biostudies-arrayexpressRosa-Maria MäättäläEscherichia colihttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17203A library of hairpins was generated using TInDel Assembly to be tested for RNA thermometer activity. This method provides variation in sequence, length, and topology at the RNA level. The library was generated in vitro and cloned into an expression vector for screening. The library was amplified via PCR from the vector for submission for NGS.biostudies-arrayexpressLibrary Construction - The purified PCR product was submitted as is without adapters.Sequencing - The library was sequenced using Genewiz (Azenta) Amplicon-EZ service which uses Illumina Short-read NGS technology and accepts read lengths ranging between 150 and 600 bp and with a read depth of 50,000 sequences.Nucleic Acid Extraction - The PCR product was extracted from a 4% agarose gel using the Monarch DNA Gel Extraction kit from New England Biolabs.Sample Collection - The library was amplified via PCR using OneTaq DNA polymerase (New England Biolabs) with the following conditions: 30 sec at 94°C; 15 cycles of 20 sec at 94°C, 30 sec at 54°C, 30 sec at 68°C; 5 min at 68°C. Primers can be found in the manuscript Supplementary Table 2.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - The initial processing of the raw FASTQ data joined paired-end reads, and filtered sequences based on sequence-quality criteria using PEAR45. Sequences were converted to FASTA (126,462 sequences) and filtered based on vector sequences to identify sequence orientation. This early processing was carried out in online Galaxy servers46 (workflow available at https://osf.io/u9kp4/overview) and isolated 118,699 sequences (93.8%) for detailed analysis.Data Transformation - A strict sequence-based filter was applied using vector sequences immediately adjacent to the cloning site, isolating 104,952 (83.0% of the total) sequences representing 28,051 unique sequences. The script in Julia (v. 1.11) is available at https://osf.io/u9kp4/overview.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina MiSeqDNA-seqEscherichia coliTopology-guided engineering of synthetic RNA thermometers via Topological InDel (TInDel) AssemblyVitor Bernardes PinheiroRosa-Maria MäättäläRosa-Maria Määttälä, Shamal Withanage, Vitor B. PinheirofalseIllumina Short-read NGS of a de novo RNA hairpin library using TInDel AssemblyA library of hairpins was generated using TInDel Assembly to be tested for RNA thermometer activity. This method provides variation in sequence, length, and topology at the RNA level. The library was generated in vitro and cloned into an expression vector for screening. The library was amplified via PCR from the vector for submission for NGS.2026-07-09T00:00:00Z2026-07-09T09:07:50.517Z2026-06-22T13:08:35.016ZE-MTAB-17203ERP195520EFO_0002944EFO_0004170EFO_0002693EFO_0004917EFO_0005518EFO_0003816EFO_0004184