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SRP067963
Arabidopsis thaliana
4 Downloadable Samples
Illumina HiSeq 2000
Description
The role of on-CG methylation in seed development and dormancy remains unknown. There are four genes in charge of non-CG methylation in Arabidopsis: drm1, drm2, cmt2 and cmt3. The majority of non-CG methylation in vegetative tissues, leaf, is gone in homozygous ddcc mutant line (Hume et al., 2014). To uncover the possible role of non-CG DNA methylation in seed development and dormancy, we characterized the transcriptome of ddcc mutant in Arabidopsis post-mature green seeds using Illumina sequencing. Meanwhile, post-mature green seeds from wild type were used as control. Overall design: Illumina sequencing of transcripts from post-mature green seeds of ddcc mutant and wild type. Two biological replicates were collected.
Publication Title
Similarity between soybean and <i>Arabidopsis</i> seed methylomes and loss of non-CG methylation does not affect seed development.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 9 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Detailed analysis comparing hiPSC lines that were newly generated and compared them to already established hiPSC lines
Publication Title
Molecular analyses of human induced pluripotent stem cells and embryonic stem cells.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 43 Downloadable Samples
- Illumina HiSeq 2000
Description
Tumors driven by activation of the transcription factor Myc generally show oncogene addiction. However, the gene-expression programs that depend upon sustained Myc activity in those tumors remain unknown. We have addressed this issue in a model of liver carcinoma driven by a reversible tet-Myc transgene, combining gene expression profiling with the mapping of Myc and RNA Polymerase II on chromatin. Switching off the oncogene in advanced carcinomas revealed that Myc is required for the continuous activation and repression of distinct sets of genes, constituting no more than half of those deregulated during tumor progression, and an even smaller subset of all Myc-bound genes. We further showed that a Myc mutant unable to associate with the co-repressor protein Miz1 is defective in the initiation of liver tumorigenesis. Altogether, our data provide the first detailed analysis of a Myc-dependent transcriptional program in a fully developed carcinoma, revealing that the critical effectors of Myc in tumor maintenance must be included within defined subsets (ca. 1,300 each) of activated and repressed genes. Overall design: RNAseq samples of control liver (n=11), tet-Myc tumors (n=16), tet-Myc tumors with short-term Myc inactivation (n=8), tet-MycVD tumors (n=11)
Publication Title
Identification of MYC-Dependent Transcriptional Programs in Oncogene-Addicted Liver Tumors.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Drosophila melanogaster
- 55 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
The sensation of hunger after a period of fasting and the sensation of satiety after eating is crucial to behavioral regulation of food intake, but the biological mechanisms regulating these sensations are incompletely understood. We studied the behavioral and physiological adaptation to fasting in the vinegar fly (Drosophila melanogaster). Here we show that flies demonstrated increased behavioral attraction to food odor when food-deprived with no corresponding increase in sensitivity in the peripheral olfactory system. Flies increased their food intake transiently in the post-fasted state, but returned to a stable baseline feeding level within 24 hr after return to food. This modulation in feeding was accompanied by a significant increase in the size of the crop organ of the digestive system, suggesting that fasted flies responded both by increasing their food intake and storing reserve food in their crop. The post-fasting feeding response was observed in both male and female flies of diverse genetic backgrounds. Expression profiling of head, body, and chemosensory tissues by microarray analysis revealed several hundred genes that are regulated by feeding state, including 247 genes in the fly head. We performed RNA interference-mediated knockdown of, takeout, one of the genes strongly downregulated by fasting in multiple tissues. When takeout was knocked down in all neurons the post-fasting feeding response was abolished. These observations suggest that a coordinated transcriptional response to internal physiological state may regulate both ingestive behaviors and chemosensory perception of food
Publication Title
Post-fasting olfactory, transcriptional, and feeding responses in Drosophila.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Drosophila melanogaster
- 14 Downloadable Samples
- Illumina HiSeq 2000
Description
Purpose: Communication between growth cones and their environment plays a central role in assembling neural circuits. We use Tandemly-Tagged Ribosome Affinity Purification (T-TRAP) of mRNA from R cells followed by RNA-seq for multiple time points during development to follow gene expression during target selection and synapse formation. Methods: We chose a ribosome trap method by modifying the N-terminus of the Drosophila ribosomal protein RpL10 with two tandemly arranged epitopes, 3X FLAG and GFP, separated by the Tobacco Etch Virus (TEV) protease site and expressed this in specific cell types using the GAL4/UAS system. cDNA libraries were prepared from mRNA associated with the affinity purified ribosomes and sequenced using an Illumina HiSeq 2000. We mapped raw reads to the D. melanogaster reference genome (release FB2013_01) with the gapped aligner Tophat. Only reads uniquely aligned were collected.Transcript expression levels were quantified using RPKM units using customized scripts written in Perl. Results: In this study, we observed massive changes in expression of cell surface proteins over short time scales (i.e. 5 fold differences in the expression of many hundreds of genes over 5 hr intervals) as R cell growth cones encounter the processes of many different neurons during their conversion from growth cones to synaptic terminals. In addition, to changes in transcripts encoding cell surface proteins, other mRNAs changed significantly as did non-coding RNAs (lincRNAs) associated with ribosomes. Although dramatic changes in transcript levels of presynaptic proteins were not observed preceding the onset of synapse formation, marked changes in the 3''-untranslated regions of these transcripts were seen. Conclusions: These studies provide a step towards merging traditional genetic and global genomic approaches to understanding cellular recognition underlying the assembly of neural circuits. Overall design: We chose 7 time points for RNA-seq analysis of R cells during pupal development corresponding to 24, 35, 40, 45, 53, 65 and 96 hrs after pupal formation (APF).
Publication Title
Rapid Changes in the Translatome during the Conversion of Growth Cones to Synaptic Terminals.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples- Caenorhabditis elegans
- 12 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
ATFS-1 has been shown to regulate transcription of mitochondrial chaperone genes such as mtHsp70/hsp-6 and hsp-60 in response to mitocondrial stress. To identify the entire ATFS-1-mediated response, we compared the transcript profiles from wild-type and atfs-1(tm4525) worms raised in the absence and presence of mitochondrial stress.
Publication Title
Mitochondrial import efficiency of ATFS-1 regulates mitochondrial UPR activation.
Sample Metadata Fields
Specimen part
View Samples- Caenorhabditis elegans
- 6 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
We previously identified a number of genes which were differentially expressed during mitochondrial stress in an ATFS-1-dependent manner using an atfs-1 loss-of-function mutant allele . To complement the findings from our previous microarray, we compared the transcript profiles from wild-type and atfs-1(et18) gain-of-function worms (which have constitutively active ATFS-1) in the absence of mitochondrial stress.
Publication Title
Maintenance and propagation of a deleterious mitochondrial genome by the mitochondrial unfolded protein response.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 155 Downloadable Samples
- Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Sleep is not just for the brain: transcriptional responses to sleep in peripheral tissues.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Mus musculus
- 78 Downloadable Samples
- Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Molecular profiles in sleep and sleep deprivation in peripheral tissues using microarrays
Publication Title
Sleep is not just for the brain: transcriptional responses to sleep in peripheral tissues.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Mus musculus
- 77 Downloadable Samples
- Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Molecular profiles in sleep and sleep deprivation in peripheral tissues using microarrays
Publication Title
Sleep is not just for the brain: transcriptional responses to sleep in peripheral tissues.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples