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Danio rerio
20 Downloadable Samples
IlluminaGenomeAnalyzerIIx
Description
This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA-seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- IlluminaGenomeAnalyzerIIx
Description
Transcriptome of human HL-60 and HEK-293 cells depending on culture cell density
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7.
Publication Title
Gene expression signature in organized and growth-arrested mammary acini predicts good outcome in breast cancer.
Sample Metadata Fields
Sex, Specimen part, Cell line, Time
View Samples- Mus musculus
- 29 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
The innate immune response is primarily mediated by the Toll-like receptors functioning through the Myd88-dependent and TRIF-dependent pathways. Despite being widely studied, it is not yet completely understood and systems-level analyses have been lacking. In this study, we identified a high-probability network of genes activated during the innate immune response using a novel approach to analyze time course gene expression profiles of activated immune cells in combination with a large gene regulatory and protein-protein interaction network. We classified the immune response into three consecutive time-dependent stages and identified the most probable paths between genes showing a significant change in expression at each stage. The resultant network contained several novel and known regulators of the innate immune response, many of which did not show any observable change in expression at the sampled time points. The response network shows the dominance of genes from specific functional classes during different stages of the immune response. It also suggests a role for the protein phosphatase 2a catalytic subunit a in the regulation of the immunoproteasome during the late phase of the response. In order to clarify the differences between the Myd88-dependent and TRIF-dependent pathways in the innate immune response, time course gene expression profiles from Myd88-knockout and TRIF-knockout dendritic cells were analyzed. Their response networks suggest the dominance of the MyD88 dependent pathway in the innate immune response, and an association of the circadian regulators and immunoproteasomal degradation with the TRIF-dependent pathway. The response network presented here provides the most probable associations between genes expressed in the early and the late phases of the immune response, while taking into account the intermediate regulators. We propose that the method described here can also be used in the identification of time-dependent gene subnetworks in other biological systems.
Publication Title
Discovery of Intermediary Genes between Pathways Using Sparse Regression.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
we performed genome-wide screening using SW480 cells with Gankyrin knockdown on an Affymetrix gene expression array to identify the transcriptional targets of Gankyrin
Publication Title
Gankyrin activates IL-8 to promote hepatic metastasis of colorectal cancer.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Caenorhabditis elegans
- 82 Downloadable Samples
- NextSeq 500
Description
We have used FACS to isolate fluorescent cells at multiple time points from synchronized embryos containing early and highly specific tissue/lineage markers. We then carried out RNA-seq, and observe dramatic differences in gene expression levels both between cell-types, and over time within the same population. Furthermore, we observe differential transcript usage between cell-types and over time, including differential promoter and differential exon usage that leads to additional differences between cell types.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples
SRP000931- Homo sapiens
- 14 Downloadable Samples
- IlluminaGenomeAnalyzerII
Description
Paired end sequencing of cDNA isolated from individual melanoma samples via the Illumina sequencing platform to identify genetic aberrations that may play a role in melanoma genesis.
Publication Title
Integrative analysis of the melanoma transcriptome.
Sample Metadata Fields
No sample metadata fields
View Samples- Escherichia coli
- 9 Downloadable Samples
- Illumina Genome Analyzer II
Description
The goal was to establish a robust and scalable RNA-seq process applicable to cultured bacteria as well as to complex community transcriptomes. To this end, we evaluated rRNA depletion methods and chose a protocol that eliminates rRNA reads efficiently and robustly, and largely irrespective of the quality of the RNA input sample.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Cell line
View Samples SRP052182- Anopheles gambiae
- 7 Downloadable Samples
- Illumina HiSeq 2000
Description
Transcriptome sequencing of arthropod cell lines
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples SRP052081- Anopheles gambiae
- 7 Downloadable Samples
- Illumina HiSeq 2000
Description
Transcriptome sequencing of arthropod cell lines
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples