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Glycine max
135 Downloadable Samples
Illumina HiSeq 2000
Description
We investigated soybean seed development because (1) soybean seeds are a major source of food and fuel, (2) soybean seeds have been an excellent system for studying the basic processes controlling seed development for over three decades, and (3) new soybean genomic resources, including the sequence of the soybean genome and the gene expression profiles for all seed compartments, tissues, and cell types, can be used to gain new insights into the regulatory processes required for seed differentiation. We sequenced messenger RNA populations of specific soybean seed compartments, which will provide new insights into gene expression that are important for “making a soybean seed.” Overall design: Seventeen compartments of the Early Maturation stage of the soybean seeds were analyzed. Three to four biological replicates were collected for each compartment.
Publication Title
Down-Regulating the Expression of 53 Soybean Transcription Factor Genes Uncovers a Role for SPEECHLESS in Initiating Stomatal Cell Lineages during Embryo Development.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Understanding the nature of the various glucose-derived signals for insulin secretion (both triggering and amplifying) is essential for gaining insight into the functional failure of the beta-cells in diabetes and the development of drugs for correcting this problem. The beta-cells uniquely couple changes in cellular metabolism to electrical activity and thus insulin release. In mice, beta-cell specific deletion of the von Hippel-Lindau (VHL) tumor suppressor protein leads to the activation of a HIF transcription program that includes genes involved in glycolysis, suppression of mitochondrial activity and lactate production. This reprogramming of cellular metabolism results in abnormal insulin secretion properties.
Publication Title
PVHL is a regulator of glucose metabolism and insulin secretion in pancreatic beta cells.
Sample Metadata Fields
Sex, Age
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
In previous studies, miR-1825 has been found to be downregulated in the serum of familial and sporadic patients with amyotrophic lateral sclerosis (ALS). In this study, we aim to identify the target mRNAs of miR-1825 using a combination of proteomic and transcriptomic approaches.
Publication Title
Dysregulation of a novel miR-1825/TBCB/TUBA4A pathway in sporadic and familial ALS.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Amyotrophic later sclerosis is a motor neuron disease accompanied by metabolic changes. PGC (PPAR gamma coactivator)-1alpha is a master regulator of mitochondrial biogenesis and function and of critical importance for all metabolically active tissues. PGC-1alpha is a genetic modifier of ALS.
Publication Title
ALS-causing mutations differentially affect PGC-1α expression and function in the brain vs. peripheral tissues.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
WT vs. Spp1-/- MPPs showed distict patterns in tgene transcription profiles when analyzed with single cell sequencing Overall design: MPPs from mice treated with thioglycollate were FACS-sorted, and gene expression profiles were compared between WT vs. Spp1-/- cells.
Publication Title
Skewing of the population balance of lymphoid and myeloid cells by secreted and intracellular osteopontin.
Sample Metadata Fields
Subject
View Samples
SRP044619- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 2000
Description
To identify isoform differential expression underlying peripheral nerve regeneration we performed RNA-Sequencing on DRG neurons after axotomy. Overall design: RNA was sequenced from peripheral Dorsal Root Ganglia (DRG) neurons from adult male mice 7 days after a conditioning lesion at the level of the sciatic nerve (Crushed samples) or after a sham surgery (Controls surgery).
Publication Title
Identification of miRNAs involved in DRG neurite outgrowth and their putative targets.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
Purpose: The goals of this study are to identify the transcriptional profile of retinal ganglion cells (RGCs) with the capacity to regenerate an axon, and contrast this profile with the profile of RGCs that cannot regenerate an axon. Methods: See sample pages for protocols for tissue preparation, RNA extraction and purification, library construction and data processing. Results: RNA from the 12 samples was sequenced to an average depth of 42 million reads. Genes were considered expressed if a gene had an expression of 1 count per million in 3 of the 12 samples. There were 13,406 genes that met this criterion. Conclusions: Our study represents the first analysis by NGS of highly-purified RGCs in the context of axonal injury Overall design: RGC mRNA profiles of melanopsin RGCs and ON-OFF Direction Selective Ganglion Cells (ooDSGCs) were generated by deep sequencing in triplicate, using Illumina HiSeq 2500.
Publication Title
Thrombospondin-1 Mediates Axon Regeneration in Retinal Ganglion Cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 104 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Clinical heterogeneity of esrtrogen receptor-negative, progesterone receptor-negative [ER(-)/PR(-)] breast cancer (BC) suggests biological heterogeneity. We performed gene expression analysis of primary BCs and BC cell lines to identify the underlying biology of ER(-)/PR(-) disease, define subsets, and identify potential therapeutic targets.
Publication Title
An estrogen receptor-negative breast cancer subset characterized by a hormonally regulated transcriptional program and response to androgen.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Treatment
View Samples- Macaca mulatta
- 32 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
The mucosa that lines the respiratory and gastrointestinal (GI) tracts is an important portal of entry for pathogens and provides the frontline of immune defense against HIV infection. Using the simian immunodeficiency virus (SIV) rhesus macaque model, we have performed a comparative analysis of host gene expression in the lung and GI mucosa in response to SIV infection and antiretroviral therapy.
Publication Title
Enhanced innate antiviral gene expression, IFN-α, and cytolytic responses are predictive of mucosal immune recovery during simian immunodeficiency virus infection.
Sample Metadata Fields
Specimen part
View Samples- Macaca mulatta, Homo sapiens
- 13 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Transcription profiling reveals potential mechanisms of dysbiosis in the oral microbiome of rhesus macaques with chronic untreated SIV infection.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Cell line, Treatment
View Samples