{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Bekkouche Louisa"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16814"],"description":["We used several cell lines and treatments to investigate the formation of DNA triplexes in human cells."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - S1-END‑seq libraries are generated by blunting and A‑tailing DNA ends, ligating Illumina-compatible adapters, size‑selecting fragments, and PCR amplifying the repaired DNA using KAPA HiFi HotStart ReadyMix (Roche)","Sequencing - Libraries were quantified using with the KAPA Library Quantification Kit (Roche) and sequenced using 75 bp single end kits on Illumina NextSeq 550 instruments, 100 bp single-end kits on Illumina NextSeq 2000 instruments, or were performed by Novogene using 150 bp paired-end on Illumina NovaSeq 6000","Sample Treatment - Benzoquinoquinoxaline (BQQ) 1uM diluted in DMSO -treatment time 24 hours. Doxycycline (DOX) 10mg/mL diluted in water -  treatment time 24 hours","Sample Collection - Cultured cells were harvested after tripsinization.","Nucleic Acid Extraction - Live cells were harvested and embedded into agarose plugs. Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - S1-END-seq reads were aligned to the reference genome (hg19 or hg38), using bowtie2 (v2.5.4) with parameters -N 1 -L 32. The hg19 genome was used for comparison with the regions with high RFD, which were annotated in this genome. All other analyses were performed using the hg38 genome as reference. The functions ‘view’ and ‘sort’ of samtools (v1.9) (29) were used to convert and sort the aligned .sam files into sorted .bam files. The .bam files were further converted to .bed files using the bedtools (v.2.28.0) bamToBed command (30)."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["DNA-seq"],"species":["Homo sapiens"],"pubmed_authors":["Bekkouche Louisa"],"additional_accession":[]},"is_claimable":false,"name":"Formation of DNA triplexes/H-DNA associated with malignant transformation in human cells","description":"We used several cell lines and treatments to investigate the formation of DNA triplexes in human cells.","dates":{"release":"2026-04-15T00:00:00Z","modification":"2026-04-17T01:01:31.69Z","creation":"2026-03-25T11:44:04.366Z"},"accession":"E-MTAB-16814","cross_references":{"ENA":["ERP191296"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}