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Caenorhabditis elegans
43 Downloadable Samples
Illumina HiSeq 1500, Illumina Genome Analyzer IIx
Description
C. elegans totalRNA profiles of worms treated with RNAi for different Integrator complex genes or L4440 (Control). Worms were grown at 15ºC and samples were taken six days after silencing Overall design: C. elegans totalRNA profiles of worms treated with RNAi for different Integrator complex genes or L4440 (Control). Three replicates per sample. Deep sequencing in Illumina HiSeq1500.
Publication Title
Disruption of the Caenorhabditis elegans Integrator complex triggers a non-conventional transcriptional mechanism beyond snRNA genes.
Sample Metadata Fields
Subject
View Samples- Caenorhabditis elegans
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
The transcriptomes of model organisms have been defined under specific laboratory growth conditions. The standard protocol for Caenorhabditis elegans growth and maintenance is 20ºC on an Escherichia coli diet. Temperatures ranging from 15ºC to 25ºC or feeding with other species of bacteria are considered physiological lab conditions, but the effect of these conditions on the worm transcriptome have not been well characterized. Here, we compare the global patterns of gene expression for the reference Caenorhabditis elegans strain (N2) grown at 15oC, 20oC, and 25oC on two different diets, Escherichia coli and Bacillus subtilis. When C. elegans were fed E. coli and the growth temperature was increased, we observed an enhancement of defense response pathways and down-regulation of genes associated with metabolic functions. However, when C. elegans were fed B. subtilis and the growth temperature was increased, the nematodes exhibited a decrease in defense response pathways and an enhancement of expression of genes associated with metabolic functions. Our results show that C. elegans undergo significant metabolic and defense response changes when the maintenance temperature fluctuates within the physiologically accepted experimental range and that the degree of pathogenicity of the bacterial diet can further alter the worm transcriptome. Overall design: C. elegans mRNA profiles at different temperatures and feeding in six samples, three replicates per sample. Deep sequencing in Illumina HiSeq2500.
Publication Title
Effect of the diet type and temperature on the <i>C. elegans</i> transcriptome.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 7 Downloadable Samples
- Illumina HiSeq 2000
Description
Gene expression analysis of wid type and Lmnb1-/- epicardial cells Overall design: Total RNA was isolated from wild type and Lmnb1-/- epicardial explants and subject ot sequencing on the Illumina platform
Publication Title
Lamin-B1 contributes to the proper timing of epicardial cell migration and function during embryonic heart development.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 20 Downloadable Samples
- IlluminaHiSeq2000
Description
We discovered that two mitotic regulators, BuGZ and Bub3, involved in splicing regulation during interphase Overall design: 8 samples from primary Human foreskin fibroblast cells (HFFs) , 12 samples from TOV21G cells. Control siRNA. BuGZ siRNA or Bub3 siRNA were transfected for 48 h before sample collection. Cells treated with pladienolide B served as positive controls. For each RNAi experiment, we had two biological replicates.
Publication Title
Splicing function of mitotic regulators links R-loop-mediated DNA damage to tumor cell killing.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 18 Downloadable Samples
- IlluminaHiSeq2000
Description
We report the transcriptional response of the zebrafish digestive organs to an acute high-fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis, storage, and dispersal of lipids. These key physiological responses to a high-fat meal all stem from the endoplasmic reticulum (ER), where lipids are formed and assigned to their fates. Overall design: A feeding time course was undertaken with 6.5-dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high-fat or low-fat food. 5% egg yolk emulsion (high-fat) feeds and 10% egg white (low-fat) feeds were prepared. At the appropriate time points, digestive organs (intestine, liver, pancreas) were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.
