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TranscriptomicsEndogenous shRNAs, siRNAs, and Other Microprocessor-independent, Dicer-dependent Small RNAs in Mouse ES Cells
Canonical microRNAs (miRNAs) require two processing steps: the first by the Microprocessor, a complex of DGCR8 and Drosha, and the second by Dicer. dgcr8delta/delta mouse embryonic stem cells (mESCs) have less severe phenotypes than dicer1delta/delta mESCs, suggesting a physiological role for Microp...
ORGANISM(S): Mus musculus 
2008-09-09 | E-GEOD-12521 | biostudies-arrayexpress
TranscriptomicsDGCR8 is required for microRNA maturation
To determine whether DGCR8 is required for maturation of all miRNAs, we performed miRNA microarray analysis. Using RNA from wild-type ES cells as our reference sample, we observed a global loss of miRNAs in DGCR8 knockout cells, but normal levels of expression in DGCR8 heterozygous cells. The simil...
ORGANISM(S): Mus musculus 
2010-06-11 | E-GEOD-6586 | biostudies-arrayexpress
TranscriptomicsMicroRNA profiling of glial progenitor cells in growth and differentiation conditions
The molecular basis of astrocyte differentiation and maturation is poorly understood. As microRNAs have important roles in cell fate transitions, we set out to study their function during the glial progenitor cell (GPC) to astrocyte transition. Inducible deletion of all canonical microRNAs in GPCs i...
ORGANISM(S): Mus musculus 
2015-03-05 | E-GEOD-64661 | biostudies-arrayexpress
TranscriptomicsFunctional non-canonical microRNAs in the mammalian hippocampus and cortex
Non-canonical microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) are distinct subclasses of small RNAs that bypass the DGCR8/Drosha Microprocessor but still require Dicer for their biogenesis. What, if any, role they have in mammals remains unknown. To identify potential roles for t...
ORGANISM(S): Mus musculus 
2011-03-23 | E-GEOD-21090 | biostudies-arrayexpress
TranscriptomicsThe effect of miR-294 and miR-181 on the transcriptome during OSK reprogramming of MEFs
Study designed to determine the immediate effects of supplementing OSK reprogramming with miR-294 or miR-181. MEFs were infected on day 0, and transfected with miR-294, miR-181 or control mimic on day 1. On day 3 RNA was extracted. OSK infected MEFs samples were compared to non-infected MEFs and to ...
ORGANISM(S): Mus musculus 
2013-09-15 | E-GEOD-49556 | biostudies-arrayexpress
TranscriptomicsExpression data from the adult hippocampus of Sox1-GFP mice
The dentate gyrus of the hippocampus continues generating new neurons throughout life. These nerve cells originate from radial astrocytes within the subgranular zone (SGZ). We find that Sox1, a member of the SoxB1 family of transcription factors, is expressed in a subset of radial astrocytes. Linea...
ORGANISM(S): Mus musculus 
2012-08-08 | E-GEOD-39992 | biostudies-arrayexpress
TranscriptomicsExpression analysis of OSK and Sall4+OSK reprogramming cells sorted for expression of miR-290 and/or miR-302.
MEFs were infected with Oct4, Sox2, Klf4 (+/- Sall4), sorted for miR-290/302 reporter expression at day 9 (OSK) or 12 (Sall4+OSK), and then profiled. Resulting iPSCs were also profiled. Mouse ES cells were differentiated and sorted for miR-290/302 reporter expression during Fgf/Activin differentiati...
ORGANISM(S): Mus musculus 
2014-03-31 | E-GEOD-54341 | biostudies-arrayexpress
GenomicsFoxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation [ChIP-seq]
Transcription factor/enhancer interactions determine cell specific gene expression. Here, we followed enhancers during differentiations of embryonic stem (ESCs) to epiblast like cells (EpiLCs). There were highly dynamic changes in histone lysine 27 acetylation at enhancer sites throughout the geno...
ORGANISM(S): Mus musculus 
2015-12-08 | E-GEOD-58407 | biostudies-arrayexpress
TranscriptomicsExpression analysis of miR-302 knockout and wild-type embryos during neurulation
Wild-type or miR-302 knockout tissue was isolated from embryos during neurulation in replicate Performed in biological triplicate except for E7.5 WT which was in duplicate and E9.5 timepoints which were in quadruplicate. Biological replicate samples represent independent embryos. Total RNA collected...
ORGANISM(S): Mus musculus 
2015-08-03 | E-GEOD-62396 | biostudies-arrayexpress
TranscriptomicsMammalian microRNAs: Experimental evaluation of novel and previously annotated genes
MicroRNAs (miRNAs) are small regulatory RNAs that derive from distinctive hairpin transcripts. To learn more about the miRNAs of mammals, we sequenced 60 million small RNAs from mouse brain, ovary, testes, embryonic stem cells, three embryonic stages, and whole newborns. Analysis of these sequences ...
ORGANISM(S): Homo sapiens 
2010-04-26 | E-GEOD-20384 | biostudies-arrayexpress
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