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Mus musculus
2 Downloadable Samples
Illumina HiSeq 2500
Description
This project aims to delineate the circular RNA complement of mouse brain at age 8-9 weeks
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Homo sapiens
- 10 Downloadable Samples
Description
TIA1 and TIAL1 encode a family of U-rich-sequence-specific mRNA-binding proteins (mRBPs) ubiquitously expressed and conserved in metazoans. By PAR-CLIP, we determined that both proteins bind target sites with identical specificity in 3' UTRs as well as within introns proximal to 5' and 3' splice sites. Double knockout (DKO) of TIA1 and TIAL1 increased target mRNA abundance proportional to the number of binding sites and impacted the accumulation of aberrantly spliced mRNAs including the dsRNA-binding protein PRKRA, whose expression was completely blocked and subsequently triggered the activation of the dsRNA-activated protein kinase EIF2AK2/PKR and stress granule formation. Ectopic expression of PRKRA cDNA or knockout of EIF2AK2 in DKO cells rescued this phenotype. Perturbation of maturation and/or stability of additional targets also compromised cell cycle progression. Our study reveals the essential role of a single mRBP family contributing to fidelity of mRNA maturation, translation and RNA stress sensing pathways in human cells.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
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SRP013842- Homo sapiens
- 1 Downloadable Sample
- Illumina HiSeq 2000
Description
This project aims to discover canonical gene fusion events from mixed human tissue cell lines.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
In the semi-dominant mouse model, Nan (neonatal anemia), heterozygotes suffer hemolytic anemia at birth and throughout life due to a missense mutation (E339D) in transcription factor KLF1 (Krüppel-like factor 1; formerly EKLF, erythroid Krüppel-like factor) Here, we focus on erythropoiesis in the adult spleen. We performed RNAseq in flow-sorted spleen erythroid precursors from adult Nan and WT littermates rendered anemic by phlebotomy as a means to identify global transcriptome changes specific to the Nan KLF1 defect, as opposed to those characterizing anemia generally. We show that (1) expression variation in adult Nan spleen is driven primarily by cell maturation, (2) genotype influences on gene expression are most prominent in late stages of erythroid differentiation when Klf1 expression is highest, (3) Nan-KLF1 produces tissue-specific differential gene expression, and (4) suboptimal stress and basal erythropoiesis with increased reactive oxygen species (ROS) contribute to anemia in adult Nan mice.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Homo sapiens
- 12 Downloadable Samples
- IlluminaHiSeq2500
Description
46BR.1G1 cell line is impaired in DNA ligase 1 (LIG1) activity resulting in an increased level of endogenous single (SSBs) and double stranded DNA breaks (DSBs). 46BR.1G1 fibroblastoid cells represent a suitable model system to investigate how cells cope with low levels of chronic DNA damage, a condition frequently encountered in tumors. Transcriptional alterations in 46BR.1G1 cells were determined by RNAseq by comparison with 7A3, a cell line in which the defect was rescued by stable expression of ectopic wild-type Lig1. The identification of genes differentially expressed in 46BR.1G1 cells would contribute to the elucidation of DNA damage response (DDR) mechanisms.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples SRP067502- Homo sapiens
- 591 Downloadable Samples
- IlluminaHiSeq2000
Description
MicroRNA down-regulation and noise regulation
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 96 Downloadable Samples
- IlluminaHiSeq1000
Description
K562 single cell RNA-seq study
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 19 Downloadable Samples
Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
The SCH9 null strain has smaller cell size, grows at a slower rate and survives three times longer than wide-type yeast.
Publication Title
Comparative analyses of time-course gene expression profiles of the long-lived sch9Delta mutant.
Sample Metadata Fields
Age
View Samples- Saccharomyces cerevisiae
- 12 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
The three yeast mutants sch9, ras2, tor1 show extended chronological life span up to three folds.
Publication Title
Significant and systematic expression differentiation in long-lived yeast strains.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 16 Downloadable Samples
- NextSeq 500
Description
To Identify new factors of GR-mediated mRNA decay.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
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