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TranscriptomicsPlacental infection single-cell and single-nuclei maps
This resource comprises a single-cell multi-lineage map of first trimester infected placental cells. We have included data from both uninfected cells and cells infected with three pathogens known to cause maternal and fetal disorders: Plasmodium falciparum, Listeria monocytogenes, and Toxoplasma gon...
ORGANISM(S): Homo sapiens 
2024-03-01 | E-MTAB-12795 | biostudies-arrayexpress
GenomicsActive DNA demethylation in plant companion cells reinforces transposon methylation in gametes
The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation prior to fertilization, but the targeting preferences and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase acco...
ORGANISM(S): Arabidopsis thaliana 
2012-09-21 | E-GEOD-38935 | biostudies-arrayexpress
TranscriptomicsscRNA-seq and snucRNA-seq of human primary trophoblast organoids (PTO) and trophoblast stem cells (TSCs) differentiation into extravillous trophoblast organoids (EVTs)
This study aims to compare in vivo human trophoblast differentiation into EVTs to different in vitro trophoblast organoids using single-cell and single-nuclei RNA sequencing. The study includes two type of systems: human primary trophoblast organoids (PTO) and trophoblast stem cells (TSCs). Tropho...
ORGANISM(S): Homo sapiens 
2023-02-09 | E-MTAB-12650 | biostudies-arrayexpress
TranscriptomicsThree-dimensional folding and functional organization principles of the Drosophila genome
Chromosomes are the physical realization of genetic information and thus form the basis for its reading, hindering and propagation. Here we present a high-resolution chromosomal contact map derived from a new genome-wide chromosome conformation capture approach (a simplified version of the Hi-C meth...
ORGANISM(S): Drosophila melanogaster 
2012-01-20 | E-GEOD-34453 | biostudies-arrayexpress
GenomicsReciprocal regulation of cardiac chromatin by the chromatin structural proteins HMGB and CTCF
Transcriptome remodeling in heart disease occurs through the coordinated actions of transcription factors, histone modifications and other chromatin features at pathology-associated genes. It remains unknown the extent to which genome-wide chromatin reorganization also contributes to the pathologic ...
ORGANISM(S): Rattus norvegicus 
2016-06-15 | E-GEOD-80453 | biostudies-arrayexpress
TranscriptomicsExpression of sense and antisense transcripts at the ribosomal locus
Epigenetic methyl-CpG silencing of the ribosomal RNA (rRNA) genes is thought to down-regulate rRNA synthesis in mammals. In contrast, we now show that CpG methylation in fact positively influences rRNA synthesis and processing. Human HCT116 cells, inactivated for DNMT1 and DNMT3b or treated with aza...
ORGANISM(S): Homo sapiens 
2010-05-16 | E-GEOD-17042 | biostudies-arrayexpress
GenomicsDeconvolution ChIP-seq profiling of UBF and RPA194 in K562 cells to identify analogous enhancer structures on mouse and human ribosomal RNA genes
The combination of Chromatin Immunoprecipitation and Massively Parallel Sequencing, or ChIP-Seq, has greatly advanced our genome-wide understanding of chromatin and enhancer structures. However, its resolution at any given genetic locus is limited by several factors. In applying ChIP-Seq to study th...
ORGANISM(S): Homo sapiens 
2017-12-31 | E-MTAB-6032 | biostudies-arrayexpress
GenomicsThe miR-155/PU.1 axis acts on Pax5 to enable efficient terminal B cell differentiation [ChIP-Seq]
miR-155 inhibits PU.1 expression, leading to the initiation of the initiation of plasma cell differentiation pathway. Additional PU.1 targets include a network of genes whose products are involved in adhesion, with direct links to B:T interactions. Sequencing analysis of PU.1 binding in B cells usin...
ORGANISM(S): Mus musculus 
2014-09-26 | E-GEOD-61424 | biostudies-arrayexpress
GenomicsLandscape of protein SUMOylation on chromatin in hIPSCs (ChiPS4) by SUMO1 CHIP-seq
SUMO1 CHIP-seq experiment was performed in untreated hiPSC line - ChiPS4, to determine the exact locations of chromatin bound SUMO1 in these cells, thus providing information about the landscape of SUMOylation of protein targets on chromatin in human pluripotent cells and as such allowing for invest...
ORGANISM(S): Homo sapiens 
2022-12-01 | E-MTAB-9960 | biostudies-arrayexpress
TranscriptomicsRNA Subcellular CAGE Localization from ENCODE/RIKEN
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Piero Carninci mailto:carninci@riken.jp). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track show...
ORGANISM(S): Homo sapiens 
2011-12-16 | E-GEOD-34448 | biostudies-arrayexpress
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