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SRP115379
Zea mays
6 Downloadable Samples
Illumina HiSeq 2000
Description
We used isolated zygotene meiocytes, corresponding anthers and 2-week-old seedlings from the Zea mays inbred line Mo17 for RNA extraction and library construction for sequencing with Illumina technology to gain insight on gene expression during a key step in meiosis when recombination initiates.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part
View Samples- Gallus gallus
- 20 Downloadable Samples
- Illumina HiSeq 2500
Description
Male broilers from two lines (n=10 per line) with different growth rate were raised at the same condition with free access to feed and drink. At day 6 and day 21, half samples of each broiler line were euthanized by cervical dislocation, and left ventricles were collected for RNA isolation. Gene expression in left ventricle was measured by RNA-seq and compared between different time points and chicken lines. The purpose of this study is to investigate gene expression change during broiler cardiac development and to compared gene expression between fast-growing modern broilers and slow-growing heritage broilers to find possible genes and pathways related to differential cardiac development and differential susceptibility to cardiac diseases between the two broiler lines.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease
View Samples- Gallus gallus
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
broilers heat stress.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
Dengue virus (DENV) infection causes profound changes in the host cells and these changes underlie the immune response-based viral clearance and pathogenesis. There are several major cell/tissue types relevant for DENV pathogenesis in vivo, including immune cells, liver, and vascular endothelial cells. We applied a directed differentiation system that produces hepatocyte-like cells (HLCs) from pluripotent stem cells to investigate various aspects of DENV- hepatic cells interaction. Human embryonic stem cells were resistant to DENV infection while progeny hepatic cells were permissive. The transition to DENV permissiveness coincided with the upregulation of entry factors for the virus. Infection of HLCs by DENV was self-limiting due to the activation of the interferon (IFN) pathways, which protected by-stander cells from infection but failed to induce the same level of interferon-induced genes (ISGs) expression in the infected cells due to the subversion of IFN signaling by DENV. Innate immunity also protected the infected cells from virus-induced apoptosis. Furthermore, DENV infection activated the NF-?B pathway, increased production of reactive oxidative species (ROS), and led to production of inflammatory cytokines which may contribute to the cytokine storm implicated in dengue hemorrhagic fever (DHF). Finally, DENV infection of HLCs resulted several in vitro phenotypes that may have relevance for acute liver failure and vascular permeability during DHF. These include the disruption of adherens junctions and the downregulation of many liver specific genes such as albumin (ALB) and coagulation factor V (F5).
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Cell line
View Samples- Pseudomonas aeruginosa
- 4 Downloadable Samples
- Illumina HiSeq 4000
Description
Pseudomonas aeruginosa transcriptomic profile exposed to Cr(VI)
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
Arabidopsis thaliana Transcriptome (Vv-circATS1-OE and WT under 4?)
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
We compared the Galpha13 knockout and wild type mouse embryonic stem cells (cell line CJ7) to analyse the gene expression levels using Affymatrix mouse MGU_74Av2 array
Publication Title
Gene Expression Analysis of Galpha13-/- Knockout Mouse Embryos Reveals Perturbations in Galpha13 Signaling Related to Angiogenesis and Hypoxia
Sample Metadata Fields
Specimen part, Cell line, Time
View Samples- Citrus sinensis
- 10 Downloadable Samples
- Affymetrix Citrus Genome Array (citrus)
Description
Huanglongbing (HLB) (=citrus greening) is a destructive disease of citrus which is caused by a fastidious, phloem-inhabiting bacterium of the genus Candidatus Liberibacter. Large-scale analysis of gene expression changes in Valencia orange leaves were studied during the course of 19 weeks after inoculation with Ca. L. asiaticus using the Affymetrix GeneChip citrus genome array to provide new insights into the molecular basis of citrus response to this pathogen. Of the more than 33,000 probe sets on the microarray 21,067 were expressed in the leaves, of which 279 and 515 were differentially expressed (FDR 0.05) five to nine and 13-17 weeks after inoculation, respectively. Results from semi-quantitative RT-PCR analysis performed on 14 selected genes were highly correlated with those observed with the microarray. Gene expression changes involved a variety of different processes including cell defense, transport, cellular organization, photosynthesis, and carbohydrate metabolism. Notable was the pathogen-induced accumulation of transcripts for a phloem-specific lectin PP2-like protein. Transcriptional changes and their relation to disease symptom development are discussed. This is the first study of transcriptional profiling in citrus in response to liberibacter infection using microarray technology.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 95 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Four different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in major radial zones of the root. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to media supplemented with 140 mM NaCl for 1 hour, 3 hours, 8 hours, 20 hours, 32 hours and 48 hours.
Publication Title
A spatio-temporal understanding of growth regulation during the salt stress response in Arabidopsis.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 36 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Six different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in all radial zones of the root. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to media supplemented with 140 mM NaCl for 1 hour.
Publication Title
Cell identity mediates the response of Arabidopsis roots to abiotic stress.
Sample Metadata Fields
No sample metadata fields
View Samples