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SRP113512
Mus musculus
12 Downloadable Samples
NextSeq 500
Description
The transcriptomes of differentiated and undifferentiated E14 (male), Pgk12.1 (female; WT) and Pgk12.1 with a KO of Rlim (RlimKO) were elucidated and examined for differences in X chromosome inactivation. No significant differences between wt and RlimKO with respect to Xist expression and global X-silencing was detected. Results confirm that Rlim is not required for XCI in female ESCs. Overall design: Transciptomes of female WT (Pgk12.1) and female RlimKO ESCs were compared to those of male ESCs (E14). State of XCI in undifferentiated and differentiated ESCs was determined by comparing expression of Xist and expression of X-linked genes female versus male.
Publication Title
Rlim-Dependent and -Independent Pathways for X Chromosome Inactivation in Female ESCs.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
In the past three years the role of inflammatory cytokines and chemokines in tumour promotion and progression has been intensively studied. The chemokine receptor CXCR4 and its ligand CXCL12 are commonly expressed in malignant cells from primary tumours, metastases and also in malignant cell lines. To investigate the biological significance of this receptor/ligand pair, we knocked-down CXCR4 expression in ovarian cancer cell line IGROV-1 using shRNA, and established stable cell lines.
Publication Title
A dynamic inflammatory cytokine network in the human ovarian cancer microenvironment.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We present evidence for an autocrine cytokine network in human ovarian cancer that has paracrine actions on the tumour microenvironment. In experiments using bioinformatics analysis of large gene expression array datasets and ovarian cancer biopsies, we found that the inflammatory cytokines TNF- and IL-6, the chemokine receptor CXCR4 and its ligand CXCL12, are co-regulated in malignant cells. We named this co-regulation the TNF network.
Publication Title
A dynamic inflammatory cytokine network in the human ovarian cancer microenvironment.
Sample Metadata Fields
Specimen part
View Samples- Oryza sativa
- 35 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
affy_rice_2011_03 - affy_compartimentation_rice_albumen_embryon - During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination. -We germinate rice seeds of the first sequenced rice cultivar i.e. Nipponbare during 0, 4, 8, 12, 16 and 24h of imbibition in sterile distilled water. Germination occurs under constant air bubbling, in the dark at 30C. These rice seeds are then manually dissected into embryo and endosperm fractions. -The embryo-derived samples are abbreviated in E while the endosperm samples are abbreviated A. The germination time-point is indicated after the letter (e.g. E8 for embryo samples harvested after 8 hours of germination). Finally, the biological repetition number is indicated before the letter and the time digit (e.g. 1-E8 for an embryo sample from the first repetition at 8 hours of imbibition).
Publication Title
Compartmentation and dynamics of flavone metabolism in dry and germinated rice seeds.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 31 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Aging is often associated with cognitive decline, but many elderly individuals maintain a high level of function throughout life. Here we studied outbred rats, which also exhibit individual differences across a spectrum of outcomes that includes both preserved and impaired spatial memory. Previous work in this model identified the CA3 subfield of the hippocampus as a region critically affected by age and integral to differing cognitive outcomes. Earlier microarray profiling revealed distinct gene expression profiles in the CA3 region, under basal conditions, for aged rats with intact memory and those with impairment. Because prominent age-related deficits within the CA3 occur during neural encoding of new information, here we used microarray analysis to gain a broad perspective of the aged CA3 transcriptome under activated conditions. Behaviorally induced CA3 expression profiles differentiated aged rats with intact memory from those with impaired memory. In the activated profile, we observed substantial numbers of genes (greater than 1000) exhibiting increased expression in aged unimpaired rats relative to aged impaired, including many involved in synaptic plasticity and memory mechanisms. This unimpaired aged profile also overlapped significantly with a learning induced gene profile previously acquired in young adults. Alongside the increased transcripts common to both young learning and aged rats with preserved memory, many transcripts behaviorally-activated in the current study had previously been identified as repressed in the aged unimpaired phenotype in basal expression. A further distinct feature of the activated profile of aged rats with intact memory is the increased expression of an ensemble of genes involved in inhibitory synapse function, which could control the phenotype of neural hyperexcitability found in the CA3 region of aged impaired rats. These data support the conclusion that aged subjects with preserved memory recruit adaptive mechanisms to retain tight control over excitability under both basal and activated conditions.
Publication Title
Behaviorally activated mRNA expression profiles produce signatures of learning and enhanced inhibition in aged rats with preserved memory.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The CMVpp65 protein contains 2 bipartite nuclear localization signals (NLS) at 415-438aa and 537-561aa near the carboxy terminus of CMVpp65 and a phosphate binding site related to kinase activity at lysine-436. A mutation of pp65 having K436N (CMVpp65mII) and further deletion of aa537-561 resulted in a novel protein (pp65mIINLSKO) that is kinase-less and has markedly reduced nuclear localization. The purpose of this report was to study the biologic characterization of this protein and its immunogenicity compared to native pp65.Using RNA microarray analysis, expression of the CMVpp65mIINLSKO had less effect on cell cycle pathways than did the native CMVpp65 and a greater effect on cell surface signalling pathways involving immune activity. It is concluded that the removal of the primary NLS motif from pp65 does not impair its immunogenicity and may actually be advantageous in the design of a vaccine.
Publication Title
Biologic and immunologic effects of knockout of human cytomegalovirus pp65 nuclear localization signal.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 40 Downloadable Samples
- IlluminaHiSeq2000
Description
The use of low quality RNA samples in whole-genome gene expression profiling remains controversial. It is unclear if transcript degradation in low quality RNA samples occurs uniformly, in which case the effects of degradation can be normalized, or whether different transcripts are degraded at different rates, potentially biasing measurements of expression levels. This concern has rendered the use of low quality RNA samples in whole-genome expression profiling problematic. Yet, low quality samples are at times the sole means of addressing specific questions – e.g., samples collected in the course of fieldwork.
Publication Title
RNA-seq: impact of RNA degradation on transcript quantification.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 40 Downloadable Samples
- Affymetrix Rat Expression 230A Array (rae230a)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Rapid encoding of new information alters the profile of plasticity-related mRNA transcripts in the hippocampal CA3 region.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 3 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Patterns of histone H3 lysine 27 monomethylation and erythroid cell type-specific gene expression.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Rattus norvegicus
- 14 Downloadable Samples
- Affymetrix Rat Expression 230A Array (rae230a)
Description
A theoretical framework for the function of the medial temporal lobe system in memory defines differential contributions of the hippocampal subregions with regard to pattern recognition retrieval processes and encoding of new information. To investigate molecular programs of relevance, we designed a spatial learning protocol to engage a pattern separation function to encode new information. After background training, two groups of animals experienced the same new training in a novel environment, however only one group was provided spatial information and demonstrated spatial memory in a retention test. Global transcriptional analysis of the microdissected subregions of the hippocampus exposed a CA3 pattern that was sufficient to clearly segregate spatial learning animals from control. Individual gene and functional group analysis anchored these results to previous work in neural plasticity. From a multitude of expression changes, increases in camk2a, rasgrp1 and nlgn1 were confirmed by in situ hybridization. Furthermore, siRNA inhibition of nlgn1 within the CA3 subregion impaired spatial memory performance, pointing to mechanisms of synaptic remodeling as a basis for rapid encoding of new information in long-term memory.
Publication Title
Rapid encoding of new information alters the profile of plasticity-related mRNA transcripts in the hippocampal CA3 region.
Sample Metadata Fields
No sample metadata fields
View Samples