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Mus musculus
4 Downloadable Samples
Illumina Genome Analyzer IIx
Description
By using a strand-specific RNA sequencing approach on growing C2C12 myoblasts and differentiated myotubes (day1, day3 and day5) we identified new murine lncRNAs which expression is dynamically ordered during in vitro differentiation. In order to do that, total RNA from myoblasts/myotubes was isolated with the RNeasy Plus mini kit (Qiagen) according to manufacturer’s instructions and quantified by Nanodrop (Thermo Scientific). RNA-seq libraries were prepared from 200 nanogramms of total RNA using TruSeq™ stranded mRNA Sample Prep Kit (Illumina) and following manufacturer’s instructions. Hence, the transcriptome measurements shown on these tracks were performed on polyA+ selected RNA with the specification of the coding strand. DNA libraries were quantified with KAPA reagent (KAPA SYBR® FAST Universal qPCR Kit, Illumina) and inspected for quality on 2100 Bioanalyzer (Agilent). Multiplexed libraries (10pM) were loaded on the cBot flowcell (TruSeq PE Cluster Kit v2 - cBot–GA) and then sequenced on the GAII (Illumina Inc.) as paired-end 2x86 base reads according to Illumina’s instructions.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 22 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Expression data of BL2 Burkitt Lymphoma cell line (controls and samples treated with different B cell specific stimuli)
Publication Title
Global gene expression changes of in vitro stimulated human transformed germinal centre B cells as surrogate for oncogenic pathway activation in individual aggressive B cell lymphomas.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Cell line
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GSE42637- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Recently global gene expression profiling of patients samples lead to a molecular definition of Burkitt Lymphoma (BL) with lymphocyte enhancer-binding factor 1 (LEF1) as a signature gene. Here we report the discovery of nucleic LEF1 in a very high proportion of BL cases (15/18) and LEF1 target genes. Germinal center B cells were devoid of detectable nuclear LEF1 expression as mantle cell lymphoma (0/5), marginal zone lymphoma (0/6), follicular lymphoma (0/12) or diffuse large B cell lymphoma (DLBCL) (1/31). Using whole genome gene expression profiling after transient knockdown of LEF1 in BL cell lines, new LEF1 target genes were identified. The joint expression of these genes in primary BL samples shows that LEF1 is not only expressed aberrantly in BL but also transcriptionally active. Our study identified aberrantly expressed LEF1 and its target genes suggesting an important functional role in BLs.
Publication Title
Aberrant lymphocyte enhancer-binding factor 1 expression is characteristic for sporadic Burkitt's lymphoma.
Alternate Accession IDs
Sample Metadata Fields
Cell line
View Samples- Danio rerio
- 6 Downloadable Samples
- Illumina HiSeq 3000
Description
The zebrafish has become a valuable model for examining ocular lens development, physiology and disease. The zebrafish cloche mutant, first described for its loss of hematopoiesis, also shows reduced eye and lens size, interruption in lens cell differentiation and a cataract likely caused by abnormal protein aggregation. To facilitate the use of the cloche mutant for studies on cataract development and prevention we characterized variation in the lens phenotype, quantified changes in gene expression by qRT-PCR and RNA-Seq and compared the ability of two promoters to drive expression of introduced proteins into the cloche lens. We found that the severity of cloche embryo lens cataract varied, while the decrease in lens diameter and retention of nuclei in differentiating lens fiber cells was constant. We found very low expression of both aB-crystallin genes (cryaba and cryabb) at 4 days post fertilization (dpf) by both qRT-PCR and RNA-Seq in cloche, cloche sibling and wildtype embryos and no significant difference in aA-crystallin (cryaa) expression. RNA-Seq analysis of 4 dpf embryos identified transcripts from 25,281 genes, with 1,329 showing statistically significantly different expression between cloche and wildtype samples. Downregulation of eight lens ß- and ?M-crystallin genes and 22 retinal related genes may reflect a general reduction in eye development and growth. Six stress response genes were upregulated. We did not find misregulation of any known components of lens development gene regulatory networks. These results suggest that the cloche lens cataract is not caused by loss of aA-crystallin or changes to lens gene regulatory networks. Instead, we propose that the cataract results from general physiological stress related to loss of hematopoiesis. Our finding that the zebrafish aA-crystallin promoter drove strong GFP expression in the cloche lens demonstrates its use as a tool for examining the effects of introduced proteins on lens crystallin aggregation and cataract prevention.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples SRP090377- Gallus gallus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
Characterization of the Gallus gallus thrombocyte transcriptome under control and LPS stimulated conditions
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment
View Samples- Arabidopsis thaliana
- 9 Downloadable Samples
- Illumina HiSeq 2500
Description
Transcriptomic data of Arabidopsis seedlings (Col-0 and cerk1-2 mutant) treated with a 1,3-b-glucan hexasaccharide
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Age, Specimen part
View Samples- Danio rerio
- 17 Downloadable Samples
- Affymetrix Zebrafish Genome Array (zebrafish)
Description
microRNAs play crucial roles in the early development of an organism. However the regulation of transcription through the action of microRNAs during the initial embyonic development has not been studied.
Publication Title
miR-34 is maternally inherited in Drosophila melanogaster and Danio rerio.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The proinflammatory cytokine, TNFalpha is critical in maintaining liver homeostasis since it is a major determiner of hepatocyte life and death. Considering this, gene transcription profiling was examined in control and TNFalpha treated HepG2 cells. Results indicated that TNFalpha could significantly alter the expression of a significant number of genes; most of them were functionally distributed among molecular functions like catalytic activity, binding, molecular transducer activity, transporter activity, translation and transcription regulator activities or enzyme regulator activity. Also, within genes up-regulated by TNFalpha, several GO terms related to lipid and fat metabolism were significantly overrepresented indicating global dysregulation of fat metabolism within the hepatocyte and those within the down-regulated dataset included genes involved in immunoglobulin receptor activity and IgE binding thereby indicating a compromise in immune defense mechanism(s) apart from those involved the DNA binding and protein binding categories. The interacting network of lipid metabolism, small molecule biochemistry was derived to be significantly affected that correlated well with the top canonical pathway of biosynthesis of steroids and molecular and cellular function of lipid metabolism. All these indicate TNFalpha to be significantly altering the transcriptome profiling within HepG2 cells with genes involved in lipid and steroid metabolism being the most favoured. This study suitably addresses the genes that determine TNFalpha mediated alterations within the hepatocyte mainly the phenotypes of hepatic steatosis and fatty liver that are associated with several hepatic pathological states.
Publication Title
Gene expression profiling and network analysis reveals lipid and steroid metabolism to be the most favored by TNFalpha in HepG2 cells.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Bos indicus
- 4 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Hypobaric Hypoxia Induced Transcriptional profiling of Bovine (Bos indicus)
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage, Subject
View Samples SRP044781- Danio rerio
- 12 Downloadable Samples
- IlluminaHiSeq2000
Description
Transcriptome analysis of 12 zebrafish tissues
Publication Title
Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database.
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
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