{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["veronica manicardi"],"instrument_platform":["NextSeq 500"],"study_type":["ATAC-seq"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13851"],"description":["Characterization 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["veronica manicardi"],"additional_accession":[]},"is_claimable":false,"name":"ATAC-seq of human ALK negative ALCL cell line (TLBR2) in parental and HELLS knockdown conditions","description":"Characterization 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.","dates":{"release":"2025-11-02T00:00:00Z","modification":"2025-11-02T02:02:29.094Z","creation":"2024-02-23T10:41:07.018Z"},"accession":"E-MTAB-13851","cross_references":{"ENA":["ERP157705"],"Biostudies":["E-MTAB-12935","E-MTAB-9918"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0004184","EFO_0003969"]}}