biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsveronica manicardiNextSeq 500ATAC-seqHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13851Characterization of chromatin accessibility in T-cell lymphoma. ATAC-seq experiments were performed in both control (CT) and HELLS knockdown (shHELLS) cells to evaluate changes in chromatin accessibility.biostudies-arrayexpressNucleic Acid Extraction - DNA was purified using DNA Clean and Concentrator-5 KIT (Zymo Research).Library Construction - Fragmented DNA amplification and barcoding was performed with NEBNext Ultra II Q5 2X Master Mix (New England Biolabs) with sample-specific adapters. Samples were quantified with NEBNext Library Quantification kit (New England Biolabs) and amplified for an additional 7 cycles.Sequencing - Sequencing was performed by Illumina Nextseq 500 instrument (High output kit v2.5, double-stranded, read length 75 bp - 2×75 cycles).Sample Collection - 50'000 cells were collected for ATAC-seq. Cell pellet was lysed in ATAC-seq Lysis Buffer then diluted in ATAC-seq Wash Buffer. Tagmentation was performed with Illumina Tagment DNA (TD) TDE1 Enzyme and Buffer (Illumina). Nuclear pellet was resuspended in Transposition Mix and incubated at 37°C.Growth Protocol - Cells were cultured in RPMI medium supplemented with 10% FBS, 1% P/S and 20U IL-2.Sample Treatment - Functional HELLS knockdown by shRNA was induced by the treatment with Doxycycline (DOX) for 48h at final concentration of 100ng/ml.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB Filesveronica manicardifalseATAC-seq of human ALK negative ALCL cell line (TLBR2) in parental and HELLS knockdown conditionsCharacterization of chromatin accessibility in T-cell lymphoma. ATAC-seq experiments were performed in both control (CT) and HELLS knockdown (shHELLS) cells to evaluate changes in chromatin accessibility.2025-11-02T00:00:00Z2025-11-02T02:02:29.094Z2024-02-23T10:41:07.018ZE-MTAB-13851ERP157705E-MTAB-12935E-MTAB-9918EFO_0002944EFO_0007045EFO_0004170EFO_0003789EFO_0005518EFO_0004184EFO_0003969