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SRP069362
Homo sapiens
40 Downloadable Samples
IlluminaHiSeq2000
Description
To define the in vivo targets of the human nuclear exosome, we performed stranded RNA-seq using polyA RNAs isolated from nuclei of HeLa cells. To compare the RNA levels in each sample in an unbiased fashion, we added spike-in controls to equal amount of total nuclear RNAs. Overall design: PolyA RNAs isolated from nuclei of control, hRRP40 or hMTR4 siRNA treated HeLa cells were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.
Publication Title
Exosome cofactor hMTR4 competes with export adaptor ALYREF to ensure balanced nuclear RNA pools for degradation and export.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 40 Downloadable Samples
- IlluminaHiSeq2000
Description
To define the in vivo targets of the human nuclear exosome, we performed stranded RNA-seq using rRNA-depleted RNAs isolated from nuclei of HeLa cells. To compare the RNA levels in each sample in an unbiased fashion, we added spike-in controls to equal amount of total nuclear RNAs. Overall design: rRNA-depleted RNAs isolated from nuclei of control, hRRP40 or hMTR4 siRNA treated HeLa cells were generated by deep sequencing, using Illumina HiSeq 2000.
Publication Title
Exosome cofactor hMTR4 competes with export adaptor ALYREF to ensure balanced nuclear RNA pools for degradation and export.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
S-adenosylmethionine (SAM) is the methyl donor for biological methylation modifications that regulate protein and nucleic acid functions. Here we show that methylation of a phospholipid, phosphatidylethanolamine (PE), is the major consumer of SAM in budding yeast. The induction of phospholipid biosynthetic genes is accompanied by induction of the enzyme that hydrolyzes S-adenosylhomocysteine (SAH), a product and inhibitor of methyltransferases. Beyond its function for the synthesis of phosphatidylcholine (PC), the methylation of PE facilitates the turnover of SAM for the synthesis of cysteine and glutathione. Strikingly, cells that lack PE methylation accumulate SAM, which leads to hypermethylation of histones and the major phosphatase PP2A, dependency on cysteine, and sensitivity to oxidative stress. Without PE methylation, particular sites on histones then become methyl sinks to enable the turnover of SAM. These findings reveal an unforeseen metabolic function for phospholipid and histone methylation intrinsic to the life of a cell. Overall design: Two biological replicates of wild type and cho2? cells in YPL media, in SL media after 1 hour and in SL media after 3 hour were collected for sequencing.
Publication Title
A Metabolic Function for Phospholipid and Histone Methylation.
Alternate Accession IDs
Sample Metadata Fields
Cell line, Subject, Time
View Samples- Mus musculus
- 15 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
How secondary CD4 T cell effectors, derived from resting memory cells, differ from primary cells, derived from nave precursors, and how such differences impact recall responses to pathogens is unknown.
Publication Title
Memory CD4+ T-cell-mediated protection depends on secondary effectors that are distinct from and superior to primary effectors.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
During reprogramming of mouse embryonic fibroblast, pluripotent genes are up-regulated. Once iPSCs are successfully reprogrammed, the global gene profiles of iPSCs are comparable to mouse ESC.
Publication Title
EpEX/EpCAM and Oct4 or Klf4 alone are sufficient to generate induced pluripotent stem cells through STAT3 and HIF2α.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 93 Downloadable Samples
- Illumina HiSeq 2500
Description
We report RNA sequencing of single olfactory neurons from mouse olfactory epithelium in developmental progression from progenitors to precursors to immature neurons to mature neurons. Most mature neurons expressed only one of ~ 1000 odorant receptor genes (Olfrs) at high levels, whereas many immature neurons expressed low levels of multiple Olfrs. Overall design: Investigating expression of odorant receptors genes in mouse olfactory sensory neurons during development.
Publication Title
Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis.
Alternate Accession IDs
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
TGF is one of most intensively studied regulators of extracellular matrix formation, and has been implicated in the development of pulmonary fibrosis in different models. However, little is know about the role of miRNAs in TGF mediated fibrogenic gene regulation. By using miRNA qRT-PCR array, we have identified miRNAs whose expression are regulated by TGF in IMR-90 cells. Among those down-regulated miRNAs are miR-29 family members. Knockdown miR-29 in IMR-90 cells results in up-regulation of a large number of extracellular matrix and fibrogenic genes including family members of collagen, laminin, integrin, ADAM and MMP, many of them are predicted or confirmed miR-29 targets. Hierarchichal clustering analysis of mRNA array data revealed that many extracellular matrix and fibrogenic genes up-regulated by TGF in IMR-90 cells, are also up-regulated in miR-29 KD cells. Moreover, the similar set of extracellular matrix and fibrogenic genes is also significantly up-regulated in bleomycin treated mouse lungs. Together, our data strongly suggest that downstream of the TGF, miR-29 is a master modulator of genes involved in extracellular matrix formation and might play a significant role in pulmonary fibrosis.
Publication Title
miR-29 is a major regulator of genes associated with pulmonary fibrosis.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
GW182 (Tnrc6a) is a key component of RISC (miRNA-Induced Silencing Complex) that plays a critical role in miRNA-mediated gene silencing. Here, we show that GW182 is expressed in the yolk sac endoderm, and that gene-trap disruption of GW182 leads to growth arrest of yolk sac endoderm, impaired hematopoiesis and embryonic lethality.
Publication Title
Trinucleotide repeat containing 6a (Tnrc6a)-mediated microRNA function is required for development of yolk sac endoderm.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
How IL-2 produced by secondary CD4 T cell effectors, derived from resting memory cells, impacts memory CD4 T cell function and survival to memory following antigen re-encounter is unknown.
Publication Title
Effector CD4 T-cell transition to memory requires late cognate interactions that induce autocrine IL-2.
Alternate Accession IDs
Sample Metadata Fields
Treatment, Time
View Samples- Mus musculus
- 37 Downloadable Samples
- Illumina HiSeq 2000, Illumina Genome Analyzer II
Description
As the most widely used mammalian model organism, mice play a critical role in biomedical research for mechanistic study of human development and diseases. Today, functional sequences in the mouse genome are still poorly annotated a decade after its initial sequencing. We report here a map of nearly 300,000 cis-regulatory sequences in the mouse genome, representing active promoters, enhancers and CTCF binding sites in a diverse set of 19 tissues and cell types. This map provides functional annotation to nearly 11% of the genome, and over 70% of conserved, non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that cis-regulatory sequences are organized into domains of coordinately regulated enhancers and promoters. Our results provide a valuable resource for the annotation of functional elements in the mammalian genome, and study of regulatory mechanisms for tissue-specific gene expression. Overall design: 19 tissues and primary cell types were examined.
Publication Title
A map of the cis-regulatory sequences in the mouse genome.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
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