Publication Title
Endoplasmic Reticulum Lipid Flux Influences Enterocyte Nuclear Morphology and Lipid-dependent Transcriptional Responses.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using transcriptome profiling (RNA-seq) to evaluate the effects of EBV infection or (and) EBV BART6-3p mimics on the global transcriptome of the BJAB cells. Methods: BJAB cells were transfected with negative control mimics or BART6-3p mimics for 48 h and then infected with EBV virons for 2h. RNAs were extracted by Trizol and sequenced by Solexa high-throughput sequencing service (Oebiotech, Shanghai, China). Data were extracted and normalized according to the manufacturer's standard protocol. Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05. There are 408 mRNAs were up-regulated and 263 were down-regulated in “EBV infection” group cells comparing to “Mock” group cells. There are 385 mRNAs were up-regulated and 246 were down-regulated in “EBV infection + Bart6-3p mimics” group cells comparing to “EBV infection + negative control mimics” group cells. Conclusions: Our study describes the global transciptome changes of BJAB cells induced by EBV infection or (and) EBV 6-3p mimics. Overall design: BJAB cells mRNA profiles of “mock” (no infection, no treatment), “EBV infection”, “EBV infection + negative control mimics”, and “EBV infection + BART6-3p mimics” were generated by RNA sequecning, using Solexa high-throughput sequencing service (Oebiotech, Shanghai, China).
Publication Title
Epstein-Barr Virus miR-BART6-3p Inhibits the RIG-I Pathway.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
Lamins, the major components of the nuclear lamina, have diverse functions in many cellular processes. Despite broad expression, lamins have been implicated in cell type-specific roles in development, aging and disease by regulating gene expression. Yet, due to the lack of in depth lineage-specific functional studies, it remains unclear whether or how lamins regulate cell type-specific functions. Using targeted knockout of lamin B1 in the olfactory sensory neuron lineage, we show that lamin B1 is not required for early stages of olfactory sensory neuron differentiation but is needed for formation of mature neurons that properly respond to odor stimulation. Lamin B1 mutant cells exhibited decreased expression of genes involved in mature neuron function, increased expression of genes atypical of the olfactory lineage and clustered nuclear pore distribution. These results demonstrate that the universally expressed lamin B1 regulates cell type-specific gene expression and terminal differentiation. Overall design: Transcriptome profiles were generated from sorted regenerated olfactory epithelium cells lacking Lamin B1 (Lmnb1) and control (heterozygous cells). Each sample is collected from one mouse. Data are from two experimental groups (G1,G2), each containing a control and a mutant sample. Different groups differ in treatment, parents, age and sex. Within a group, treatment, sample preparation, sequencing, animal sex, age, and parents are the same.
Publication Title
Lamin B1 is required for mature neuron-specific gene expression during olfactory sensory neuron differentiation.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Homo sapiens
- 2 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Epstein-Barr virus (EBV) is highly successful virus infecting the majority of the human population worldwide. During the latent infection period, there are only a few of EBV-encoded proteins can be detected, whereas EBV-encoded non-coding RNAs are highly activated, especially microRNAs. Recent studies found that those BART microRNAs not only disturb EBV genes expression, but also interfere many host genes expression, thus modulating cellular proliferation and immune regulation. In the present study, we investigate the effect of EBV BART6-3p on gene expression profile of the human PBMCs.
Publication Title
Epstein-Barr Virus miR-BART6-3p Inhibits the RIG-I Pathway.
Sample Metadata Fields
No sample metadata fields
View Samples
GSE46708- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Gene expression were identified with or without CD24 gene silencing in Du145 cells.
Publication Title
Intracellular CD24 disrupts the ARF-NPM interaction and enables mutational and viral oncogene-mediated p53 inactivation.
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Glycine max
- 12 Downloadable Samples
- Affymetrix Soybean Genome Array (soybean)
Description
A soybean ortholog of the Arabidopsis MADS-domain transcription factor (called GmAGL15) enhanced somatic embryogenesis from immature cotyledon explants of soybean when expressed via the 35S promoter compared to non transgenic tissue (cultivar Jack). To better understand how this occurs an expression microarray experiment was performed.
Publication Title
Alterations in the transcriptome of soybean in response to enhanced somatic embryogenesis promoted by orthologs of Agamous-like15 and Agamous-like18.
Sample Metadata Fields
Specimen part, Time
View Samples