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GenomicsIdentification of N6-adenine methylation in C. elegans DNA
In mammalian cells, DNA methylation on the 5th position of cytosine (5mC) plays an important role as an epigenetic mark. However, DNA methylation was considered to be absent in C. elegans because of the lack of detectable 5mC as well as homologs of the cytosine DNA methyltransferases. Here, using mu...
ORGANISM(S): Caenorhabditis elegans 
2015-05-05 | E-GEOD-66504 | biostudies-arrayexpress
TranscriptomicsRapid reprogramming of primary human astrocytes into potent tumor initiating cells with defined genetic factors
Cancer stem cells play key roles in human malignancies. However, their cellular and molecular origins are still poorly understood. Here we report the successful generation of cancer stem cells from primary human astrocytes by use of defined genetic factors. Combined transduction of four factors —m...
ORGANISM(S): Homo sapiens 
2016-11-07 | E-MTAB-4771 | biostudies-arrayexpress
UnknownNatural products for migraine: Data-mining analyses of Chinese Medicine classical literature.
Not available
S-EPMC9650126 | biostudies-literature
GenomicsBase-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics
5-methylcytosine (5mC), the predominant epigenetic modification on DNA, plays critical roles in mammalian development and is dysregulated in various human pathologies. In mammals, the TET family of dioxygenases can oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5...
ORGANISM(S): Mus musculus 
2015-01-20 | E-GEOD-56429 | biostudies-arrayexpress
TranscriptomicsPosterior brain organoids multi-omics atlas
Here, we generated multiome (coupled scRNA-seq and scATAC-seq) data over a time course of mid- and hindbrain organoid development to map cell composition and explore the regulatory mechanisms underlying cell type maturation. The dataset incorporates 5 time points from day 7 to day 120 from 3 human i...
ORGANISM(S): Homo sapiens 
2026-03-17 | E-MTAB-15659 | biostudies-arrayexpress
TranscriptomicsscRNA-seq of posterior brain organoid morphogen screen
To pattern novel posterior brain regions, we used a multiplexed morphogen screen with a single-cell sequencing readout to test 48 concentrations and combinations of 10 morphogens involved in brain patterning. This screen revealed the emergence of regions harboring under-represented cell types, such ...
ORGANISM(S): Homo sapiens 
2026-03-16 | E-MTAB-15660 | biostudies-arrayexpress
TranscriptomicsExpression profiling of BMP9-stimulated mesenchymal stem cells
To identify potential target genes regulated by BMP9 in MSCs, we used microarray to profile expression patterns of BMP9- vs. GFP-stimulated MSCs. Subconfluent mouse C3H10T1/2 cells were transduced with adenoviral vector expressing BMP9 or GFP for 30h. Total RNA was isolated for microarray analysis u...
ORGANISM(S): Mus musculus 
2013-07-16 | E-GEOD-48882 | biostudies-arrayexpress
TranscriptomicsNgn2 induces diverse neuronal lineages from human pluripotency
Human neurons engineered from induced pluripotent stem cells (iPSCs) through Neurogenin 2 (Ngn2) overexpression are widely used to study neuronal differentiation mechanisms and to model neurological diseases. However, the differentiation paths and heterogeneity of emerged neurons have not been fully...
ORGANISM(S): Homo sapiens 
2021-08-05 | E-MTAB-10632 | biostudies-arrayexpress
TranscriptomicsscRNA-seq CRISPR screening of human posterior brain organoids
We used a pooled, multiplexed CRISPR/Cas9 gene knock-out (KO) experiment with single-cell transcriptomic readout to perturb and validate selected TF regulomes . We designed gRNAs and generated a pooled lentiviral library targeting 12 TFs with specific midbrain or hindbrain expression or high regulat...
ORGANISM(S): Homo sapiens 
2026-03-17 | E-MTAB-15826 | biostudies-arrayexpress
TranscriptomicsStructural basis of YTH domain as m6A reader
The N6-methyladenosine (m6A) is the most abundant internal modification in almost all eukaryotic messenger RNAs, and is dynamically regulated. Therefore, identification of m6A readers is especially important in determining the cellular function of m6A. YTHDF2 has recently been characterized as the f...
ORGANISM(S): Homo sapiens 
2014-09-18 | E-GEOD-58352 | biostudies-arrayexpress
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