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GSE87330
Rattus norvegicus
16 Downloadable Samples
Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Inflammation is a key component of pathological angiogenesis. Here we monitor gene expression profiles of the pre-sprouting phase of corneal angiogenesis in the rat model, as influenced by topically applied treatments.
Publication Title
Genome-wide expression differences in anti-Vegf and dexamethasone treatment of inflammatory angiogenesis in the rat cornea.
Sample Metadata Fields
Sex, Specimen part
View Samples- Rattus norvegicus
- 15 Downloadable Samples
- Affymetrix Rat Gene 2.0 ST Array (ragene20st)
Description
Inflammation is a key component of pathological angiogenesis. Here we induce cornea neovascularisation using sutures placed into the cornea, and sutures are removed to induce a regression phase.
Publication Title
Factors regulating capillary remodeling in a reversible model of inflammatory corneal angiogenesis.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 1 Downloadable Sample
Illumina Genome Analyzer II
Description
The hair of all mammals consists of terminally differentiated cells that undergo a specialized form of apoptosis called cornification. While DNA is destroyed during cornification, the extent to which RNA is lost is unknown. Here we find that multiple types of RNA are incompletely degraded after hair shaft formation in both mouse and human. Notably, mRNAs and short regulatory microRNAs (miRNAs) are stable in the hair as far as 10 cm from the scalp. To better characterize the post-apoptotic RNAs that escape degradation in the hair, we performed sequencing (RNA-seq) on RNA isolated from hair shafts pooled from several individuals. This hair shaft RNA library, which encompasses different hair types, genders, and populations, revealed 7,193 mRNAs, 449 miRNAs and thousands of unannotated transcripts that remain in the post-apoptotic hair. A comparison of the hair shaft RNA library to that of viable keratinocytes revealed surprisingly similar patterns of gene coverage and indicates that degradation of RNA is highly inefficient during apoptosis of hair lineages. The generation of a hair shaft RNA library could be used as months of accumulated transcriptional history useful for retrospective detection of disease, drug response and environmental exposure.
Publication Title
The post-apoptotic fate of RNAs identified through high-throughput sequencing of human hair.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
Cultured epidermal keratinocyte controls used for IFNg, TNFa and IL1 treatment.
Publication Title
Unique keratinocyte-specific effects of interferon-gamma that protect skin from viruses, identified using transcriptional profiling.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
The heat-shock stress response was studied at the level of exons using Affymetrix Exon-array profiling for both sense and anti-sense transcripts. Sense transcript profiling was done as per the protocol of Affymetrix Exon 1.0 ST array and anti-sense transcript array profiling was done using a modified protocol (Xijin Ge et al., BMC Genomics. 2008 Jan 22;9:27).
Publication Title
Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism.
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip
Description
The repertoire of transcripts that are differentially regulated in response to Heat-shock were studied using Illumina WG-6 v2.0 BeadChip.
Publication Title
Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism.
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Escherichia coli
- 12 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Over expression of recombinant proteins is known to cause a metabolic burden to the host cells which leads to down regulation of both growth rates and protein expression. Most studies in this regard have been conducted in low density shake flask cultures which does not capture the essential features of an industrial scale bioprocess. In the present work we studied the transcriptomic profiling at different specific growth rates while expressing the recombinant human interferon beta in fed batch cultures with complex media. These conditions mimicked the industrial fermentations for recombinant proteins.
Publication Title
Comparative transcriptomic profile analysis of fed-batch cultures expressing different recombinant proteins in Escherichia coli.
Sample Metadata Fields
No sample metadata fields
View Samples- Escherichia coli
- 12 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
The objective of this work was to design an improved host platform for recombinant protein expression in E. coli. The approach involves first to create a library of the E. coli genomic DNA in different expression vectors and screen for probable transcripts which may lead to slow growing colonies and also simultaneously over-expression of recombinant proteins. To observe its effect on host performance, these genes were knocked out from the E. coli genome. A CG2 strain has been created by knocking in vhb gene gene downstream of the acetate promoter and knocking down ribB gene in DH5 and transformed with Recombinant GFP cloned in pBAD33.
Publication Title
Comparative transcriptomic profile analysis of fed-batch cultures expressing different recombinant proteins in Escherichia coli.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Identifying PDEF regulated genes may shed light on the mechanism by which PDEF may induce breast cancer progression. To that purpose, we have used the MCF-7 human breast tumor cell line model to identify PDEF induced genes. Briefly, PDEF expression was down regulated by shRNA in MCF-7 cells and RNA probes from PDEF-down regulated and control MCF-7 cells were used to screen the Affymetrics HG-U133A Gene Chips. This analysis found 62 genes that were induced 2-fold or higher by PDEF. Further analysis of 3 of these genes namely S100A7, CEACAM6 and B7-H4 in primary breast tumors showed CEACAM6 as a frequently elevated and co-exressed gene with PDEF in these tumors.
Publication Title
Prostate derived Ets transcription factor and Carcinoembryonic antigen related cell adhesion molecule 6 constitute a highly active oncogenic axis in breast cancer.
Sample Metadata Fields
Cell line
View Samples- Escherichia coli
- 3 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Strong production of recombinant proteins interfere with cellular processes in many ways. The extent of the bacterial stress response is determined by the specific properties of the recombinant protein, and by the rates of transcription and translation. The consideration of bacterial stress and starvation responses is of crucial importance for the successful establishment of an industrial large scale bioprocess. Stress genes can be used as marker genes in order to monitor the fitness of industrial bacterial hosts during fermentation processes. For this purpose, here in our study we have applied transcriptome analysis for the description of general and specific stress and starvation responses of Escherichia coli. Producing recombinant protein (Xylanase) in high cell density fed batch culture.
Publication Title
Comparative transcriptomic profile analysis of fed-batch cultures expressing different recombinant proteins in Escherichia coli.
Sample Metadata Fields
Treatment
View Samples