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Oryza sativa
8 Downloadable Samples
Affymetrix Rice Gene 1.1 ST Array (rcngene11st)
Description
Using microarray, the anther transcript profiles of the three indica rice CMS lines revealed 622 differentially expression genes (DEGs) in each of the three CMS lines. GO and Mapman analysis indicated that these DEGs were mainly involved in lipid metabolic and cell wall organization. Comprised with the gene expression of sporophytic and gametophytic CMS lines, 303 DEGs were differentially expressed and 56 of them were down-regulated in all the CMS lines. Co-expression network analysis suggested that many genes were significantly differentially expressed in the CMS lines. These down-regulated DEGs in the CMS lines were found to be involved in tapetum or cell wall formation and their suppressed expression might be related to male sterility. The present study will give some information for the nuclear gene regulation by different cytoplasmic genotypes and provide some candidate genes for pollen development in rice.
Publication Title
Comparative transcript profiling of alloplasmic male-sterile lines revealed altered gene expression related to pollen development in rice (Oryza sativa L.).
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 29 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Calcium acts as a universal second messenger to regulate gene expression in both developmental processes and responses to environmental stresses. Previous studies showed that a number of stimuli can induce calcium increases in the cytoplasm and nucleus, independently. However, the gene expression network deciphering [Ca2+]cyt and/or [Ca2+]nuc signaling pathway remain obscure.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
Illumina HiSeq 2500
Description
compare the transcriptome changes under high ambient temperature
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 9 Downloadable Samples
- Illumina HiSeq 2500
Description
To delineate the mechanism underlying SRSF1/delta133p53-mediated alterations in vascular smooth muscle cell (VSMC) proliferation, we analyzed the genome-wide gene expression profiles in cultured human aortic smooth muscle cells (HASMCs) with delta133p53-overexpression and Ang II treatment versus GFP controls using RNA-Seq approach.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 9 Downloadable Samples
- Illumina HiSeq 2000
Description
The RNA-seq data was used to study alternative splicing in Arabidopsis
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease
View Samples- Arabidopsis thaliana
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
Plant seedlings undergo distinct developmental processes in the dark and in the light. Using an activation-tagging approach, we identified SRS5ox, which overexpresses SHI-RELATED SEQUENCE 5 (SRS5) following induction with estradiol in Arabidopsis thaliana. SRS5 overexpression in SRS5ox seedlings results in a constitutive photomorphogenesis phenotype in the dark. To investigate potential downstream genes of SRS5, the expression levels of genes assayed by RNA-seq in 5-day-old SRS5ox seedlings grown under white light treated with or without estradiol for 2 hours, respectively.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples
SRP162200- Danio rerio
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
The transcriptome of zebrafish mutant and wt embryos.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
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.
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.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
Compare m1A levels in the 16S (large) mitochondrial ribosomal RNA in TRMT61B knockdown cells and control.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples