biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsChara MastrokalouNAIllumina iSeq 100DNA-seqHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17181The project aims to compare the rate of recombination events between loxP sites at various timepoints in the conditional sgRNA system to induce the expression of guide RNA after Cre-recombinase mediated induction.biostudies-arrayexpressLibrary Construction - NGS amplicon libraries were generated with a two-step PCR protocol. First, the lentiviral cassette containing the gRNA, was amplified from genomic DNA with specific primers that also contain Illumina specific adapter sequences. In the second PCR, 8 nucleotide Nextera indices were added using Indexing primers with complementary sequences to the 1st PCR primers and contained P5 and P7 Illumina compatible sequences necessary for cluster generation. Final amplicon NGS libraries were cleaned up using AMPure XP beads. The samples were pooled into single library.Sample Collection - Cells were collected at various time points on day 0,4,7,11,14 after Cre mRNA induction. The cells were pelleted, washed once with D-PBS and then stored at -20°C before processing.Nucleic Acid Extraction - Genomic DNA was extracted using the Qiagen Blood and Cell culture DNA kit (order number 13343) according to the manufacturer’s protocol. https://www.qiagen.com/us/products/discovery-and-translational-research/dna-rna-purification/dna-purification/genomic-dna/blood-and-cell-culture-dna-kits?catno=13343Sequencing - The pooled samples were sequenced via a 300bp Paired-End sequencing.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesChara MastrokaloufalseAmplicon DNA-sequencing of time series of loxP-recombination events within conditional sgRNA system in HT29 colon cancer cell line.The project aims to compare the rate of recombination events between loxP sites at various timepoints in the conditional sgRNA system to induce the expression of guide RNA after Cre-recombinase mediated induction.2026-09-20T00:00:00Z2026-09-20T01:00:37.938Z2026-06-10T19:16:23.075ZE-MTAB-17181ERP194849EFO_0002944EFO_0004170EFO_0002693EFO_0005518EFO_0004184