We've run our ATAC-seq pipeline, including ataqv, on a selection of freely available public ATAC-seq datasets.
ataqv viewer Paper (linked to PubMed) Authors Organism Source material
PRJNA207663 Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ Homo sapiens GM12878 cells, CD4+ T cells
PRJNA259243 Individuality and variation of personal regulomes in primary human T cells. Qu K, Zaba LC, Giresi PG, Li R, Longmire M, Kim YH, Greenleaf WJ, Chang HY Homo sapiens CD4+ T cells
PRJNA279685 A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63. Bao X, Rubin A, Kun Q, Chang HY, Khavari P Homo sapiens neonatal keratinocyte
PRJNA290920 ATAC-seq on biobanked specimens defines a unique chromatin accessibility structure in naïve SLE B cells. Scharer CD, Boss J Homo sapiens CD19+ B cells
PRJNA296371 Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation. Mazumdar C, Shen Y, Xavy S, Zhao F, Reinisch A, Li R, Corces MR, Flynn RA, Buenrostro JD, Chan SM, Thomas D, Koenig JL, Hong WJ, Chang HY, Majeti R Homo sapiens CD34+ HSPC
PRJNA306754 Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes. Ackermann AM, Wang Z, Schug J, Naji A, Kaestner KH Homo sapiens pancreatic islets
PRJNA319573 Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types. Loh KM, Chen A, Koh PW, Deng TZ, Sinha R, Tsai JM, Barkal AA, Shen KY, Jain R, Morganti RM, Shyh-Chang N, Fernhoff NB, George BM, Wernig G, Salomon REA, Chen Z, Vogel H, Epstein JA, Kundaje A, Talbot WS, Beachy PA, Ang LT, Weissman IL Homo sapiens embryonic stem cell
PRJNA326967 p53 regulates enhancer accessibility and activity in response to DNA damage. Younger ST, Rinn JL Homo sapiens fetal skin fibroblasts
PRJNA358685 A c-Myb mutant causes deregulated differentiation due to impaired histone binding and abrogated pioneer factor function. Fuglerud BM, Lemma RB, Wanichawan P, Sundaram AYM, Eskeland R, Gabrielsen OS Homo sapiens erythroleukemic cell line (K562)
PRJNA396048 Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers. Kelso TWR, Porter DK, Amaral ML, Shokhirev MN, Benner C, Hargreaves DC Homo sapiens HCT116 and TOV21G cells
PRJNA242521 Genomic-wide transcriptional profiling in primary myoblasts reveals Runx1-regulated genes in muscle regeneration. Umansky KB, Feldmesser E, Groner Y Mus musculus Primary proliferating myoblasts
PRJNA274006 Single-cell chromatin accessibility reveals principles of regulatory variation. Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ Homo sapiens; Mus musculus Human: H1 human embryonic stem cells [ESCs], K562 chronic myelogenous leukemia cells; GM12878 lymphoblastoid cells; TF-1 (erythroblast); HL-60 (promyeloblast); BJ fibroblasts (foreskin fibroblast)
Mouse: mouse ESCs; EML1 (mouse hematopoietic progenitor)
PRJNA290471 Structural organization of the inactive X chromosome in the mouse. Giorgetti L, Lajoie BR, Carter AC, Attia M, Zhan Y, Xu J, Chen CJ, Kaplan N, Chang HY, Heard E, Dekker J Mus musculus neural progenitor cells; embryonic stem cells
PRJNA261246 Hematopoietic Differentiation Is Required for Initiation of Acute Myeloid Leukemia. Ye M, Zhang H, Yang H, Koche R, Staber PB, Cusan M, Levantini E, Welner RS, Bach CS, Zhang J, Krivtsov AV, Armstrong SA, Tenen DG Mus musculus MLL-AF9 leukemic cells
PRJNA323617.PRJNA341508 Neuronal activity modifies the chromatin accessibility landscape in the adult brain. Su Y, Shin J, Zhong C, Wang S, Roychowdhury P, Lim J, Kim D, Ming GL, Song H Mus musculus dentate granule neurons
PRJNA325538 Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors. Hughes AE, Enright JM, Myers CA, Shen SQ, Corbo JC Mus musculus rods; green cones; Nrl-/- photoreceptors
PRJNA330723 Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells. Carter AC, Xu J, Chang HY Mus musculus embryonic stem cells; neural progenitor cells
PRJNA345167 Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex. Gray LT, Yao Z, Nguyen TN, Kim TK, Zeng H, Tasic B Mus musculus adult mouse cortex
PRJNA349462 Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells. Mognol GP, Spreafico R, Wong V, Scott-Browne JP, Togher S, Hoffmann A, Hogan PG, Rao A, Trifari S Mus musculus CD8 T cell
PRJNA352791 Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes. Semenkovich NP, Planer JD, Ahern PP, Griffin NW, Lin CY, Gordon JI Mus musculus intraepithelial lymphocyte; peripheral blood lymphocyte
PRJNA369195 Functional characterisation of cis-regulatory elements governing dynamic Eomes expression in the early mouse embryo. Simon CS, Downes DJ, Gosden ME, Telenius J, Higgs DR, Hughes JR, Costello I, Bikoff EK, Robertson EJ Mus musculus definitive endoderm; embryonic stem cell
PRJNA371831 Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation. Nelson AC, Mould AW, Bikoff EK, Robertson EJ Mus musculus differentiated trophoblast stem cells; trophoblast stem cells
PRJNA380283 An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, Orloff LA, Risca VI, Kundaje A, Khavari PA, Montine TJ, Greenleaf WJ, Chang HY Homo sapiens; Mus musculus CD19/20+ B cells, fresh from peripheral blood; CD4+ T cells, fresh from peripheral blood; Human acute T cell leukemia cell line; Human B lymphoblastoid cell line; Human chronic myelogenous leukemia cell line; Human embryonic kidney cell line; Human fibrosarcoma cell line; Human urinary bladder transitional cell carcinoma cell line; mESC v6.5; Murine bulk colon, C57BL/6; Murine bulk heart, C57BL/6; Murine bulk liver, C57BL/6; Murine bulk lung, C57BL/6; Murine bulk spleen, C57BL/6; Occipital lobe; Primary human keratinocytes, from foreskin; Primary human thyroid cancer, unspecified
PRJNA380816 Clonally stable Vκ allelic choice instructs Igκ repertoire. Levin-Klein R, Fraenkel S, Lichtenstein M, Matheson LS, Bartok O, Nevo Y, Kadener S, Corcoran AE, Cedar H, Bergman Y Mus musculus Bone marrow derived pre-B cell
PRJNA388786 Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts. Lawlor N, Youn A, Kursawe R, Ucar D, Stitzel ML Mus musculus Alpha TC1 (αTC1) and Beta-TC-6 (βTC6) mouse islet cell lines
PRJNA394116 Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons. Wapinski OL, Lee QY, Chen AC, Li R, Corces MR, Ang CE, Treutlein B, Xiang C, Baubet V, Suchy FP, Sankar V, Sim S, Quake SR, Dahmane N, Wernig M, Chang HY Mus musculus mouse embryonic fibroblasts; TauEGFP+ cells
PRJNA412907 Epigenetic mechanisms underlying maternal diabetes-associated risk of congenital heart disease. Basu M, Zhu JY, LaHaye S, Majumdar U, Jiao K, Han Z, Garg V Mus musculus atrioventricular mesenchymal (AVM) cells