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SRP055912
Mus musculus
4 Downloadable Samples
Illumina HiSeq 2000
Description
Genes are up and down regualted in DRG and spinal dorsal cord after peripheral nerve injury Overall design: WT male adult with sciatic and femoral nerve transection 7 days, RNA was purified from ipilateral or contralateral L4-L6 DRGs or lumbar spinal dorsal cords
Publication Title
Injured sensory neuron-derived CSF1 induces microglial proliferation and DAP12-dependent pain.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 176 Downloadable Samples
- Illumina HiSeq 2500
Description
We report the application of low cell number sequencing of identifiable Drosophila melanogaster neurons following behavior. We demonstate the feasibility of identifying the transcriptome of 5 Mushroom Body output Neurons and 2 classes of Kenyon Cells. We find these neurons display a diverse repertoire of receptors and signaling transcripts. This information alone seems to be enough to identify each class of neurons in the study. In additional we show that aversive long-term memory induces changes in gene transcript levels in a subset of these neurons. This study provides a framework for identifying neuronal classes in Drosophila melanogaster and gaining insight into the interplay between behavior and gene regulation. Overall design: 5 Mushroom Body output neurons and 2 classes of kenyon cells are used to look at general gene expression and changes following aversive long term memory. Paired control and trained animals were used and a minimum of 4 pairs up to 6 pairs. Animals were of the same background (w1118). Animals were aged and parental matched. Cells were harvested at the same chronological time for the animals across all experiments. All animals were exposed to 1 minute of each odor and 1 minute of a series of 12 5second 60V shocks. This was considered one block and then the animals had spaced training of each block so there was a 10 minute break between 8 blocks of training. Trained animals had an odor paired with a shock, control animals received the shock then the odor stimulus. All cells were harvested usign a patch pipet from living animals on an electrophysiology rig within a half hour of the end of training. Cells were amplified using the Clontech SMARTer Ultra Low Input RNA version 2 High Volume kit. 2 Brain samples were also collected and 3-4 whole fly samples for each genotype were collected to account for background differences across flies.
Publication Title
Cell-Type-Specific Transcriptome Analysis in the Drosophila Mushroom Body Reveals Memory-Related Changes in Gene Expression.
Sample Metadata Fields
Subject
View Samples- Rattus norvegicus
- 12 Downloadable Samples
Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
In this study we showed that rat XEN cells grown in the presence of a GSK3 inhibitor exhibited enhanced formation of cell contacts and decreased motility. In contrast, treatment with forskolin induced the PE formation and epithelial-mesenchymal transition (EMT) in rat XEN cells. Using microarray and real-time PCR assays, we found that VE versus PE formation of rat XEN cells was correlated with change in expression levels of VE or PE marker genes. Similar to forskolin, EMT was prompted upon treatment of rat XEN cells with recombinant parathyroid hormone related peptide (PTHRP), an activator of the cAMP pathway in vivo. Taken together, our data suggest that rat XEN cells are PrE-like cells. The activation of Wnt pathway in rat XEN cells leads to the acquisition of VE characteristics, whereas the activation of the PTHRP/cAMP pathway leads to EMT and the formation of PE.
Publication Title
Activation of the PTHRP/adenylate cyclase pathway promotes differentiation of rat XEN cells into parietal endoderm, whereas Wnt/β-catenin signaling promotes differentiation into visceral endoderm.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Salt stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a novel calcium-binding protein and used the Affymetrix whole-genome arrays to define downstream targets of this important protein.
Publication Title
A nuclear calcium-sensing pathway is critical for gene regulation and salt stress tolerance in Arabidopsis.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
BMP3 stimulates mesenchymal stem cell proliferation, but the down-stream molecular targets of BMP3 are unknown
Publication Title
Wisp1 mediates Bmp3-stimulated mesenchymal stem cell proliferation.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Salt stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified an essential regulator of salt stress RSA3 and used the Affymetrix whole-genome arrays to study the effect of rsa3-1 mutation on global gene expression under salt stress. A set of genes differentially expressed in rsa3-1 under salt stress are identified.
Publication Title
A bi-functional xyloglucan galactosyltransferase is an indispensable salt stress tolerance determinant in Arabidopsis.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Rattus norvegicus
- 9 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Degenerative retinal diseases like age-related macular degeneration (AMD) are the leading cause of blindness. Cell transplantation showed promising therapeutic effect for such diseases, and retinal progenitor cell (RPC) derived from embryonic stem cell (ESC) is one of the sources of such donor cells. Here, we established two protocols through which two types of rat ESC-derived RPCs (rESC-RPCs) were obtained and both contained some NPCs and committed retina lineage cells. As P-RPCs have been reported to successfully integrate into host eyes, we sough to identify differentially expressed genes among P-RPCs, rESC-RPC1s and rESC-RPC2s through genome-wide transcript profiling. rESC-RPC2 can integrate into the host retina, form synaptic connections and restore visual function after transplanted into the degenerative retinal disease model RCS rat.
Publication Title
Transplantation of rat embryonic stem cell-derived retinal progenitor cells preserves the retinal structure and function in rat retinal degeneration.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- IlluminaGenomeAnalyzerIIx
Description
We profiled the dynamic, comprehensive transcriptome during human erythroid differentiation in vitro. The erythroid cells at day 4, 8, 11 and 14 differentiation stages were harvested and sequenced by Illumia 72 bp paired-end sequencing format, respectively. Overall design: Expression profiling of erythroid cells on differentiation days 4, 8, 11 and 14 and performed mRNA-seq on two biological replicates at each stage.
Publication Title
Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified an essential regulator of cold-responsive genes and used the Affymetrix whole-genome arrays to define downstream targets of this important protein.
Publication Title
A DEAD box RNA helicase is critical for pre-mRNA splicing, cold-responsive gene regulation, and cold tolerance in Arabidopsis.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Tumor formation constitutes a major obstacle to the clinical application of embryonic stem cells (ESCs). As P-RPCs could successfully integrate into host eyes without development of teratomas or NOG, we sought to identify differentially expressed genes between P-RPCs and ESC-RPCs through genome-wide transcript profiling. Inhibition of Wnt signaling by DKK1 promotes the commitment of ESC-RPCs to more mature retinal cells and reduces the occurrence of NOG to 3%. DKK1-treated ESC-RPCs efficiently integrate to the host retina, form synaptic connections and restore visual function.
Publication Title
WNT signaling determines tumorigenicity and function of ESC-derived retinal progenitors.
Sample Metadata Fields
Specimen part, Treatment
View Samples