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Drosophila melanogaster
66 Downloadable Samples
Illumina HiSeq 2000
Description
This study crossed Drosophila melanogaster genotypes from four populations to the reference genome line. RNAseq data was then generated to study natural variation in allele specific expression.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Saccharomyces cerevisiae
- 338 Downloadable Samples
- Illumina HiSeq 2500
Description
WT cells and mutants during growth on low phosphate levels and recovery
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Saccharomyces cerevisiae
- 200 Downloadable Samples
- Illumina HiSeq 2500
Description
WT and mutants cells during growth in low phosphate levels and recovery into 20mM phosphate
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Homo sapiens
- 5 Downloadable Samples
- IlluminaHiSeq2000
Description
RNA sequences are generally identical to the underlying DNA sequences but there are known exceptions. These RNA-DNA differences (RDDs) have been found in the nuclear genomes of human cells and in the mitochondria of plants and animals but not in human mitochondria. Here by deep sequencing of DNA and RNA of human mitochondria, we identified 3 RDD sites including an A-to-U and an A-to-G RDD at position 2617. Examination of the precursor polycistronic mitochondrial transcripts shows that the RDD formation occurs post-transcriptionally. Phylogenetic analysis shows that the ancestral allele at position 2617 was a thymine or a guanine. Thus the RDD formation recapitulates the ancestral form of 16S rRNA. Our findings show that RDD formation like other RNA processing steps is conserved across species and likely has functional significance.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 4000
Description
RNA-sequencings of TSPY1-overexpressed A549 and HepG2 cells were performed to systematically explore the signaling pathways in which TSPY1 is involved during tumor progression.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment
View Samples
SRP015012- Gallus gallus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
Using HiSeq2000 to sequence white leghorn different parts (ovary, magnum, isthmus and uterus) of oviduct at 40-weeks.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
In this study, we performed a NGS analysis to identify transcriptome landscape of the human placenta during uncomplicated single and twin pregnancy, to establish a pattern of normal placental genes expression for further comprehensive analyses. Additionall aim of these studies was to identify the differentially expressed transcripts of genes in single and twin pregnancy that may participate in human pregnancy.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples- Sus scrofa
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
Identification of candidate genes for drip loss
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Equus caballus
- 3 Downloadable Samples
- Illumina HiSeq 2000
Description
The equine hoof is a specialized structure in which the distal skeleton is suspended within the capsule by interdigitated structures known as laminae. Inflammation of this tissue, known as laminitis, is a devastating disease that is the second leading cause of both lameness and euthanasia in the horse. Current research on the laminitic transcriptome focuses on the expression of known genes. However, as this tissue is quite unique and equine annotation is largely derived from computational predictions and gene models from other species, there are likely yet uncharacterized transcripts expressed in the laminae that may be involved in the etiology of laminitis. In order to create a novel annotation resource, we performed whole transcriptome sequencing of sagittal lamellar sections from one control and two laminitis affected horses. Assembly of 113 million 100bp reads resulted in around 75,000 transcripts. Of these, 36,000 corresponded to known annotation in NCBI's non-redundant protein database. RT-PCR of 12 selected annotations confirmed structure and expression in lamellar tissue. Transcriptome sequencing represents a powerful tool to expand on equine annotation and identify novel targets for further laminitis research.
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