Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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).

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Noboru Sakabe

PROVIDER: E-MTAB-10257 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.

Sobreira Débora R DR Joslin Amelia C AC Zhang Qi Q Williamson Iain I Hansen Grace T GT Farris Kathryn M KM Sakabe Noboru J NJ Sinnott-Armstrong Nasa N Bozek Grazyna G Jensen-Cody Sharon O SO Flippo Kyle H KH Ober Carole C Bickmore Wendy A WA Potthoff Matthew M Chen Mengjie M Claussnitzer Melina M Aneas Ivy I Nóbrega Marcelo A MA

Science (New York, N.Y.) 20210601 6546

Whereas coding variants often have pleiotropic effects across multiple tissues, noncoding variants are thought to mediate their phenotypic effects by specific tissue and temporal regulation of gene expression. Here, we investigated the genetic and functional architecture of a genomic region within the FTO gene that is strongly associated with obesity risk. We show that multiple variants on a common haplotype modify the regulatory properties of several enhancers targeting IRX3 and < ...[more]

PMID: 34083488

Similar Datasets

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.

2018-04-06 | E-MTAB-6720 | biostudies-arrayexpress

ATAC-seq of Oesophageal Cell Lines

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

2016-09-12 | E-MTAB-4209 | 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

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

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.

2016-01-15 | E-GEOD-74977 | biostudies-arrayexpress

ATAC-seq of human lymphoblastoid cells (LCL)

Project description:We generated these data to compare two modifications of the original ATAC-seq protocol. One was the cleavage of mtDNA using CRISPR/Cas9 and 100 gRNAs targeting mtDNA. The other was the removal of detergent from the cell lysis step. There are 27 sample pairs, untreated and treated with anti-mt CRISPR/Cas9 grouped by sample pair number. Refer to Supplemental File 1 of the article describing this data set for more information on the samples.

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

ATAC-seq of BMP response in glioblastoma-derived neural stem cells

Project description:Chromatin accessibility was profiled by ATAC-seq in normal and glioblastoma-derived neural stem (GNS) cells, in self-renewing conditions and in response to differentiation stimulus with bone morphogenic protein (BMP).

2015-10-01 | E-MTAB-3868 | biostudies-arrayexpress

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.

Project description:In vertebrates, body axis elongation is fuelled by bipotent neuromesodermal progenitors (NMPs), which support the development of both spinal cord and paraxial mesoderm (PM). WNT signalling sustains both NMP expansion and PM differentiation, but the mechanism by which it distinguishes between these alternative fates is unknown. HOX transcription factors have been historically implicated in axial elongation, with their sequential activation playing a fundamental role in timing PM development. PBX1 and PBX2 are obligate anterior HOX cofactors, and therefore they represent prominent candidates for controlling the distinct response to individual HOX factors. In our work, we have demonstrated that PBX/HOX complexes establish a permissive chromatin landscape for de novo recruitment of the WNT-effector LEF1 on PM genes, including the master regulator Mesogenin1 (Msgn1). To assess the PBX-dependent changes in chromatin accessibility during PM differentiation, we performed ATAC-seq of wild-type (WT) and Pbx1/Pbx2 double-knockout (Pbx1/2-DKO) EpiSCs differentiated in vitro to pre-somitic mesoderm (PSM) at different time-points (EpiSCs, 6 hours, 12 hours, 24 hours, 36 hours, 48 hours). To assess the direct consequence of PBX/HOX binding on chromatin accessibility, we employed the CRISPR/Cas9 technology to generate lines carrying base-pair substitutions on the Msgn1 promoter (pMsgn1-mut) that abrogate the recruitment of PBX/HOX complexes, and we performed ATAC-seq of pMsgn1-mut EpiSCs differentiated in vitro to PSM at different time-points (12 hours, 24 hours, 36 hours, 48 hours).

2021-07-21 | E-MTAB-9776 | biostudies-arrayexpress

ATAC-seq of CP-A Barrett's oesophagus cells

Project description:The open chromatin of Barrett's oesophagus cell line CP-A has been profiled by ATAC-seq.

2020-09-30 | E-MTAB-8994 | biostudies-arrayexpress

ATAC-seq of primary mesenchymal stem cell (MSC)-derived osteoblasts (differentiated with BMP2) from 4 human donors

Project description:ATAC-seq was performed to map open chromatin regions in hMSC-derived osteoblasts

2019-03-20 | E-MTAB-6834 | biostudies-arrayexpress