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GSE11852
Arabidopsis thaliana
23 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Relative expression data from germinating seeds of Columbia (wt), the pkl mutant (pkl), Columbia plus uniconazole-P (Uwt) and the pkl-mutant plus uniconazole-P (Upkl).
Publication Title
The CHD3 remodeler PICKLE promotes trimethylation of histone H3 lysine 27.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 24 Downloadable Samples
IlluminaHiSeq2000
Description
Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However, non-mammalian animals (e.g. birds, amphibian and fish) regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates, we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA-Seq analyses on regenerating support cells purified by fluorescence activated cell sorting (FACS). The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration, because these cells can be acutely killed by exposure to neomycin, after which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. Tg(sqET20) larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 days post fertilization (dpf) Tg(sqET20) larvae at 1, 3 and 5 hours post neomycin treatment, as well as from a non-treated control. Overall design: Transgenic zebrafish Tg(sqET20) larvae at 5 days post fertilization were exposed to neomycin, dissociated, and FACS sorted into GFP positive and GFP negative populations at 1, 3, and 5 hours following treatment, along with a mock treated 1 hr control. The experiment was performed in triplicate, for a total of 24 samples.
Publication Title
Gene-expression analysis of hair cell regeneration in the zebrafish lateral line.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Tamoxifen, a selective estrogen receptor modulator, is widely used in research and clinically in patients. Tamoxifen injection (3 consecutive days, intraperitoneal, 5mg/20g mouse body weight) causes dramatic rearrangement of the gastric mucosa with loss of > 90% of PCs, a 6-fold increase in proliferation in stem/progenitor cells, and morphological changes in the ZCs in the bases of gastric-units.
Publication Title
Identification of alanyl aminopeptidase (CD13) as a surface marker for isolation of mature gastric zymogenic chief cells.
Sample Metadata Fields
Time
View Samples- Rattus norvegicus
- 20 Downloadable Samples
- Affymetrix Rat Gene 1.1 ST Array (ragene11st)
Description
Identify differentially expressed genes related to the neurodegenerative process in a new animal model of hepatic encephalopathy (HE).
Publication Title
Cerebellar neurodegeneration in a new rat model of episodic hepatic encephalopathy.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 100 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Triple negative breast cancer (TNBC) represents a challenging tumor type due to their poor prognosis and limited treatment options. It is well recognize that clinical and molecular heterogeneity of TNBC is driven in part by mRNA and lncRNAs. To stratify TNBCs, we profiled mRNAs and lncRNA in 158 adjuvant TNBC tumors using an Affymetrix microarray platform. Lehmann clustering analysis allowed us to identify TNBC subtypes featuring unique lncRNA expression patterns, disease free and overall survival rates and particular gene ontology enrichments (performed with GSEA algorithm).
Publication Title
Loss of function of miR-342-3p results in MCT1 over-expression and contributes to oncogenic metabolic reprogramming in triple negative breast cancer.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 58 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Triple negative breast cancer (TNBC) represents a challenging tumor type due to their poor prognosis and limited treatment options. It is well recognize that clinical and molecular heterogeneity of TNBC is driven in part by mRNA and lncRNAs. To stratify TNBCs, we profiled mRNAs and lncRNA in 158 adjuvant TNBC tumors using an Affymetrix microarray platform. Lehmann clustering analysis allowed us to identify TNBC subtypes featuring unique lncRNA expression patterns, disease free and overall survival rates and particular gene ontology enrichments (performed with GSEA algorithm).
Publication Title
Loss of function of miR-342-3p results in MCT1 over-expression and contributes to oncogenic metabolic reprogramming in triple negative breast cancer.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 88 Downloadable Samples
- Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)
Description
We performed systems analyses of immune responses to the meningococcal polysaccharide (MPSV4) and conjugate (MCV4) vaccines in healthy adults.
Publication Title
Molecular signatures of antibody responses derived from a systems biology study of five human vaccines.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Mus musculus
- 45 Downloadable Samples
- Illumina HiSeq 2500
Description
We report the RNA-seq results from mouse T-cell precursors in different developmental stages including DN1, DN2a, DN2b, DN3 and DP in order to study the gene regulation network in T cell development. Some of the samples also have certain kind of perturbations, such as Bcl11b knockout and the treatment of Notch signaling pathway inhibitor GSI, in order to study the roles of these factors in T cell development. Overall design: Examine the transcriptome of 47 mouse T-cell precursor samples from five developmental stages (DN1, DN2a, DN2b, DN3 and DP). Among them, 19 have Bcl11b knockout and 4 have GSI treatment.
Publication Title
Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 54 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Breast cancer (BC) is the most commonly diagnosed neoplasm in women worldwide and a well-recognized heterogeneous pathology classified into four molecular subtypes: Luminal A, Luminal B, HER2-enriched and Basal-like, each one with different biological and clinical characteristics. It is well recognize that clinical and molecular heterogeneity of BC is driven in part by mRNA and lncRNAs. We profiled mRNAs and lncRNA in 75 adjuvant tumors using an Affymetrix microarray platform.
Publication Title
A lncRNA landscape in breast cancer reveals a potential role for AC009283.1 in proliferation and apoptosis in HER2-enriched subtype.
Sample Metadata Fields
Specimen part
View Samples- Sus scrofa
- 20 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
The transcriptome changes of the ileal mucosa in suckling piglets during early postnatal life were analysed to contribute to the knowledge of a pigs gut development. In addition, the ileal transcriptome of suckling piglets was compared with that of age-matched weaned piglets (weaned at the age of 21 days) to elucidate the effect of weaning on the developing gut.
Publication Title
Weaning Markedly Affects Transcriptome Profiles and Peyer's Patch Development in Piglet Ileum.
Sample Metadata Fields
Specimen part
View Samples