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SRP157873
Mus musculus
22 Downloadable Samples
Illumina HiSeq 2500
Description
The dual leucine zipper kinase (DLK) is a mitogen-activated kinase kinase kinase that can activate the downstream cJun N terminal kinase (JNK) pathway (ref). We have previously reported that DLK is a positive regulator of the retrograde injury signaling and axon regeneration that unfolds after sciatic nerve injury (ref). Since DLK is required for activities of injury-associated transcription factors such as cJun and STAT3, we hypothesized that DLK is also necessary for the transcriptional responses to peripheral nerve injury. In the current study, we identify DLK-dependent transcriptome in dorsal root ganglion (DRG) neurons using a sciatic nerve injury paradigm. The DEG analysis reveals that DLK regulates regeneration/injury-associated genes in both basal and injured conditions. By performing gene ontology analysis, we suggest functional annotations and the involved genes as regulatory components of the axonal regeneration program. Finally, our comparative analysis indicates that DLK is required for a specific retrograde signaling pathway that regulates a regeneration program shared between PNS and CNS models.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 14 Downloadable Samples
- NextSeq 500
Description
we have compared the injury-induced transcriptomic changes between the regenerating proximal segment and the degenerating distal segment of a transected nerve, at different post-injury time points
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Zea mays
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
This study analyzed the regulation of polyaspartic acid on the nitrate response of maize at transcriptional level.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part, Treatment
View Samples- Oryza sativa
- 35 Downloadable Samples
Affymetrix Rice Genome Array (rice)
Description
Abiotic stresses such as salinity are very important factors limiting rice growth and productivity around the world. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice responsive to salinity stress, try to elucidate the difference of genome-wide gene expression profiling of two contrasting rice genotypes in response to salt stress and to discover the salinity related genes and gene interaction and networks. Under salinity condition, the number of differentially expressed genes (DEGs) in 177-103 was more than that in IR64, and most of up-regulated DEGs in 177-103 are response to stress. But in IR64, most of up-regulated DEGs are transcription related genes. The DEGs under salinity showed very strong tissue specificity, the number of DEGs in leaf was more than that in root. A lot of genes differentially expressed by exogenous ABA treatment under salinity condition, such as Leaf senescence protein, 1-deoxy-D-xylulose 5-phosphate synthase 2 precursor and Protein of unknown function DUF26 were induced by ABA and contributed to salinity tolerance.
Publication Title
Complex molecular mechanisms underlying seedling salt tolerance in rice revealed by comparative transcriptome and metabolomic profiling.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 62 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Evaluation of pretreatment gene expression profiling features in elderly CLL patients; correlation with clinical outcome
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 25 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
We describe 9 CLL patients who underwent a spontaneous clinical regression. CD38 and ZAP-70 were negative in all cases. Immunoglobulin heavy chain variable region (IgVH) genes, mutated in all 7 evaluable patients, were restricted to the VH3 family in 6, with the usage of VH3-30 gene in 2. The light chain variable region genes were mutated in 6/8 cases, with the usage of V4-1 gene in 3. Microarray analysis of CLL cells revealed a distinctive genomic profile. The number of activated T lymphocytes expressing IFN-, TNF- and IL-4 was similar between CLL in spontaneous regression and healthy individuals.
Publication Title
Spontaneous regression of chronic lymphocytic leukemia: clinical and biologic features of 9 cases.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Since the role of cord blood (CB) regulatory T cells (Tregs) for the suppression of the allogeneic T-cell response is under investigation, we analyzed and compared the functional properties and gene expression profile of Tregs expanded from CB units or from the peripheral blood (PB) of helathy donors. Tregs were purified from 23 CB units and from the PB of 13 donors and expanded for 6 days with anti-CD3, anti-CD28 and IL-2. Immunophenotypic analyses were performed, and suppressor activity of expanded Tregs was measured in mixed lymphocyte reaction (MLR) cultures. The IL-10 production capacity was tested and gene expression profile experiments were performed on 6 Tregs from PB and 4 from CB. CB and PB Tregs had similar immunophenotypic features. Tregs from CB presented a higher expansion capacity and genomic characterization showed in CB-derived Tregs a significant enrichments of genes involved in cell proliferation, chromatin modification and regulation of gene expression in CB-derived Tregs. All samples were positive for the Foxp3 gene and protein after expansion. CB and PB expanded Tregs exerted a comparable and potent suppressive function of MLR and presented a high in vitro IL-10 production capacity. Gene profile analysis also revealed for PB Tregs a significant enrichments of genes involved in the adaptive immune response.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 10 Downloadable Samples
- IlluminaHiSeq2500
Description
Mesenchymal stem cells (MSC) are self-renewing multipotent cells which hold great potential in stem cell-based therapy. MSC can be derived from multiple adult tissues but require invasive harvesting and imply donor-to-donor differences. MSC derived from embryonic stem cells (ESC) may provide an alternative source not suffering from those limitations, but to what extend they correspond to the adult counterpart is not known. Here we characterized human ESC-derived MSC in-depth and compared them to human adult tissue-derived MSC (bone marrow BM-MSC) as well as to hESC using next-generation RNA sequencing. In MSC we observed enrichment of proteins involved in cell adhesion, wound healing, extracellular matrix generation, as well as vesicle-mediated transport and exosomes, with the latter pointing towards paracrine signaling. The enrichment and variety of developmental terms associated with MSC further suggest the support function in tissue regeneration. The observed differences between ESC-and adult tissue derived-MSC are similar in magnitude to those reported for MSC of different origin and the former may thus represent an alternative source for therapeutic applications.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 5 Downloadable Samples
- Illumina HiSeq 2000
Description
AGO1 RIP-Seq from chromatin associated RNAs
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Rattus norvegicus
- 30 Downloadable Samples
- Affymetrix Rat Expression 230A Array (rae230a), Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Gene expression profiling of the medial (MGE), lateral (LGE) and caudal (CGE) ganglionic eminence, and cerebral cortex (CTX) at various embryonic stages (E12.5, E14 and E16).
Publication Title
Comprehensive spatiotemporal transcriptomic analyses of the ganglionic eminences demonstrate the uniqueness of its caudal subdivision.
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part
View Samples