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Homo sapiens
9 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
We identified two isoforms of human MKL1 that differ in their N-terminal domains. Since MKL1 is a transcriptional coactivator of SRF and regulates many SRF target genes, we wanted to analyze if transcription is differentially regulated by the two isoforms upon stimulation of the Rho-actin-MKL1-SRF pathway.
Publication Title
TGF-β-induced differentiation into myofibroblasts involves specific regulation of two MKL1 isoforms.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 13 Downloadable Samples
IlluminaHiSeq2000
Description
It has been unclear whether ischemic stroke induces neurogenesis or neuronal DNA-rearrangements in the human neocortex. We show here that neither is the case, using immunohistochemistry, transcriptome-, genome- and ploidy-analyses, and determination of nuclear bomb test-derived 14C-concentration in neuronal DNA. A large proportion of cortical neurons display DNA-fragmentation and DNA-repair short time after stroke, whereas neurons at chronic stages after stroke show DNA-integrity, demonstrating the relevance of an intact genome for survival. Overall design: Analyze of potential fusion transcripts in 13 samples, seven cortical ischemic stroke tissue and six control cortex, by deep sequencing using Illumina HiSeq 2000
Publication Title
The age and genomic integrity of neurons after cortical stroke in humans.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 73 Downloadable Samples
- IlluminaHiSeq2000
Description
Gene expression analysis of purified hematopoietic stem and progenitor cells isolated from low to intermediate risk MDS patients and age-matched normal healthy controls. Overall design: Analysis of lineage associated genes and PCA clustering of populations
Publication Title
Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo.
Sample Metadata Fields
No sample metadata fields
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SRP071058- Mus musculus
- 48 Downloadable Samples
- Illumina HiSeq 2500
Description
B cells provide humoral immunity by differentiating into antibody secreting plasma cells. Differentiation is dependent upon division and transcriptional changes, with commitment to B cell lineages associated with epigenetic changes. Analysis of early transcriptional and epigenetic events in B cell differentiation revealed that plasmablasts and plasma cells undergo dynamic changes in gene expression and a progressive DNA hypomethylation targeted to at least 10% of genes/loci. Of the differentially methylated loci, more than 99.7% were demethylated during differentiation and these clustered in cis-regulatory features such as enhancers and transcription factor binding sites. Changes in gene expression and DNA methylation coincided with each other at specific divisions during differentiation and inhibition of DNA methylation resulted in augmented plasma cell commitment in a division-dependent manner. These data identify a major epigenetic reprogramming event during early B cell differentiation coupled division and provide an approach to modulating humoral immune responses. Overall design: Splenic B cells (B220+ CD43-) from naïve C57/BL6J mice were labeled with CFSE or CTV and transferred into uMT mice and allowed to rest overnight prior to challenge with LPS. Three days post challenge adoptively transferred B cells representing distinct divisions were sorted out for molecular analysis. These divisions are labelled Div0, Div1, Div3, Div5, Div8- and Div8+. Division 8- refers to cells that divided at least 8 times but were CD138-, whereas Division 8+ refers to cells that divided at least 8 times but were CD138+. Cells were subjected to RNA-seq and Reduced Representation Bisulfite Sequencing.
Publication Title
Plasma cell differentiation is coupled to division-dependent DNA hypomethylation and gene regulation.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 7 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Plasma cell differentiation is coupled to division-dependent DNA hypomethylation and gene regulation.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 7 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
B cells provide humoral immunity by differentiating into antibody secreting plasma cells. Differentiation is dependent upon division and transcriptional changes, with commitment to B cell lineages associated with epigenetic changes. Analysis of early transcriptional and epigenetic events in B cell differentiation revealed that plasmablasts and plasma cells undergo dynamic changes in gene expression and a progressive DNA hypomethylation targeted to at least 10% of genes/loci. Of the differentially methylated loci, more than 99.7% were demethylated during differentiation and these clustered in cis-regulatory features such as enhancers and transcription factor binding sites. Changes in gene expression and DNA methylation coincided with each other at specific divisions during differentiation and inhibition of DNA methylation resulted in augmented plasma cell commitment in a division-dependent manner. These data identify a major epigenetic reprogramming event during early B cell differentiation coupled division and provide an approach to modulating humoral immune responses.
Publication Title
Plasma cell differentiation is coupled to division-dependent DNA hypomethylation and gene regulation.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 45 Downloadable Samples
- Illumina HiSeq 2500
Description
To understand the role of Ezh2 in B cell differentiation B cells were stimulated ex vivo with LPS, Il2, and Il5 in the presence of DMSO or the selective Ezh2 inhibitor GSK343. Following 3 days culture, activated B cells and Plasmablasts were FACS isolated and RNA-seq was performed to identify the molecular effects of Ezh2 inhibition on B cell subsets during differentiation. Overall design: RNAseq on ex vivo differentiated B cell subsets treated with GSK343 or DMSO
Publication Title
Plasma cell differentiation is controlled by multiple cell division-coupled epigenetic programs.
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment, Subject
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip, Affymetrix Human Genome U133A Array (hgu133a)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
To understand the role of LSD1 in B cell differentiation, mice with B cell conditional deletion of LSD1 were intravenously inoculated with LPS. After 3 days, B220+GL7-CD138- naïve B cells and CD138+ plasmablasts were FACS-sorted from the spleens and RNA-seq was performed to identify LSD1-target regulated genes. Overall design: RNA-seq on control or LSD1-deficient murine naïve B cells or plasmablasts.
Publication Title
The Histone Demethylase LSD1 Regulates B Cell Proliferation and Plasmablast Differentiation.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip
Description
SOX4 is a critical developmental transcription factor in vertebrates and is required for precise differentiation and proliferation in multiple tissues. In addition, SOX4 is overexpressed in many human malignancies, but the precise role of SOX4 in cancer progression is not well understood. Here we have performed an expression profiling experiment of LNCaP cells either overexpressing SOX4 or GFP to identify SOX4 target genes.
Publication Title
Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer cells.
Sample Metadata Fields
No sample metadata fields
View Samples