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Homo sapiens
4 Downloadable Samples
IlluminaHiSeq2000
Description
Several studies have shown that long non-coding RNAs (lncRNAs) may play anessential role in Epithelial-mesenchymal transition (EMT), which is an important step in tumor metastasis, however, little is known about the global change of lncRNA transcriptome during EMT. To investigate how lncRNA transcriptome alteration contributes to EMT progression regulation, we performed a whole-transcriptome strand-specific RNA deep sequencing of MCF10A induced EMT by TGF-ß. Deep sequencing results showed that the long RNA (>=200-nt) transcriptome of MCF10A was undergone a global changed in EMT, and this alteration was determined as early as 8h after being induced using TGF-ß. 8703 linear novel genes with ambiguous protein-coding potential were identified, 512 of which were further determined to be novel lncRNAs. After analyzing the expression of 5473 known and novel lncRNAs, as well as 2208 known and novel circRNAs during EMT, we found a large numbers of lncRNAs might be involved in the regulation of EMT. Intriguingly, we identified 216 gene clusters constituted by lncRNAs and/ornovel genes in “gene desert” region. The expressions of all genes in these clusters were changed concurrently during EMT, indicating that these clusters might play important role in EMT. Our study reveals a global reprogramming of lncRNAs transcriptome in EMT and provides clues to the study of the molecular mechanism of EMT.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples
SRP076058- Zea mays
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
This study presented the differentially expressed genes post maize infected by Rhizoctonia solani.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part
View Samples SRP094817- Zea mays
- 2 Downloadable Samples
- Illumina HiSeq 3000
Description
Transposons in maize may be involved in the formation of circRNAs and further modulate phenotypic variation. To test our hypothesis, we performed circRNA-Seq(RNase R treated) on B73 seedlings(third leaves of V3 stage), and uncovered 1,572 high-confidence maize circRNAs, which show distinct genomic features compared to linear transcripts. Comprehensive analyses showed that LINE1-like elements (LLE) and their reverse complementary pairs (RCPLLEs) are significantly enriched in the flanking regions of circRNAs.
Publication Title
Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize.
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part, Disease
View Samples- Gallus gallus
- 8 Downloadable Samples
- Illumina Genome Analyzer II
Description
The transcriptome sequencing reveals the divergence of the genetic mechanism of reproductive traits in two Chinese native breeds. XH chicken was meat-type breed with low reproduction ability, with a 70~80% incidence of broodiness in population, with the duration of 15~30 d brooding, and with a production of 60~90 eggs per year. BEH chicken was layer-type breed with high reproduction ability, with a 10%~15% incidence of broodiness in population, with the duration of 7~20 d brooding, and with a production of 180 eggs per year.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part
View Samples- Saccharomyces cerevisiae
- 34 Downloadable Samples
- Illumina HiSeq 2500
Description
As an ancient winning strategy of microorganisms, glucose repression mechanism has become specialized to perfection in Saccharomyces cerevisiae. The galactose (GAL) metabolism network is stringently regulated by glucose repression in yeast and has been a classic system for studying gene regulation. We show here that the population of S. cerevisiae living in fermented milks has autonomously reinstated an ancient version of the structural GAL genes through introgression. The introgressed GAL network has completely abolished the glucose repression and conversed from a strictly inducible to a constitutive system through coordinative polygenic changes in the regulatory components of the network, including transitions in the upstream repressing sequence site of GAL4 that impair Mig1p-mediated repression and loss of function of the inducer Gal3p and the repressor Gal80p. In addition, the introgressed GAL2 gene has been duplicated while the native HXT6 and HXT7 genes have been inactivated, resulting in galactose-over-glucose preference and elevated galactose utilization rate. Relying on the reverse evolution of the GAL network, the non-lactose fermenting yeast has become a dominant species co-existing with other lactose fermenting microorganisms in fermented milks. Our results also provide new clues for developing yeast strains devoid of barriers to co-utilization of different sugars.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples SRP165652- Homo sapiens
- 3 Downloadable Samples
- Ion Torrent S5
Description
This study presented the preliminary mechanistic studies of teniposide analogs for toxicity reduction
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
The differential expression of gene in bone marrow derived macrophages from Ckip-1 KO mice and WT mice.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Homo sapiens
- 16 Downloadable Samples
Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
Human cytomegalovirus (HCMV) induces pro-inflammatory monocytes following infection and we have evidence that EGFR is a key mediator in this early activation. To begin to address how this signalling pathway is responsible for the rapid activation of infected monocytes, we examined the role this pathway played in the transcriptome of infected monocytes. Global transcriptional profiling using cDNA microarrays revealed a significant number of genes, including inflammatory genes, were regulated in a EGFR-dependent manner, identifying this pathway as a key cellular control point in the conversion of monocytes to an activated pro-inflammatory state following HCMV infection.
Publication Title
Activation of EGFR on monocytes is required for human cytomegalovirus entry and mediates cellular motility.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
Human cytomegalovirus induces a pro-inflammatory monocyte following infection and we have evidence that NF-B and phosphatidylinositol 3-kinase [PI(3)K] are key mediators in this early activation. To begin to address how these signalling pathways are responsible for the rapid activation of infected monocytes, we examined the role these pathways played in the transcriptome of infected monocytes. Global transcriptional profiling using cDNA microarrays revealed a significant number of genes, including inflammatory genes, were regulated in a NF-B- and/or PI(3)K-dependent manner, identifying these pathways as key cellular control points in the conversion of monocytes to an activated pro-inflammatory state following HCMV infection.
Publication Title
Transcriptome analysis of NF-kappaB- and phosphatidylinositol 3-kinase-regulated genes in human cytomegalovirus-infected monocytes.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
Human cytomegalovirus induces a pro-inflammatory monocyte following infection. To begin to address how HCMV induces these rapid changes in infected monocytes, we examined the transcriptome of infected monocytes. Global transcriptional profiling using cDNA microarrays revealed a significant number of pro-inflammatory genes were upregulated within 4 hours post infection.
Publication Title
Transcriptome analysis reveals human cytomegalovirus reprograms monocyte differentiation toward an M1 macrophage.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
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