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Saccharomyces cerevisiae
10 Downloadable Samples
Illumina HiSeq 2000
Description
Transcriptomic profiling of chemical exposure reveals roles of Yap1 in protecting yeast cells from oxidative and other types of stresses
Publication Title
No associated publication
Sample Metadata Fields
Disease, Cell line
View Samples- Danio rerio
- 2 Downloadable Samples
- IlluminaHiSeq2000
Description
Zebrafish ZF4 cell exposed to MMS.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 188 Downloadable Samples
Description
Individual CD27+ CD38+ individual human B cells were analyze with a new RNAseq protocol that captures the 5'' end of transcripts
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 71 Downloadable Samples
- Illumina HiSeq 2500
Description
Here, we characterize differential expression patterns associated with two chromosomal inversions found in natural Drosophila melanogaster populations. To isolate the impacts of genome structure, we engineered synthetic chromosomal inversions on controlled genetic backgrounds with breakpoints that closely match each natural inversion.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
To investigate the basic principles of epigenetic control, we established an orthogonal epigenetic regulatory system in mammalian cells using N6-methyladenine (m6A), a DNA modification not commonly found in metazoan epigenomes. We developed a synthetic initiator module (synI) capable of establishing m6A marks in a sequence-specific manner at designer reporter loci integrated in the human genome, and a synthetic readout module (synR) which selectively reads m6A and consequently induces transcriptional changes. To ensure our orthogonal m6A system has minimal interaction with endogenous human transcriptional machineries, we performed RNA-sequencing analysis and determined that both synI and synR expression have minimal effect on 293FT transcriptome.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Mus musculus
- 3 Downloadable Samples
- Illumina HiSeq 2500
Description
Recent advancements in cell-based therapies for the treatment of cardiovascular disease (CVD) show continuing promise for the use of transplanted stem and cardiac progenitor cells (CPCs) to promote cardiac restitution. However, a detailed understanding of the molecular mechanisms that control the development of these cells remains incomplete and is critical for optimizing their use in such therapy. Long non-coding (lnc) RNA has recently emerged as a crucial class of regulatory molecules involved in directing a variety of critical biological and cellular processes including development, homeostasis and disease. As such, a rising body of evidence suggests that they also play key regulatory roles in CPC development, though many questions remain regarding the expression landscape and specific identity of lncRNA involved in this process. To address this, we performed whole transcriptome sequencing of two murine CPC populations – Nkx2-5 EmGFP reporter-sorted embryonic stem (ES) cell-derived and ex vivo, cardiosphere-derived – in an effort to characterize their lncRNA profiles and potentially identify novel CPC regulators. The resulting sequencing data revealed an enrichment in both CPC populations for a panel of previously-identified lncRNA genes associated with cardiac differentiation. Additionally, a total of 1,678 differentially expressed and as-of-yet unannotated, putative lncRNA genes were found to be enriched for in the two CPC populations relative to undifferentiated ES cells.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage, Cell line, Treatment
View Samples
SRP163049- Homo sapiens
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
Comparing beta catenin knock out hESCs and wildtype hESCs to understand transcript differences between the two cell types
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Homo sapiens
- 2 Downloadable Samples
- NextSeq500
Description
To understand the impact of alternative translation initiation on a proteome, we performed the first study on protein turnover using positional proteomics and ribosome profiling to distinguish between N-terminal proteoforms of individual genes. Overall, we monitored the stability of 1,941 human N-terminal proteoforms, including 147 N-terminal proteoform pairs that originate from alternative translation initiation, alternative splicing or incomplete processing of the initiator methionine. Study design: ribosome profiling of lactimidomycin and cycloheximide treated human Jurkat T-lymphocytes
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Zea mays
- 1 Downloadable Sample
- Illumina HiSeq 2000
Description
The leaf transcriptome of salt-treated maize (Tianta5)
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 36 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Multipotent progenitors (MPP) and common dendritic cell progenitors (CDP) were obtained from mouse bone marrow, followed by in vitro culture with a specific cytokine cocktail and FACS sorting (Felker et al., 2010; Ser et al., 2012). Cells were treated with 10 ng/ml recombinant human TGF-1 (R&D Systems, Minneapolis, USA) for 2, 4, 8, 12 and 24 h as described (Felker et al., 2010) or left untreated.
Publication Title
TGF-β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level.
Sample Metadata Fields
Specimen part
View Samples