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GSE81602
Homo sapiens
5 Downloadable Samples
Illumina HiSeq 2000, Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
A Long Noncoding RNA Regulates Sister Chromatid Cohesion.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 5 Downloadable Samples
Affymetrix Human Transcriptome Array 2.0 (hta20), Illumina HiSeq 2000
Description
Long noncoding RNAs (lncRNAs) have appeared to be involved in the most diverse cellular processes through multiple mechanisms. Here we describe a previously uncharacterized human lncRNA, CONCR (cohesion regulator noncoding RNA), transcriptionally activated by MYC, which is upregulated in multiple cancer types. The expression of CONCR is cell cycle-regulated, and it is required for cell cycle progression and DNA replication. Moreover, cells depleted of CONCR show severe defects in sister chromatid cohesion, suggesting an essential role for CONCR in cohesion establishment during cell division. CONCR interacts with and regulates the activity of DDX11, a DNA-dependent ATPase and helicase involved in DNA replication. These findings suggest a novel mechanism of action for CONCR in the modulation of DDX11 enzymatic activity, unveiling the direct involvement of a lncRNA in the establishment of sister chromatid cohesion.
Publication Title
A Long Noncoding RNA Regulates Sister Chromatid Cohesion.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
During organogenesis, PAX6 is required for establishment of various progenitor subtypes within the central nervous system, eye and pancreas. PAX6 expression is maintained in a variety of cell types within each organ, although its role in each lineage and how it acquires cell-specific activity remain elusive. Herein, we aimed to determine the roles and the hierarchical organization of the PAX6-dependent gene regulatory network during the differentiation of the retinal pigmented epithelium (RPE). Somatic mutagenesis of Pax6 in the differentiating RPE revealed that PAX6 functions in a feed-forward regulatory loop with MITF during onset of melanogenesis. PAX6 both controls the expression of an RPE isoform of Mitf and synergizes with MITF to activate expression of genes involved in pigment biogenesis. This study exemplifies how one kernel gene pivotal in organ formation accomplishes a lineage-specific role during terminal differentiation of a single lineage.
Publication Title
PAX6 regulates melanogenesis in the retinal pigmented epithelium through feed-forward regulatory interactions with MITF.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 33 Downloadable Samples
- Illumina HiSeq 2000, Illumina Genome Analyzer IIx
Description
We describe a novel quantitative cDNA expression profiling strategy, involving amplification of the majority of mouse transcriptome using a defined set of 44 heptamer primers. The amplification protocol allows for efficient amplification from as low as 50pg of mRNA and did not alter the expression of the transcripts even with 200 fold dilution of the minimum requirement of the starting material (10ng of mRNA) for standard RNA-seq protocols. We implemented our methodology on embryological lineage segregation, achieved by graded activation of Activin A/TGFß signaling in mouse embryonic stem cells (mESCs). The fold changes in transcript expression were in excellent agreement with quantitative RT-PCR and we observed a dynamic range spanning more than five orders of magnitude in RNA concentration with a reliable estimation of low abundant transcripts. Our transcriptome data identified key lineage markers, while the high sensitivity showed that novel lineage specific transcripts anticipate the differentiation of specific cell types. We compared our strategy with Std. RNA-seq (Mortazavi et al. 2008) and SMART-seq (Ramsköld et al. 2012). We also showed potential of our methodology to suppress the representation of highly expressing ribosomal transcripts. Overall design: Sequencing was performed on day 4 differentiating mouse ESCs treated for two days with 3 different dosages of Activin A (3ng/mL, 15ng/mL and 100ng/mL). The cells were also treated with SB-431542. Serial dilutions of mRNA derived Activin A(3ng/mL) samples were used to detemine the minimum amount of mRNA required to construct relaible sequencing library. SMARTseq libraries were prepared for both Activin A(3ng/mL) and Activin A(100ng/mL) samples. Three Different primer sets were designed to suppress the representaiton of Ribosomal transcripts.
