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E-MTAB-3558
Arabidopsis thaliana
6 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
SWP73 subunits of SWI/SNF chromatin remodeling complexes (CRCs) are involved in key developmental pathways in Arabidopsis. We found, using microarray that inactivation of SWP73B caused altered expression of genes belonging to various regulatory pathways, including leaf and flower development. On the basis of this experiment and our other data we concluded that SWP73B modulates major developmental pathways.
Publication Title
SWP73 Subunits of Arabidopsis SWI/SNF Chromatin Remodeling Complexes Play Distinct Roles in Leaf and Flower Development.
Sample Metadata Fields
Specimen part
View Samples- Hordeum vulgare
- 18 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
The wheat gene Lr34 (Yr18/Pm38/Sr57/Ltn1) encodes a putative ABCG-type of transporter and is a unique source of disease resistance providing durable and partial resistance against multiple fungal pathogens. Lr34 has been found to be functional as a transgene in barley.
Publication Title
The wheat resistance gene Lr34 results in the constitutive induction of multiple defense pathways in transgenic barley.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 5 Downloadable Samples
NextSeq 500
Description
Purpose: We tested global gene transcriptome changes by RNA-sequencing analysis in the offspring breast tumors of SV40 transgenic mice to further identify key epigenetic-controlled genes in regulation of the prenatal/maternal BSp diet-mediated early breast cancer prevention. Method: Mouse offspring mammary tumor mRNA from control and maternal BSp treatment were generated by deep sequencing, in duplicate or triplicate, using Illumina NextSeq500 platform (GPL19057). The sequence reads that passed quality filters were analyzed. We utilized the R/Bioconductor package DESeq to evaluate differential gene expression for sequence count data by the use of negative binomial distributio. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Conclusions: Our data showed differential transcriptome distribution in the breast tumors of mouse offspring between the control and prenatal/maternal BSp treatment groups. Overall design: Total RNA obtained from the offspring breast tumors of SV40 transgenic mice with mothers fed either control or BSp diets, and analyzed by Illumina NextSeq500 platform (GPL19057).
Publication Title
Temporal Efficacy of a Sulforaphane-Based Broccoli Sprout Diet in Prevention of Breast Cancer through Modulation of Epigenetic Mechanisms.
Sample Metadata Fields
Age, Cell line, Treatment, Subject
View Samples- Arabidopsis thaliana
- 22 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Due to limited bio-availability of Fe, plants evolved adaptive alterations in development regulated at the transcriptional level. We investigated the early transcriptional response to Fe deficiency.
Publication Title
Early iron-deficiency-induced transcriptional changes in Arabidopsis roots as revealed by microarray analyses.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- Illumina Genome Analyzer
Description
Several recently emerging ChIP-seq (chromatin immunoprecipitation followed by sequencing) based methods perform chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for bioinformatics and data quality analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. Application of this method allowed for discovery of a novel CTCF binding motif from ChIP-exo data. Overall design: HeLa cells were transfected with either a scrambled siRNA or one of two CTCF siRNAs (Thermo Fisher Scientific ? Life technologies) using Lipofectamine RNAiMAX (Thermo Fisher Scientific - Life technologies) and incubated for 24 hr.
Publication Title
PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 9 Downloadable Samples
- Illumina Genome Analyzer
Description
The emerging correlation between aberrant DNA methylation patterns leading to transcriptional responses that promote and progress many cancers has prompted an interest in discerning the associated regulatory mechanisms. ZBTB33 (also known as Kaiso) is a specialized transcription factor that selectively recognizes mCpG-containing sites as well as a sequence-specific DNA target (termed the KBS) utilizing three Cys2His2 zinc fingers. Increasing reports link ZBTB33 overexpression and transcriptional activities with metastatic potential and poor prognosis, though the specific cellular consequences appear to be dependent on disease phenotype. There is currently little mechanistic insight into how various cellular phenotypes are then able to harness the transcriptional capabilities of ZBTB33 to differentially promote and progress the disease state. Here we have mechanistically interrogated the cell cycle responses mediated by the transcriptional activities of ZBTB33 in two different cell lines. Utilizing a series of ZBTB33 depletion and overexpression studies, we have determined that in HeLa cells ZBTB33 directly occupies the promoter regions of cyclin D1 and cyclin E1 in a KBS and methyl-specific manner, respectively, inducing increased proliferation by promoting RB1 hyper-phosphorylation, allowing for E2F transcriptional activity that coordinates an accelerated G1- to S-phase transition. Conversely, in HEK293 cells ZBTB33 indirectly regulates Cyclin E abundance resulting in reduced RB1 phosphorylation, decreased E2F activity and a decelerated transition through G1-phase. Thus, we have identified a novel mechanism by which ZBTB33 directly mediates the highly coordinated cyclin D1/cyclin E1/RB1/E2F signaling pathway controlling the passage through the G1-phase restriction point and accelerating cellular proliferation in a cancer cell line. Overall design: Determination of cellular and transcriptional consequences for ZBTB33 depletion in HeLa cells.
