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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ATAC-seq of primary human airway smooth muscle cells from 4 donors

ABSTRACT: Generation of genome-wide maps of putative regulatory regions in human airway smooth muscle cells (ASMC) to aid in fine mapping of asthma GWAS. The cells were cultured and maintained in 10% FBS in PBS for 24 hours with no additional treatment given. MACS2 peaks provided in this submission were mapped to hg19.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-14267 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP162182E-MTAB-14295

REPOSITORIES: biostudies-arrayexpress

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ATAC-seq of iPSC-derived hypothalamic arcuate-like neuron cells

Project description:We performed ATAC-seq on iPSC-derived hypothalamic arcuate-like neuron cells to identify putative regulatory elements. All samples were derived from the same individual and from the same differentiation/cell line but ATAC-seq was performed in 3 separate experiments (3 technical replicates).

2021-04-01 | E-MTAB-10257 | biostudies-arrayexpress

ATAC-seq of oesophageal adenocarcinoma cell line MFD-1

Project description:The open chromatin of new esophageal adenocarcinoma cell line MFD-1 has been profiled by ATAC-seq.

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ATAC-seq of Oesophageal Cell Lines

Project description:ATAC-seq in oesophageal cell lines, OE33 (OAC), FLO1 (OAC), HET1A (Normal)

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ATAC-sequencing mice small intestinal epithelium with intestinal epithelium specific LSD1 knock out compared to wild type

Project description:To study the epigenetic regulation of intestinal epithelium we focus on the role of chromatin modulators. Lysine-specific histone demethylase 1a (KDM1A, LSD1) is one of the enzymes that can erase the H3K4me1/2 mark. To assess the role of LSD1 in intestinal epithelium we studied wild type (WT) (Villin-Cre -; Lsd1f/f) and intestinal-epithelial-specific knock-out (KO) (Villin-Cre+; Lsd1f/f) mice. We found that KO mice completely lack Paneth cells, and have altered stem cell characteristics compared to WT littermates. To assess genome-wide ATAC levels in WT and KO small intestines, we isolated intestinal epithelium tissue from wild type mice and LSD1 KO mice. This tissue was digested to single cells and performed ATAC seq as described in the protocols.

2021-03-23 | E-MTAB-8718 | biostudies-arrayexpress

ATAC-seq of oesophageal cell lines and tissue samples

Project description:ATAC-seq in oesophageal cell lines: OE19, HEEPIC, and human eosophageal tissue samples

2017-07-07 | E-MTAB-5169 | biostudies-arrayexpress

The LRF/ZBTB7A transcription factor is a BCL11A-independent repressor of fetal hemoglobin

Project description:Hemoglobinopathies, including sickle cell disease and _-thalassemia, are global public health concerns. Induction of fetal-type hemoglobin (HbF) is a promising means to treat these disorders; however, precisely how HbF expression is silenced in adult erythroid cells is not fully understood. Here, we show that the LRF/ZBTB7A transcription factor is a potent repressor of HbF production. LRF inactivation derepresses embryonic/fetal _-globin expression in mouse and human adult erythroid cells. We employed genome-wide analysis of the transcriptome, chromatin accessibility and LRF occupancy sites, and demonstrate that LRF occupies the _-globin loci and maintains nucleosome density necessary for _-globin silencing. LRF confers its repressive activity through a unique NuRD repressor complex independent of BCL11A. Strikingly, human erythroid lines lacking both LRF and BCL11A exhibited almost a complete switch in expression from adult- to fetal-type globin, suggesting that these two factors cumulatively represent the near entirety of _-globin repressive activity in adult erythroid cells. RNA-seq, LRF ChIP-seq and ATAC-seq assays were used to investigtae LRF binding, effect of LRF depletion on transcription and chromatin landscape in mouse and human cells.

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ATAC-seq of wild-type, Pbx1/Pbx2 double-knockout and pMsgn1-mut EpiSCs differentiated in vitro to pre-somitic mesoderm in the first 48 hours of differentiation.

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ATAC-seq of human lymphoblastoid cells (LCL)

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2017-02-28 | E-MTAB-5205 | biostudies-arrayexpress

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