":"E-MTAB-16601","cross_references":{"ENA":["ERP188295"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}