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SRP049028
Homo sapiens
3 Downloadable Samples
IlluminaHiSeq2500
Description
Generating human serotonergic neurons from fibroblasts
Publication Title
Generation of functional human serotonergic neurons from fibroblasts.
Sample Metadata Fields
No sample metadata fields
View Samples- Sus scrofa
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
Transcriptome of connective tissue of swine affected and non-affected with scrotal hernia
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples- Saccharomyces cerevisiae
- 43 Downloadable Samples
- Illumina HiSeq 2500
Description
We studied gene expression by RNA-seq in yeast cells in various CDK1-cyclin-depleted states.
Publication Title
The CDK-APC/C Oscillator Predominantly Entrains Periodic Cell-Cycle Transcription.
Sample Metadata Fields
Disease, Cell line
View Samples- Populus trichocarpa
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
Our analysis provides a comprehensive picture of how P. trichocarpa responds to drought stress at physiological and transcriptome levels which may help to understand molecular mechanisms associated with drought response and could be useful for genetic engineering of woody plants.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 1 Downloadable Sample
- Illumina HiSeq 2000
Description
Urechis unicinctus, a benthic marine worm inhabiting widely in the coast of Russia, Japan, Korean Peninsula and China, present special biological characteristics in morphology, reproductive and developmental biology as well as physiology. It could exist in condition of low oxygen, high sulfide and pollution where most animals could not live. However, the molecular mechanisms of resistance are still unknown and the main obstacle to further study is the limited genomic and genetic information. In order to improve the situation, we performed and acquired its transcriptome database.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Zea mays
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
This study provide a dynamic atlas of endosperm development from Shaanxi within China
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Populus trichocarpa
- 3 Downloadable Samples
- Illumina HiSeq 2000
Description
The goal of this study is to investigate the genes regulated by histone acetylation during root development.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 1 Downloadable Sample
- Illumina HiSeq 2000
Description
Urechis unicinctus, a benthic marine worm inhabiting widely in the coast of Russia, Japan, Korean Peninsula and China, presents special biological characteristics in morphology, reproductive and developmental biology as well as physiology. It could exist in condition of low oxygen, high sulfide and pollution where most animals could not live.However, the molecular mechanisms of resistance are still unknown and the main obstacle to further study is the limited genomic and genetic information.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 82 Downloadable Samples
- Illumina HiSeq 2000
Description
Post-transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal-to-Zygotic Transition (MZT), thousands of maternal transcripts are regulated, however, how different cis-elements and trans-factors are integrated to determine mRNA stability is still poorly understood. Here, we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay, we identified cis-regulatory sequences in the 3'-UTR, including poly-U motifs that are associated with mRNA stability. In contrast, miR-430 target sequences, UAUUUAUU AU-rich elements (ARE), CCUC and CUGC elements emerged as destabilizing motifs, with miR-430 and AREs causing mRNA deadenylation upon genome activation. We identified trans-factors by profiling RNA-protein interactions and found that poly-U binding proteins are preferentially associated with 3'-UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly-C motifs and correlated with protein binding. Finally, we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA-seq timecourse part of the study.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment
View Samples- Danio rerio
- 25 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA folding plays a crucial role in RNA function. However, our knowledge of the global structure of the transcriptome is limited to steady-state conditions, hindering our understanding of how RNA structure dynamics influences gene function. Here, we have characterized mRNA structure dynamics during the maternal-to-zygotic transition in zebrafish. We observe that on a global level, translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions, and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast, we find that 3'-UTRs form highly folded structures in vivo, which can affect gene expression by modulating miRNA activity. Furthermore, we find that dynamic 3'-UTR structures are enriched in RNA decay elements, including regulatory elements in nanog, and cyclin A1, key maternal factors orchestrating the maternal-to-zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA-seq timecourse part of the study.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment
View Samples