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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
Alternate Accession IDs
None
Sample Metadata Fields
Age, Specimen part
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
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 259 Downloadable Samples
- Illumina HiSeq 2500
Description
Fetal, perinatal and adult mouse mammary epithelial single cell transcriptomes
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line
View Samples- Rattus norvegicus
- 40 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
NRVMs were subjected to varying durations of ischemia or ischemia+reperfusion using coverslip hypoxia. Expression profiling was used to identify genes that are differentially regulated in either event.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 33 Downloadable Samples
- Illumina HiSeq 2000
Description
These RNA-seq data are from dorsolateral prefrontal cortex (DLPFC) tissue from 5 individuals left off ice at room temperature for 0, 15, 30, and 60 minutes. Resulting RNA was extracted and sequenced with both polyA+ and RiboZero protocols.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Race
View Samples- Arabidopsis thaliana
- 31 Downloadable Samples
- NextSeq 500, Illumina HiSeq 2500
Description
This study was designed to understand the mechanism by which floral organ abscission mutants'' phenotypes arise.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part, Treatment
View Samples- Saccharomyces cerevisiae
- 18 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Global restriction of protein synthesis is a hallmark of cellular stress. Using hydrogen peroxide, we monitor the transcript level and also the translation status for each RNA using cycloheximide to freeze elongating ribosomes. Polyribosome fractionation of cell extracts was used to separate highly translated and poorly translated mRNAs that were then separately analysed.
Publication Title
Global translational responses to oxidative stress impact upon multiple levels of protein synthesis.
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Compound
View Samples- Saccharomyces cerevisiae
- 12 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
One common form of translational control is mediated by proteins that bind to the mRNA 5' cap-binding protein eIF4E. These proteins are collectively called 4E binding proteins (4EBPs). Saccharomyces cerevisiae possesses two 4EBPs that are encoded by non-essential genes called CAF20 and EAP1. To determine the impact of gene deletion on gene expression, we monitored the transcript level and also the translation status for each RNA using cycloheximide to freeze elongating ribosomes in wild-type, caf20 and eap1 cells. Polyribosome fractionation of cell extracts was used to separate highly translated and poorly translated mRNAs that were then separately analyzed.
Publication Title
Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins.
Alternate Accession IDs
None
Sample Metadata Fields
Sex
View Samples- Mus musculus
- 8 Downloadable Samples
- NextSeq 500
Description
Neuro-2a cells were infected with ZIKV (MOI = 0.5) for 48 h and total RNA was extracted and purified using TRI Reagent and RNeasy Mini kit (Qiagen). RNA-seq was performed at the Molecular and Genomics Core Facility of the University of Mississippi Medical Center. Differential expression analysis between mock and ZIKV infected cells was done using Tophat and cuffdiff programs from the tuxedo suite.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line
View Samples- Mus musculus
- 5 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Effect of FGF2 on the transcriptional profile of microvascular endothelial cells
Publication Title
A pro-inflammatory signature mediates FGF2-induced angiogenesis.
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part, Cell line, Compound
View Samples