Filters
Technology
Platform
SRP032999
Homo sapiens
6 Downloadable Samples
IlluminaHiSeq2000
Description
We employed next generation sequencing to examine whether knocking down the steroid receptor RNA activator (SRA) gene significantly affect the expression levels of certain genes in MCF-7 cells. MCF-7 cells were transfected with either a pool of four non-target control siRNAs or a pool of four SRA siRNAs for 32 hrs. 157 million reads were generated from triplicate samples of the control group; 151 million reads were generated from triplicate samples of the SRA knockdown group. Six genes were identified as significantly changed in the expression levels with the cutoff of q value = 0.05, fold change = 0.5 or = 2, and reads per kilobase per million mapped reads (RPKM) = 1. However, except for SRA itself, the other five genes were shown by real-time PCR to be only affected by one siRNA in the SRA siRNA pool. Further analysis of this dataset with different cuttoff setting may reveal true SRA-regulated genes in MCF-7. Overall design: MCF-7 cells were cultured in high glucose DMEM with 10% fetal bovine serum, 2 mM Glutamax-1, 100 units/ml penicillin and 100 µg/ml streptomycin. ON-TARGETplus SMARTpool for human SRA (Thermo Scientific, L-027192-00-0005) was used to knockdown SRA (siSRA) and ON-TARGETplus Non-targeting Pool Thermo Scientific, D-001810-10-05) was used as a negative control (siCtrl). A total of 25 nM siRNA was transfected in 6-well dishes using Lipofectamine™ RNAiMAX Reagent (Life Technologies, Invitrogen) following the manufacturer’s recommendations. Polyadenylated RNA was purified from the cells 32 hrs after transfection. cDNA libraries were prepared and double-stranded cDNA was fragmented using DNase I according to Illumina specifications, prior to adaptor ligation. Sequencing libraries were amplified and sequenced using an Illumina HiSeq 2000 sequencer.
Publication Title
Structure and function of steroid receptor RNA activator protein, the proposed partner of SRA noncoding RNA.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The p53 tumor suppressor is a DNA damage responsive sequence-specific transcriptional activator. The sustained activation of the p53 response is incompatible with cell growth and viability. To circumvent this issue, a variety of negative feedback loops exist to limit the duration of p53 activation. Despite our understanding of p53-regulation, very little is known about the effect of transient p53 activation on the long term expression of p53 target genes. Here we used a temperature sensitive variant of p53 and oligonucleotide microarrays to monitor gene expression during and following reversible p53 activation. The expression of most p53-induced transcripts was rapidly reversible, consistent with active mRNA decay. Representative 3UTRs derived from short-lived transcripts (i.e. DDB2 and GDF15) conferred instability on a heterologous mRNA while 3UTRs derived from more stable transcripts (i.e. CRYAB and TP53I3) did not. The 3UTRs derived from unstable p53-induced mRNAs were significantly longer than those derived from stable mRNAs. These 3UTRs had high uridine and low cytosine content, leading to a higher density of U-, AU- and GU-rich sequences. Remarkably, short-lived p53 targets were induced faster reaching maximum transcript levels earlier than the stable p53-targets. Taken together, the p53 transcriptional response has evolved with primarily short-lived target mRNAs and that post-transcription processes play a prominent role in the p53 response.
Publication Title
The role of mRNA decay in p53-induced gene expression.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Arabidopsis thaliana
- 154 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Physiological genomics of response to soil drying in diverse Arabidopsis accessions.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 59 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
These data provide a basis for exploration of gene expression differences between physiologically diverse Spring annual accessions of Arabidopsis thaliana.
Publication Title
Physiological genomics of response to soil drying in diverse Arabidopsis accessions.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 41 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
These data provide a basis for exploration of gene expression differences between physiologically diverse accessions of Arabidopsis thaliana.
Publication Title
Physiological genomics of response to soil drying in diverse Arabidopsis accessions.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 30 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
These data provide a basis for the detection of sequence based polymorphisms between 10 Spring annual accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies.
Publication Title
Physiological genomics of response to soil drying in diverse Arabidopsis accessions.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 24 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
These data provide a basis for exploration of gene expression differences between physiologically extreme accessions of Arabidopsis thaliana.
Publication Title
Exploring genetic and expression differences between physiologically extreme ecotypes: comparative genomic hybridization and gene expression studies of Kas-1 and Tsu-1 accessions of Arabidopsis thaliana.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 24 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
These data provide a basis for the detection of sequence based polymorphisms between 10 Spring annual accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies.
Publication Title
Physiological genomics of response to soil drying in diverse Arabidopsis accessions.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
These data provide a basis for the detection of sequence based polymorphisms between the Col-1, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies.
Publication Title
Exploring genetic and expression differences between physiologically extreme ecotypes: comparative genomic hybridization and gene expression studies of Kas-1 and Tsu-1 accessions of Arabidopsis thaliana.
Sample Metadata Fields
Specimen part
View Samples- Anopheles gambiae
- 16 Downloadable Samples
- Affymetrix Plasmodium/Anopheles Genome Array (plasmodiumanopheles)
Description
Insect hemocytes mediate important cellular immune responses including phagocytosis and encapsulation, and also secrete immune factors such as opsonins, melanization factors, and antimicrobial peptides. In Anopheles, they contribute to the defense against malaria parasite invasion during the early sporogonic cycle. We used microarrays to identify transcripts that are specific or enriched in circulating hemocytes compared to either neuronal or to the rest of the body.
Publication Title
Discovery of Plasmodium modulators by genome-wide analysis of circulating hemocytes in Anopheles gambiae.
Sample Metadata Fields
Specimen part, Treatment
View Samples