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TranscriptomicsExon array analysis of resting and activated primary murine CD4+ T-cells
The stability, localization and translation of mammalian mRNAs are largely determined by sequences in the 3' untranslated region (UTR). Here, we describe a conserved program of increased upstream polyadenylation site usage following activation of primary murine CD4+ T lymphocytes. This program, re...
ORGANISM(S): Mus musculus 
2010-05-26 | E-GEOD-10666 | biostudies-arrayexpress
TranscriptomicsSingle cell RNA-seq of individual cells from dorsal skin of a F1 mouse cross-breed (C57BL/6JxCAST/EiJ)
Sequencing of diverse cell types present in the dorsal skin of a F1 mouse cross-breed in order to study the regulation of transcription on an allele-resolved level.
ORGANISM(S): Mus musculus 
2022-10-07 | E-MTAB-12181 | biostudies-arrayexpress
TranscriptomicsGenomic encoding of transcriptional burst kinetics
We used single-cell RNA-sequencing to generate allele-resolution expression levels in individual cells that we used for inference of transcriptional burst kinetics.
ORGANISM(S): Mus musculus 
2018-09-30 | E-MTAB-6362 | biostudies-arrayexpress
TranscriptomicsSingle-cell RNA-Seq reveals dynamic, random monoallelic gene expression in mammalian cells
In the diploid genome, genes come in two copies, which can have different DNA sequence and where one is maternal and one is paternal. In a particular cell, a gene could potentially be expressed from both copies (biallelic expression) or only one (monoallelic). We performed RNA-Sequencing on individu...
ORGANISM(S): Mus musculus 
2014-01-10 | E-GEOD-45719 | biostudies-arrayexpress
TranscriptomicsCTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing [RNA-Seq]
The goal of this study was to investigate the role of intragenic CTCF in alternative pre-mRNA splicing through a combined CTCF-ChIP-seq and RNA-seq approach. CTCF depletion led to decreased inclusion of weak upstream exons. CTCF ChIP-seq was performed in BJAB and BL41 B cell lines and normalized rel...
ORGANISM(S): Homo sapiens 
2011-10-06 | E-GEOD-31486 | biostudies-arrayexpress
GenomicsCTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing [ChIP-Seq]
The goal of this study was to investigate the role of intragenic CTCF in alternative pre-mRNA splicing through a combined CTCF-ChIP-seq and RNA-seq approach. CTCF depletion led to decreased inclusion of weak upstream exons. CTCF ChIP-seq was performed in BJAB and BL41 B cell lines and normalized rel...
ORGANISM(S): Homo sapiens 
2011-10-06 | E-GEOD-31485 | biostudies-arrayexpress
TranscriptomicsMorphological, electrophysiological and transcriptomic profiling of single neurons using Patch-seq
The mammalian neocortex is a layered sheet of neural tissue that mediates complex cognitive processes including perception and cognition. Despite its importance, we still lack detailed knowledge of the cellular components of the neocortex. Integrating morphological, electrophysiological and molecula...
ORGANISM(S): Mus musculus 
2016-01-25 | E-MTAB-4092 | biostudies-arrayexpress
TranscriptomicsSingle-cell RNA-seq analysis of human pancreas from healthy individuals and type 2 diabetes patients
We used single-cell RNA-sequencing to generate transcriptional profiles of endocrine and exocrine cell types of the human pancreas. Pancreatic tissue and islets were obtained from six healthy and four T2D cadaveric donors. Islets were cultured and dissociated into single-cell suspension. Viable indi...
ORGANISM(S): Homo sapiens 
2016-09-22 | E-MTAB-5061 | biostudies-arrayexpress
TranscriptomicsSequentially acting Sox transcription factors in neural lineage development [RNA-seq]
We report sequential binding but unique functions of different Sox transcription factors during distinct stages of neural differentiation Loss of function experiment for Sox2/Sox3 in neural progenitor cells and gene expression profile for Sox11 expressing (PSA NCAM sorted) early formed neurons.
ORGANISM(S): Mus musculus 
2011-11-01 | E-GEOD-33060 | biostudies-arrayexpress
GenomicsSequentially acting Sox transcription factors in neural lineage development [ChIP-seq]
We report sequential binding but unique functions of different Sox transcription factors during distinct stages of neural differentiation Examination of genome-wide Sox2, Sox3 and Sox11 transcription factor binding during different stages of neurogenesis.
ORGANISM(S): Mus musculus 
2011-11-01 | E-GEOD-33059 | biostudies-arrayexpress
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