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SRP128491
Homo sapiens
3 Downloadable Samples
Illumina HiSeq 2500
Description
The goals of this study are to compare NGS-derived whole transcriptome profiles (RNA-seq) of H5N1 infected A549 cells overexpressing either negative control mimic or miR-324-5p mimic Overall design: A549 cells were either mock transfected or transfected with either negative control or mir-324-5p mimic. After 12 hours cells were either mock infected (mock transfected cells) or infected with A/duck/India/02CA10/2011 - H5N1 virus (negative control and miR-324-5p overexpressing cells)
Publication Title
MicroRNA hsa-miR-324-5p Suppresses H5N1 Virus Replication by Targeting the Viral PB1 and Host CUEDC2.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Analyses of expression differences in flower bud and leaf of scion and rootstock, in homografts of Arabidopsis
Publication Title
Grafting triggers differential responses between scion and rootstock.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
We previously identified TLR-independent expression of 4933430F08Rik, encoding Batf2, in T. cruzi-infected bone marrow-derived dendritic cells (BMDCs) (Kayama et al., 2009). To determine the functions of Batf2 in innate immune responses, we performed a comprehensive gene expression analysis in wild-type and Batf2-/- bone marrow-derived macrophages (BMMf). RNA-seq analysis showed that 98 genes are upregulated in Batf2-/- BMMf stimulated with LPS following IFN-? treatment, when compared with that in wild-type cells. Among these genes, we focused on Il23a, encoding IL-23p19, because IL-23 is able to promote expression of Il17a in Th17 cells. Overall design: mRNA of wild-type and Batf2-/- BMMf were subjected to deep sequencing profiling using Illumina HiSeq 2000.
Publication Title
BATF2 inhibits immunopathological Th17 responses by suppressing <i>Il23a</i> expression during <i>Trypanosoma cruzi</i> infection.
Sample Metadata Fields
Specimen part, Treatment, Subject, Time
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
The goal of this study is to compare downstream genes of Sema6D signaling in both M1 and M2 macrophages. Overall design: Bone marrow derived macrophage mRNA profiles of 7 weeks of wild type (WT) and Sema6D-/- mice were stimulated by IL-4 for 24 hrs.
Publication Title
Semaphorin 6D reverse signaling controls macrophage lipid metabolism and anti-inflammatory polarization.
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
Purpose: The goal of this study is to compare downstream genes of Sema6D signaling in LPS plus IFNg stimulated macrophages. Methods: Bone marrow derived macrophage mRNA profiles of 7 weeks of wild type (WT) and Sema6D-/- mice were stimulated by LPS for 4 hrs. Results: According to this comparison, we found that 550 genes were downregulated in Sema6D-/- macrophages than WT macrophages in response to LPS. Conclusions: Our study represents 62 genes were supressed in both M1 and M2 Sema6D-/- macrophage than WT macrophages, suggesting of Sema6D reverse sigaling genes. Overall design: Bone marrow derived macrophage mRNA profiles of 7 weeks of wild type (WT) and Sema6D-/- mice were stimulated by LPS for 4 hrs, then isolated total RNA by RNeasy kit.
Publication Title
Semaphorin 6D reverse signaling controls macrophage lipid metabolism and anti-inflammatory polarization.
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Non-metastatic 2 (NME2)-mediated suppression of lung cancer metastasis involves transcriptional regulation of key cell adhesion factor vinculin.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
The goal of this study is to evaluate the function of eosinophil-derived neurotoxin (EDN) in eosinophilic chronic rhinosinusitis (ECRS) pathogenesis and assess its potential as a disease activity marker. Overall design: To determine the pathological role of eosinophil-derived neurotoxin (EDN) in eosinophilic chronic rhinosinusitis (ECRS), we performed RNA sequencing to analyze gene expression in human nasal epithelial cells (HNEpCs) stimulated with EDN.
Publication Title
Eosinophil-derived neurotoxin enhances airway remodeling in eosinophilic chronic rhinosinusitis and correlates with disease severity.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Gossypium hirsutum
- 30 Downloadable Samples
- Affymetrix Cotton Genome Array (cotton)
Description
Cotton is one of the most commercially important Fiber crops in the world and used as a source for natural textile Fiber and cottonseed oil. The fuzzless-lintless ovules of cotton mutants are ideal source for identifying genes involved in Fiber development by comparing with Fiber bearing ovules of wild-type. To decipher molecular mechanisms involved in Fiber cell development, transcriptome analysis has been carried out by comparing G. hirsutum cv. MCU5 (wild-type) with its fuzzless-lintless mutant (MUT). Cotton bolls were collected at Fiber initiation (0 dpa/days post anthesis), elongation (5, 10 and 15 dpa) and secondary cell wall synthesis stage (20 dpa) and gene expression profiles were analyzed in wild-type and MUT using Affymetrix cotton GeneChip Genome array.
Publication Title
Functional genomics of fuzzless-lintless mutant of Gossypium hirsutum L. cv. MCU5 reveal key genes and pathways involved in cotton fibre initiation and elongation.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Background: Multiple sclerosis (MS) is a demyelinating autoimmune disease of the central nervous system and the leading cause of lasting neurological disabilities in young adults. Increasing evidence suggests that early treatment prevents the development of disability. However, there have been no reliable serum markers to assist the early diagnosis. In addition, interferon (IFN)-, which is the major treatment for MS, is not always effective. Therefore, the development of simple serological test to help the early diagnosis and predict responsiveness to IFN- is of clinical importance. On the other hand, a transmembrane-type semaphorin, Sema4A, has been implicated in experimental autoimmune encephalomyelitis (EAE) by regulating helper T (Th) cell differentiation. Thus, we aimed to identify the implications of Sema4A in diagnosis and pathogenesis of MS. Methods: We assayed serum Sema4A in 59 patients with relapsing-remitting MS (RRMS), 22 patients with clinically isolated syndrome (CIS) and 126 patients with other neurological diseases (OND) by developing a sandwich ELISA. To identify a source of soluble Sema4A and characteristics of MS patients with high levels of Sema4A, we analyzed peripheral blood mononuclear cells (PBMCs) from MS patients and healthy controls by flow cytometry (FACS) and gene chip analysis. The effect of Sema4A was examined in vitro and in vivo using an EAE model. Findings: Sema4A was significantly increased in sera of patients with MS and CIS compared to controls. Sema4A expression was increased on the surface of DCs in MS patients and shed from these cells in a metalloproteinase-dependent manner, affecting the Th17skewing. In addition, patients with high Sema4A levels exhibited more severe disabilities, and IFN- treatment was not beneficial to those patients. Interpretation: Measuring Sema4A is a practical laboratory test to help diagnose MS and to predict responsiveness to IFN- therapy.
Publication Title
Elevation of Sema4A implicates Th cell skewing and the efficacy of IFN-β therapy in multiple sclerosis.
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage
View Samples- Gossypium hirsutum
- 30 Downloadable Samples
- Affymetrix Cotton Genome Array (cotton)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Genome-wide transcriptomic analysis of cotton under drought stress reveal significant down-regulation of genes and pathways involved in fibre elongation and up-regulation of defense responsive genes.
Sample Metadata Fields
Specimen part, Treatment
View Samples