Publication Title
Cell-specific Kaiso (ZBTB33) Regulation of Cell Cycle through Cyclin D1 and Cyclin E1.
Sample Metadata Fields
Cell line, Subject
View Samples- Rattus norvegicus
- 16 Downloadable Samples
- Illumina HiSeq 4000
Description
Hypertension remains a poorly understood condition, and the understanding of the sympathetic nervous systems role in this disease remains even more limited. In this study, RNA-sequencing is used to identify transcriptomal differences in the sympathetic stellate ganglia between the 16-week-old normotensive wistar strain and the spontaneously hypertensive rat strain.This dataset should allow for further molecular characterisation of hypertensive changes in a cardiac-innervating sympathetic ganglion. Overall design: Comparison of normotensive and hypertensive rat stellate ganglia. 4 biological replicates for both 16 week wistar and SHR stellate ganglia samples were contrasted
Publication Title
Neurotransmitter Switching Coupled to β-Adrenergic Signaling in Sympathetic Neurons in Prehypertensive States.
Sample Metadata Fields
No sample metadata fields
View Samples- Gallus gallus
- 12 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
The mycotoxin deoxynivalenol (DON) is a secondary metabolite from Fusarium species and is frequently present on wheat and other cereals. The main effects of DON are a reduction of the feed intake and reduced weight gain of broilers. At the molecular level DON binds to the 60S ribosomal subunit and inhibits subsequently protein synthesis at the translational level. It has been suggested that cells and tissues with high protein turnover rate, like the liver and small intestine, are most affected by DON. However, little is known about other effects of DON e.g. at the transcriptional level. Therefore we decided to perform a microarray analysis, which allows us the investigation of thousands of transcripts in one experiment.
Publication Title
Fusarium mycotoxin-contaminated wheat containing deoxynivalenol alters the gene expression in the liver and the jejunum of broilers.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
Transcriptome profiling using RNA-seq of ß-TC3 cell, a mouse pancreatic cell line used in the study of novel Cis-regulatory elements for the Pax6 gene . Overall design: Total RNA was collected and a Illumina sequencing libraries prepared from two biological replicates of cultured ß-TC3 cells.
Publication Title
Functional characteristics of novel pancreatic Pax6 regulatory elements.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Background: The prefrontal cortex is important in regulating sleep and mood. Diurnally regulated genes in the prefrontal cortex may be controlled by the circadian system, by the sleep-wake states, or by cellular metabolism or environmental responses. Bioinformatics analysis of these genes will provide insights into a wide-range of pathways that are involved in the pathophysiology of sleep disorders and psychiatric disorders with sleep disturbances. Results: We examined gene expression in the mouse prefrontal cortex at four time points during the 24-hour (12-hour light:12-hour dark) cycle by microarrays, and identified 3,890 transcripts corresponding to 2,927 genes with diurnally regulated expression patterns. We show that 16% of the genes identified in our study are orthologs of identified clock, clock controlled or sleep/wakefulness induced genes in the mouse liver and SCN, rat cortex and cerebellum, or Drosophila head. The diurnal expression patterns were confirmed in 16 out of 18 genes in an independent set of RNA samples. The diurnal genes fall into eight temporal categories with distinct functional attributes, as assessed by the Gene Ontology classification and by the analysis of enriched transcription factor binding sites. Conclusions: Our analysis demonstrates that ~10% of transcripts have diurnally regulated expression patterns in the mouse prefrontal cortex. Functional annotation of these genes will be important for the selection of candidate genes for behavioural mutants in the mouse and for genetic studies of disorders associated with anomalies in the sleep:wake cycle and circadian rhythms.
Publication Title
Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex.
Sample Metadata Fields
No sample metadata fields
View Samples