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GenomicsIn vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse (Bisulfite-Seq)
Methylation of cytosines (5meC) is a widespread heritable DNA modification. During mammalian development, two global demethylation events are followed by waves of de novo DNA methylation. In vivo mechanisms of DNA methylation establishment are largely uncharacterized. Here we use Saccharomyces cerev...
ORGANISM(S): Saccharomyces cerevisiae 
2015-04-02 | E-GEOD-66905 | biostudies-arrayexpress
TranscriptomicsMosaic perturbation of transcription factors in human retinal organoid development
To begin to understand how TFs regulate retinal cell type identity in human tissues, we established a pooled loss of function (LOF) experiment based on the CROP-seq protocol in developed retinal organoids. We targeted five TFs (OTX2, NRL, CRX, VSX2, and PAX6) that are important for retinal developme...
ORGANISM(S): Homo sapiens 
2023-02-24 | E-MTAB-12622 | biostudies-arrayexpress
TranscriptomicsExpression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell type specificity
Background: Although genome-wide association studies (GWAS) have identified hundreds of variants associated with risk of autoimmune and immune-related disorders (AID), our understanding of the diseases mechanisms is limited. In particular, more than 90% of the risk variants lie in non-coding regions...
ORGANISM(S): Homo sapiens 
2014-10-16 | E-GEOD-62408 | biostudies-arrayexpress
TranscriptomicsThe bile acid CoA ligase, FATP5, is necessary for NAT synthesis in the liver
This study aimed to investigate the overlap between hepatic NAT and the bile acid synthesis to identify additional enzymes involved in NAT synthesis in the liver. We sequenced livers high-fat fed mice the were either wild-type or with a single-amino acid substitution in fatty acid amide hydrolase (F...
ORGANISM(S): Mus musculus 
2026-03-02 | E-MTAB-15752 | biostudies-arrayexpress
GenomicsMolecular role of the PAX5-ETV6 oncoprotein in promoting B cell acute lymphoblastic leukemia
PAX5 is a tumor suppressor in B-ALL, while the role of PAX5 fusion proteins in B-ALL development is largely unknown. Here we studied the function of PAX5-ETV6 and PAX5- FOXP1 in mice expressing these proteins from the Pax5 locus. Both proteins arrested Blymphopoiesis at the pro-B-to-pre-B cell trans...
ORGANISM(S): Mus musculus 
2016-07-30 | E-GEOD-84987 | biostudies-arrayexpress
TranscriptomicsDynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity [RNA-Seq]
T cell development comprises a stepwise process of commitment from a multipotent precursor. To define molecular mechanisms controlling this progression, we probed five stages spanning the commitment process using deep sequencing RNA-seq and ChIP-seq methods to track genome-wide shifts in transcripti...
ORGANISM(S): Mus musculus 
2012-04-13 | E-GEOD-31234 | biostudies-arrayexpress
TranscriptomicsFate and State Transitions during Human Blood Vessel Organoid Development: Perturbation
Human blood vessel organoids (hBVOs) have emerged as a system to model human vascular development and disease. Here, we use genetic and signaling pathway perturbations to reconstruct hBVO development. We use single-cell genetic perturbations to identify transcription factors (TFs) and receptors invo...
ORGANISM(S): Homo sapiens 
2025-03-01 | E-MTAB-14839 | biostudies-arrayexpress
TranscriptomicsFate and State Transitions during Human Blood Vessel Organoid Development: Time Course
Human blood vessel organoids (hBVOs) derived from human pluripotent stem cells have emerged as a novel system to understand human vascular development, model disorders, and develop regenerative therapies. However, it was unclear which molecular states constitute hBVOs and how cells differentiate and...
ORGANISM(S): Homo sapiens 
2025-03-21 | E-MTAB-14807 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of Phytobacterium profundum SS9 strain cells grown at two different pressure conditions 0.1 MPa and at 28 MPa
P. profundum SS9 strain cells were grown at two different pressure conditions 0.1 MPa and at 28 MPa. RNA extracted from the two different cultures was labelled with Cy5 and Cy3 and competitively hybridized on the same slide.
ORGANISM(S): Photobacterium profundum 
2005-07-28 | E-MEXP-210 | biostudies-arrayexpress
UnknownGuidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).
Not available
S-EPMC4835977 | biostudies-literature
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