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SRP062850
Homo sapiens
32 Downloadable Samples
IlluminaHiSeq2000
Description
To better understand transcriptional regulation during human oogenesis and pre-implantation embryonic development, we defined stage-specific transcription, which revealed cleavage stage as highly distinctive. We present multiple lines of evidence that two cleavage-specific homologs, mouse mDUX and human DUX4, each activate hundreds of cleavage-specific endogenous genes (e.g. ZSCAN4, ZFP352, KDM4E) and retroviral elements (MERVL/HERVL-family). Remarkably, mDux expression converts mouse ESCs into two-cell embryo-like (2C-like) cells by binding to MERVL promoters/enhancers and restoring the chromatin landscape (via ATACseq) to the pattern of mouse two-cell embryos Overall design: We derived and analyzed transcriptomes from seven stages of developing human oocytes and embryos. The blastocyst stage embryos were dissected into inner cell mass (ICM) and trophectoderm lineages and processed independently. Cells from each stage were pooled and RNA was extracted. Two stranded libraries were prepared from each stage. Each library was then split and amplied for 12 or 14 PCR cycles, resulting in four technical replicates per developmental stage. 12 and14 cycle replicates from the same library prep were merged after sequencing
Publication Title
Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The purpose of this experiment was to identify genes responding differently to a 24 h low red to far red ratio (R:FR) treatment in plants grown at 16 and 22 degrees
Publication Title
Light-quality regulation of freezing tolerance in Arabidopsis thaliana.
Sample Metadata Fields
Age
View Samples- Homo sapiens
- 38 Downloadable Samples
- IlluminaHiSeq2000
Description
Motivation: RNA-seq is replacing microarrays as the primary tool for gene expression studies. Many RNA-seq studies have used insufficient biological replicates, resulting in low statistical power and inefficient use of sequencing resources. Results: We show the explicit trade-off between more biological replicates and deeper sequencing in increasing power to detect differentially expressed (DE) genes. In the human cell line MCF-7, adding more sequencing depth after 10M reads gives diminishing returns on power to detect DE genes, while adding biological replicates improves power significantly regardless of sequencing depth. We also propose a cost-effectiveness metric for guiding the design of large scale RNA-seq DE studies. Our analysis showed that sequencing less reads and perform more biological replication is an effective strategy to increase power and accuracy in large scale differential expression RNA-seq studies, and provided new insights into efficient experiment design of RNA-seq studies Overall design: Treatment (10nM E2 treatment for 24h) and control MCF7 cells are both replicated 7 times, and collected for mRNA-seq. Reads are then subsampled for statistical analysis.
Publication Title
RNA-seq differential expression studies: more sequence or more replication?
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
In the present study, we hypothesized that C/EBPa (CCAAT/enhancer-binding protein alpha) plays a role in cell regeneration in response to bronchiolar epithelial cell injury. C/EBPa mediated ciliated cell regeneration after naphthalene bronchiolar epithelial cell injury in vivo. Furthermore, we demonstrated that C/EBPa regulates protease/anti-protease balance after lung injury, and intratracheal treatment with anti-protease (BPTI) restored ciliated cell regeneration after naphthalene injury in CebpaD/D mice.
Publication Title
CCAAT/enhancer binding protein-α regulates the protease/antiprotease balance required for bronchiolar epithelium regeneration.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Drosophila melanogaster
- 13 Downloadable Samples
- Affymetrix Drosophila Genome Array (drosgenome1)
Description
Ewg differentially regulated genes in 16-18 h Drosophila embryos. The experiment contains expression measurements from wild type, ewg l1 protein null allele and ewg l1 elavEWG (elavEWG rescue construct expressing a ewg cDNA from the elav promoter) mutants.
Publication Title
Erect wing regulates synaptic growth in Drosophila by integration of multiple signaling pathways.
Sample Metadata Fields
Age
View Samples- Bos taurus
- 12 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Growth plate chondrocytes were isolated from the distal metacarpus of young dairy cattle (all under 10 mo of age), the chondrocytes were released from the extracellular matrix by digestion with Collagenase P for 4 hours, and the various zones of the growth plate were separated by density centrifugation. The least-dense Hypertrophic Zone (HZ) cells were compared to the most-dense Reserve Zone (RZ) cells. 6 pairs of HZ vs RZ were compared by microarray.
Publication Title
SCF, BDNF, and Gas6 are regulators of growth plate chondrocyte proliferation and differentiation.
Sample Metadata Fields
Sex, Specimen part
View Samples- Drosophila melanogaster
- 9 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
The expression of a very large number of genes changes as male germ cells pass through differentiation into spermatids and then sperm. Much of this transcriptional programme requires the activity of the meiotic arrest genes.
Publication Title
The RNA export factor, Nxt1, is required for tissue specific transcriptional regulation.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Affymetrix Arabidopsis Genome Array (ag)
Description
This experiment was a time course performed over 24 hours to look at the effects on gene expression of exposure to low red:far-red ratio light in Arabidopsis thaliana plants. In this way genes involved in the shade avoidance response might be identified. This experiment was designed for gene identification only and containes no replicates,genes identified were verified by quantitative PCR for publication.
Publication Title
Gating of the rapid shade-avoidance response by the circadian clock in plants.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject
View Samples- Homo sapiens
- 1 Downloadable Sample
- IlluminaHiSeq2000
Description
We performed NGS-based transcript profiling (RNA-seq) to profile transcripts that are expressed in MCF10A cells. 12,332 genes with FPKM>1 were considered as expressed in MCF10A cells. Overall design: mRNA profiles of MCF10A cells were generated by deep sequencing using Illumina Hiseq 2000.
Publication Title
Widespread genetic epistasis among cancer genes.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 106 Downloadable Samples
- Illumina HiSeq 2000
Description
The CCA-adding enzyme adds CCA to the 3'' ends of transfer RNAs (tRNAs), a critical step in tRNA biogenesis that generates the amino acid attachment site. We found that the CCA-adding enzyme plays a key role in tRNA quality control by selectively marking unstable tRNAs and tRNA-like small RNAs for degradation. Instead of adding CCA to the 3'' ends of these transcripts, CCA-adding enzymes from all three kingdoms of life add CCACCA. Here, we report deep sequencing analysis of the 3'' ends of tRNA-Ser-CGA and tRNA-Ser-UGA from S. cerevisiae strains and show that hypomodified mature tRNAs are subjected to CCACCA (or poly(A) addition) as part of a rapid tRNA decay pathway in vivo. We conjecture that CCACCA addtion is a universal mechanism for controlling tRNA levels and preventing errors in translation. Overall design: 121 samples analyzed in total, representing time courses of 10 different yeast strains; Biological replicates for each time point are included
Publication Title
tRNAs marked with CCACCA are targeted for degradation.
Sample Metadata Fields
Cell line, Subject
View Samples