Publication Title
Quantitative transcriptomics using designed primer-based amplification.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 52 Downloadable Samples
- Illumina HiSeq 2000
Description
Transcriptomics data obtained from limiting amounts of mRNA is often noisy, providing primarily qualitative changes in transcript expressions. So far, technical variations arising out of the library preparation protocols have not been adequately characterized at reduced levels of mRNA. Here, we generated sequencing libraries from limiting amounts of mRNA using three amplification-based methods, viz. Smart-seq, DP-seq and CEL-seq, and demonstrated significant technical variations in these libraries. Reduction in mRNA levels led to inefficient amplification of the majority of low to moderately expressed transcripts. Furthermore, stochasticity in primer hybridization and/or enzyme incorporation was magnified during the amplification step resulting in significant distortions in fold changes of the transcripts. Consequently, the majority of the differentially expressed transcripts identified were either high-expressed and/or exhibited high fold changes. High technical variations, which were sequencing depth independent, ultimately masked subtle biological differences mandating the development of improved amplification-based strategies for quantitative transcriptomics from limiting amounts of mRNA. Overall design: Sequencing libraries were prepared from serial dilutions of mRNA, ranging from 1 ng to 25 pg, using three amplification-based methods, viz. Smart-seq, DP-seq and CEL-seq. The mRNA was derived from an in vitro model of lineage segregation achieved by modulating TGF beta signaling pathway in differentiating mouse embryonic stem cells.
Publication Title
Technical variations in low-input RNA-seq methodologies.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 14 Downloadable Samples
- Illumina HiSeq 2000
Description
In this study, we confirmed that transformed dedifferentiated astrocytes and neurons acquired a stem/progenitor cell state, although they still retained gene expression memory from their parental cell-type. Transcriptional network analysis on transformed cells revealed up-regulation of genes involved in three signaling pathways: Wnt signaling, cell cycle and focal adhesion with the gene Spp1, also known as osteopontin (OPN) serving as a key node connecting these three pathways. Inhibition of OPN blocked the formation of aggregated neurospheres, affected the proliferative capacity of transformed cell-types and reduced the expression levels of neural stem cell markers. Specific inhibition of OPN in murine glioma tumors prolonged mice survival. We conclude that OPN is an important player in dedifferentiation of cells during tumor formation, hence its inhibition can be a therapeutic target for glioblastoma. Overall design: Cortical neurons and astrocytes were derived from 11 days old SynapsinI-Cre and GFAP-Cre mice, respectively. The cells were cultured in their respective media to maintain their identity. These cells were then transduced with HRas-shp53 lentivirus with a transduction efficiency of >90%. The transduced neurons and astrocytes were later switched to neural stem cell media devoid of serum and supplemented with FGF-2 (NSC media). Within one week, these cells became proliferative and aggregated to form free-floating neurospheres. These cells, hereinafter referred to as NSynR53 and AGR53, respectively, were later harvested and mRNA collected for sequencing library generation using DP-seq. To assess the regression of these cells to an undifferentiated state along the differentiation axis, enriched populations of mESC and NSC were also grown in vitro and mRNA obtained from these cells were subjected to sequencing library preparation.
Publication Title
Identification of therapeutic targets for glioblastoma by network analysis.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina MouseWG-6 v2.0 R2 expression beadchip
Description
Genome wide gene expression analysis in G9a knockdown myoblasts
Publication Title
G9a promotes proliferation and inhibits cell cycle exit during myogenic differentiation.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 13 Downloadable Samples
- Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Natural killer T (NKT) cells are important therapeutic targets in various disease models and under clinical trials for cancer patients. However, their function in obesity and type 2 diabetes remains unclear. Our data show that adipose tissues of both mice and humans contain a population of type-1 NKT cells, whose abundance decreases with increased adiposity and insulin resistance. Although loss-of-function of NKT cells had no effect on glucose tolerance in animals with prolonged high-fat diet (HFD) feeding, activation of NKT cells by lipid agonist -galactosylceramide (GalCer) enhances alternative macrophage polarization in adipose tissue and improves glucose homeostasis in animals at different stages of obesity. Furthermore, the effect of NKT cells is largely mediated by the IL-4/STAT6 signaling axis in obese adipose tissue. Thus, our data identifies a novel therapeutic target for the treatment of obesity-associated inflammation and type-2 diabetes.
Publication Title
Activation of natural killer T cells promotes M2 Macrophage polarization in adipose tissue and improves systemic glucose tolerance via interleukin-4 (IL-4)/STAT6 protein signaling axis in obesity.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Aim of this experiment was to look at the gene expression differences in the benzyladenine-treated and untreated Arabidopsis seedlings grown in light
Publication Title
Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis.
Sample Metadata Fields
Age, Specimen part, Compound
View Samples- Arabidopsis thaliana
- 3 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Aim was to look at the gene profile changes in 10 days old Arabidopsis seedlings grown in light and treated with either Zeatin or BA and compared to non-treatment
Publication Title
Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis.
Sample Metadata Fields
Age, Compound
View Samples