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Saccharomyces cerevisiae
644 Downloadable Samples
Illumina HiSeq 2000
Description
High-throughput RNA sequencing (RNA-seq) is now the standard method to determine differential gene expression. Here, a 48 replicate, two condition RNA-seq experiment was designed specifically to test assumptions about RNA-seq read count variability models and the performance of methods for differential gene expression analysis by RNA-seq. Samples were run on an Illumina HiSeq for 50 cycles single-end and included ERCC RNA spike-ins. The high-replicate data allowed for strict quality control and screening of 'bad' replicates. The experiment allowed the effect of bad replicates to be assessed as well as providing guidelines for the number of replicates required for differential gene expression analysis and the most appropriate statistical tools. The mapping between technical replicates and biological replicates is provided via FigShare http://dx.doi.org/10.6084/m9.figshare.1416210 The gene read counts are also available on FigShare: https://dx.doi.org/10.6084/m9.figshare.1425503 https://dx.doi.org/10.6084/m9.figshare.1425502
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (Probe Name version), Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st), Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (Probe Name version)
Description
DNA methylation is tightly regulated throughout mammalian development and altered DNA methylation patterns are a general hallmark of cancer. The methylcytosine dioxygenase TET2 is frequently mutated in hematological disorders, including acute myeloid leukemia (AML), and has been suggested to protect CpG islands and promoters from aberrant DNA methylation. In this study, we present a novel Tet2-dependent leukemia mouse model that closely recapitulates gene expression profiles and hallmarks of human AML1-ETO induced AML. Using this model, we show that the primary effect of Tet2 loss in pre-leukemic hematopoietic cells is progressive and widespread DNA hypermethylation affecting up to 25% of active enhancer elements. In contrast, CpG island and promoter methylation does not change in a Tet2-dependent manner, but increase relative to population doublings. We confirm this specific enhancer hypermethylation phenotype in human AML patients with TET2 mutations. Analysis of immediate gene expression changes reveals rapid deregulation of a large number of genes implicated in tumorigenesis, including many downregulated tumor suppressor genes. Hence, we propose that TET2 prevents leukemic transformation by protecting enhancers from aberrant DNA methylation, and that it is the combined silencing of several tumor suppressor genes in TET2-mutated hematopoietic cells that contribute to increased stem cell proliferation and leukemogenesis.
Publication Title
Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
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
Alternate Accession IDs
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
Alternate Accession IDs
None
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
Alternate Accession IDs
None
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
Alternate Accession IDs
None
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
Alternate Accession IDs
None
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
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
In cytotoxic T cells (CTL), Protein Kinase B /Akt is activated by the T cell antigen receptor (TCR) and the cytokine Interleukin 2 (IL2), in part by phosophorylation of Akt by Phospholipid dependent kinase 1 (PDK1).
Publication Title
Protein kinase B controls transcriptional programs that direct cytotoxic T cell fate but is dispensable for T cell metabolism.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples