{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Robert Dallmann"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15036"],"description":["A549 lung cells were infected with pGIPZ carrying shBMAL1 hairpin. Knockdown was confirmed by Western blot before sequencing experiment.  Both parental and knockdown cells lines were then synchronised with forskolin and 12 or 24 hours later triplicates of both cell lines were collected and RNA was extracted with the Quiagen RNAEasy kit. RNA was send to Novogen for library generation and sequencing on a NovaSeq platform with a 150bp paired-ended kit."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Nova-Seq, non-stranded, paired-end, 150bp to a depth of at least 15mi reads","Nucleic Acid Extraction - Quiagen RNAeasy column with DNA clean up column","Growth Protocol - Cells were grown in DMEM, 10% FCS, P/S, glutamax.","Library Construction - PolyA enrichment for mRNA of all samples.","Sample Collection - Dishes were washed with PBS and frozen at -80C till RNA extraction.","Sample Treatment - Cells were seeded 24hours before forskolin treatment for synchronisation and then collected 12 and 24hours post FSK."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - FastQ files were aligned with Kalisto using BioJupies."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Robert Dallmann"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of human lung epithelial A549 cells compared to A549 cells with shBMAL1 mediated knockdown of BMAL1 at two circadian phases","description":"A549 lung cells were infected with pGIPZ carrying shBMAL1 hairpin. Knockdown was confirmed by Western blot before sequencing experiment.  Both parental and knockdown cells lines were then synchronised with forskolin and 12 or 24 hours later triplicates of both cell lines were collected and RNA was extracted with the Quiagen RNAEasy kit. RNA was send to Novogen for library generation and sequencing on a NovaSeq platform with a 150bp paired-ended kit.","dates":{"release":"2026-04-05T00:00:00Z","modification":"2026-04-05T01:01:00.493Z","creation":"2025-04-15T13:20:11.515Z"},"accession":"E-MTAB-15036","cross_references":{"ENA":["ERP171657"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}