{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["charles girardot"],"organism":["Drosophila melanogaster"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17016"],"description":["Three biological replicates of RNA-seq were performed using S2 cells incubated for 72 hours with RNAi targeting Clamp or LacZ (control) transcripts. For each target, 10 µg of each purified dsRNA was combined to a total of 30 µg and directly added to 1.5 × 10⁶ S2 cells seeded in a 6-well plate. Cells were incubated for 72 hours at 25 °C.  Total RNA was extracted from treated cells using the RNeasy Mini Kit (Qiagen, 74104). RNA-seq libraries were prepared from the isolated RNA using the NEBNext UltraExpress RNA Library Prep Kit (NEB, E3330S), following the manufacturer’s protocol. Libraries were sequenced on an Illumina NextSeq 2000 platform, generating 122-base single-end reads."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - RNA-seq libraries were prepared from the isolated RNA using NEBNext UltraExpress RNA Library Prep Kit (NEB, E3330S) following manufacturer protocol and RNA library were sequenced using Illumina NextSeq 2000 and produced 100 bases single-end reads.","Sample Treatment - 10 μg of each purified dsRNA was mixed for each target to a total of 30 μg and directly added to 1.5x10^6 of S2 cells in a 6 well plate and incubated for 72 hr at 25 °C.","Sample Collection - D. melanogaster S2 cells are cultured at 25C in Schneider's Drosophila medium (Gibco) supplemented with 10% of inactivated fetal bovine serum. For maintenance, cells were split every 3 to 5 days at ~1-2 million cells per mL for no more than 20 passages.","Nucleic Acid Extraction - 2.5 million cells were collected for each treatment condition in biological triplicates.  RNA was extracted following manufacturer instructions using the Qiagen RNeasy Mini kit including the optional DNase digestion step, eluting twice in 35 ul and quantity was measured using Nanodrop.","Sequencing - Libraries were single-end sequenced on Illumina NextSeq 2000"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Processed data were analyzed using the nf-core/rnaseq pipeline (v3.23.0)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA"],"species":["Drosophila melanogaster"],"pubmed_authors":["Yuliya Badayeva","charles girardot","Mathias Boulanger","Arnaud Krebs","Chatsirisupachai Kasit"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq S2 Clamp RNAi knockdown","description":"Three biological replicates of RNA-seq were performed using S2 cells incubated for 72 hours with RNAi targeting Clamp or LacZ (control) transcripts. For each target, 10 µg of each purified dsRNA was combined to a total of 30 µg and directly added to 1.5 × 10⁶ S2 cells seeded in a 6-well plate. Cells were incubated for 72 hours at 25 °C.  Total RNA was extracted from treated cells using the RNeasy Mini Kit (Qiagen, 74104). RNA-seq libraries were prepared from the isolated RNA using the NEBNext UltraExpress RNA Library Prep Kit (NEB, E3330S), following the manufacturer’s protocol. Libraries were sequenced on an Illumina NextSeq 2000 platform, generating 122-base single-end reads.","dates":{"release":"2026-08-04T00:00:00Z","modification":"2026-08-04T01:00:49.633Z","creation":"2026-05-06T11:58:54.408Z"},"accession":"E-MTAB-17016","cross_references":{"ENA":["ERP193082"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}