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TranscriptomicsDifferentiation and specification of resident tissue macrophages
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Mus musculus 
2016-08-08 | E-GEOD-81774 | biostudies-arrayexpress
GenomicsSingle-cell DNA methylome sequencing and bioinformatic inference of epigenetic cell state dynamics
Here we describe a method for whole genome bisulfite sequencing in very small cell populations (µWGBS) and in single cells (scWGBS). Our method is optimized for profiling DNA methylation in many samples at low coverage, and we developed a bioinformatic method that uses collections of single-cell met...
ORGANISM(S): Mus musculus 
2015-02-25 | E-GEOD-65196 | biostudies-arrayexpress
TranscriptomicsSingle-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
We report the single-cell RNA-seq based identification of 6 known human islet cell types (alpha cells, beta cells, delta cells, pp cells, acinar cells and duct cells) based on the expression of known marker genes. We further assess cell type specific gene expression and suggest novel marker genes fo...
ORGANISM(S): Homo sapiens 
2016-01-05 | E-GEOD-73727 | biostudies-arrayexpress
GenomicsChromatin accessibility maps of chronic lymphocytic leukemia identify subtype-specific epigenome signatures and transcription regulatory networks
Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ...
ORGANISM(S): Homo sapiens 
2016-06-26 | E-GEOD-81274 | biostudies-arrayexpress
GenomicsSequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here we present sequential ChIP-bisulfite-sequencing (ChIP- BS-seq) as an approach to quantitatively ...
ORGANISM(S): Homo sapiens 
2012-03-27 | E-GEOD-28254 | biostudies-arrayexpress
GenomicsGenome wide DNA methylation analysis of leukemia and reprogrammed leukemia cells
We apply cellular reprogramming to an induced pluripotent cell state to human cell lines and primary samples exhibiting Chronic Myoloid Leukemia (CML). Addtionally, we generated an inducible CML BCR-ABL transgenic mouse model. Biological replicates (duplicates) were available for all samples. DNA me...
ORGANISM(S): Homo sapiens 
2015-07-14 | E-GEOD-50456 | biostudies-arrayexpress
TranscriptomicsPaternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals (dye swap)
Epigenetic information can be inherited through the mammalian germline, and represents a plausible transgenerational carrier of environmental information. To test whether transgenerational inheritance of environmental information occurs in mammals, we carried out an expression profiling screen for g...
ORGANISM(S): Mus musculus 
2011-01-14 | E-GEOD-25895 | biostudies-arrayexpress
TranscriptomicsPaternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals (Affymetrix)
Epigenetic information can be inherited through the mammalian germline, and represents a plausible transgenerational carrier of environmental information. To test whether transgenerational inheritance of environmental information occurs in mammals, we carried out an expression profiling screen for g...
ORGANISM(S): Mus musculus 
2011-01-14 | E-GEOD-25896 | biostudies-arrayexpress
GenomicsPaternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals (meDIP)
Epigenetic information can be inherited through the mammalian germline, and represents a plausible transgenerational carrier of environmental information. To test whether transgenerational inheritance of environmental information occurs in mammals, we carried out an expression profiling screen for g...
ORGANISM(S): Mus musculus 
2011-01-14 | E-GEOD-25898 | biostudies-arrayexpress
TranscriptomicsPaternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals
This SuperSeries is composed of the following subset Series: GSE25895: Paternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals (dye swap) GSE25896: Paternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammal...
ORGANISM(S): Mus musculus 
2011-01-14 | E-GEOD-25899 | biostudies-arrayexpress
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