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

Promoter capture Hi-C of human SGBS (Simpson-Golabi-Behmel syndrome preadipocyte) cells and iPSC-derived hypothalamic cells

ABSTRACT: To identify distal chromatin contacts between promoters and their putative regulatory elements in SGBS preadipocytes and hypothalamic arcuate-like neurons derived from iPSC, we performed Hi-C with a capture step to enrich the library for contacts involving promoters. Hi-C with a capture step was performed according to PMID: 29988018

ORGANISM(S): Homo sapiens

SUBMITTER: Marcelo Nobrega

PROVIDER: E-MTAB-10200 | 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

Promoter Capture-HiC in Ring1a KO and Ring1a/b dKO mouse ES cells

2015-08-01 | E-MTAB-3109 | biostudies-arrayexpress

In situ promoter capture Hi-C data of differentiated SGBS human preadipocytes (days 0, 2, 8 and 16 of differentiation to adipocytes) and iPSC-derived hypothalamic neurons (days 12, 16 and 27 of differentiation)

Project description:Human SGBS preadipocytes were differentiated into adipocytes, and human iPSCs were differentiated into hypothalamic neurons. Cells were collected for in situ promoter capture Hi-C [PMID: 29988018] at several differentiation stages. The differentiations were performed in one biological replicate, with two technical replicates (different wells of the differentiation that were also processed individually during library preparation). SGBS Day0: Represents the preadipocyte state. SGBS Day2: Represents immature adipocytes. SGBS Day8: Represents early mature adipocytes. SGBS Day16: Represents mature adipocytes. Hypothalamic Day 12: Represents early hypothalamic neurons. Hypothalamic Day 16: Represents mid hypothalamic neurons. Hypothalamic Day 27: Represents mature hypothalamic neurons.

2021-05-29 | E-MTAB-10488 | biostudies-arrayexpress

Promoter capture mESC and fetal liver

Project description:Genome organization influences transcriptional regulation by facilitating interactions between gene promoters and distal regulatory elements. To analyse distal promoter contacts we used Capture Hi-C (CHi-C) to enrich for promoter-interactions in HiC libraries from mouse ESC and E14.5 fetal liver. Please note additional files included. These files were created using the following protocol: Significantly interacting regions were called using the GOTHiC BioConductor package (http://www.bioconductor.org/packages/devel/bioc/html/GOTHiC.html) as described in (Mifsud et al.). Update on December 2015: the original additional file E-MTAB-2414.additional.1.zip contained an earlier iteration of processed data and not the one that was used for the published paper. The file now contains the correct list of interactions.

2015-02-01 | E-MTAB-2414 | biostudies-arrayexpress

Promoter capture GM12878 CD34

2015-03-01 | E-MTAB-2323 | biostudies-arrayexpress

Promoter capture Hi-C of human SGBS (Simpson-Golabi-Behmel syndrome preadipocyte) cells and iPSC-derived hypothalamic cells

Project description:Promoter capture Hi-C of human SGBS (Simpson-Golabi-Behmel syndrome preadipocyte) cells and iPSC-derived hypothalamic cells

| PRJEB43592 | ENA

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of lincRNA genes in human cells

Project description:Characterizing the relationship between genome form and function requires methods both for zooming out, to globally survey the genomic architectural landscape, and for zooming in, to investigate regions of interest at high resolution. High throughput methods based on chromosome conformation capture (3C) have greatly advanced our understanding of the three-dimensional (3D) organization of genomes, but are limited in resolution by their reliance on restriction enzymes. Here we describe a method for comprehensively mapping global chromatin contacts that uses DNaseI for chromatin fragmentation, leading to greatly improved efficiency and resolution. Coupling this method with DNA capture technology provides a high-throughput approach for targeted mapping of fine-scale chromatin architecture. We applied targeted DNase Hi-C to characterize the 3D organization of 1,030 lincRNA promoters in two human cell lines, and identified thousands of high-confidence lincRNA promoter-associated chromatin contacts at 1 kilobase pair (kbp) resolution. Detailed analysis of these contacts reveals that expression of lincRNAs is tightly controlled by complex mechanisms involving both super-enhancers and the polycomb repressive complex. Our results provide the first glimpse of the cell-type-specific 3D organization of lincRNA genes. DNase Hi-C assay (x1 replicate) in H1 and K562 cells, respectively. Targeted DNase Hi-C assays of the 220kb promoter-enhancer library (x1 replicate) and the 5Mb lincRNA promoter library (x2 replicate), in H1 and K562 cells, respectively.

2014-11-01 | E-GEOD-56869 | biostudies-arrayexpress

HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [Capture Hi-C]

Project description:We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. To determine whether distal REs come into contact with promoters, instead of using a classical Hi-C, we further combined Hi-C with a capture enrichment step. We generated a biotinylated RNA bait library specifically targeting 212,735 promoter regions and performed a capture Hi-C after 0h, 1h and 6h after stress.

2023-01-03 | GSE206356 | GEO

Expression data from human SGBS adipocytes under hypoxic conditions

Project description:Hypoxia in adipose tissue is suggested to be involved in the development of a chronic mild inflammation, which in obesity can further lead to insulin-resistance. The effect of hypoxia on gene expression in adipocytes seems to play a central role in this inflammatory response observed in obesity. However, the global impact of hypoxia on transcriptional changes in human adipocytes is unclear. Therefore, we compared gene expression profiles of human Simpson-Golabi-Behmel syndrome (SGBS) adipocytes under normoxic or hypoxic conditions to detect hypoxia-responsive genes in adipocytes by using whole human genome microarrays. Human SGBS adipocytes were cultured in a hypoxic environment (1% O2) for 3, 6 and 16 hours and the control group was cultured under normoxic conditions (21% O2). Total RNA was prepared from control and treated SGBS cells, in triplicate experiments, and probes were hybridized on ‘Human Genome U133 2.0’ arrays (Affymetrix).

2011-04-14 | E-GEOD-28603 | biostudies-arrayexpress

Proteomic characterization of SGBS cells

Project description:In this study, SGBS preadipocytes were differentiated for 12 days into mature preadipocytes.

2021-09-16 | PXD023266 | Pride

High throughput analysis of three human adipose cell lines PAZ6, SGBS and SW872

Project description:We report molecular characterization of human brown and white adipocytes. We showed that PAZ6 and SW872 cells exhibit classical molecular and phenotypic markers of brown and white adipocytes, respectively. However, SGBS cells presented a versatile phenotype of adipocyte Sequencing of three human adipocytes cell lines (SGBS, SW872 and PAZ6) in undifferentiated and differentiated stages.

2015-01-01 | E-GEOD-63190 | biostudies-arrayexpress