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SRP052991
Homo sapiens
8 Downloadable Samples
IlluminaHiSeq2500
Description
Injury to anterior cruciate ligament (ACL) is common in young individuals and a frequent cause of functional instability and early onset of osteoarthritis. The healing potential of an injured ACL is known to decay over time. The molecular origin of this healing deficiency largely remains elusive but plausibly involves gene transcripts associated with tissue healing. To explore this possibility, we set out to identify transcript expression differences in injured ACL remnants recovered at the time of surgical reconstruction, via microarray (n=24) and RNA-seq (n=8) technologies in transcriptome profiling. We found that time-from-injury was an important determinant of changes in gene expression signatures predominately resulting in repression of several biological processes as identified by gene ontology. The most interesting observation was a time-dependent decline in the gene transcripts as well as the biological processes common to both microarray and RNA-seq analyses. Compared to acute tears, in chronic several important biological processes were namely extracellular matrix organization, angiogenesis, cell adhesion, wound healing, mesenchyme transition, and response to hypoxia. Furthermore, the cross-platform concordance in terms of differentially expressed transcripts or enriched pathways was linearly correlated (r=0.64). Microfluidic digital PCR confirmed the expression of selected differentially expressed transcripts. These intriguing findings suggest an initial attempt of the injured ACL to repair, which drops with time. These findings have implications for efforts to repair the ACL and may be relevant for its reconstruction. These findings also emphasize the utility of differentially expressed transcripts as prognostic biomarkers in patients with ACL injury. Overall design: Examination of transcript expression differences by time-from-injury in anterior cruciate ligament
Publication Title
Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 31 Downloadable Samples
Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Spinal cord injury leads to impaired motor and sensory functions. After spinal cord injury there is a an initial phase of hypo-reflexia followed by a developing hyper-reflexia, often termed spasticity. Previous studies have suggested a relationship between the reappearence of plateau potentials in motor neurons and the development of spasticity after spinalizaion. To understand the moleclar mechanism behind this pheneomona we examined the transcriptional response of the motor neurons after spinal cord injury as it progress over time.
Publication Title
Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Genes specific to Sox9+ pancreatic progenitors were identified by comparing the gene expression in embryonic and adult Sox9+ cells.
Publication Title
A Notch-dependent molecular circuitry initiates pancreatic endocrine and ductal cell differentiation.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- IlluminaGenomeAnalyzerIIx
Description
Sequencing of 5' ends of RNA molecules from control and exosome-depleted HeLa-S3 cells. Overall design: CAGE library construction from RNA extracted from control and exosome-depleted cells.
Publication Title
Nuclear stability and transcriptional directionality separate functionally distinct RNA species.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
Gene expression programs change during cellular transitions. It is well established that a network of transcription factors and chromatin modifiers regulate RNA levels during embryonic stem cell (ESC) differentiation, but the full impact of post-transcriptional processes remains elusive. While cytoplasmic RNA turnover mechanisms have been implicated in differentiation, the contribution of nuclear RNA decay has not been investigated. Here, we differentiate mouse ESCs, depleted for the ribonucleolytic RNA exosome, into embryoid bodies to determine to which degree RNA abundance in the two states can be attributed to changes in transcription vs. RNA decay by the exosome. As a general observation, we find that exosome depletion mainly leads to the stabilization of RNAs from lowly transcribed loci, including several protein-coding genes. In particular, transcripts that are differentially expressed between states tend to be more exosome sensitive in the state where expression is low. We conclude that the RNA exosome contributes to down-regulation of transcripts with disparate expression, often in conjunction with transcriptional down-regulation. Overall design: CAGE experiments were carried out in mouse embryonic stem cells and embryoid bodies differentiated for three days upon depletion of RRP40 with shRNAs, using a scrambled shRNA as control. The experiments were performed in duplicates
Publication Title
The RNA exosome contributes to gene expression regulation during stem cell differentiation.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To investigate genes possibly regulated by TTF-1 in small cell lung cancer cell lines, we compared gene expression profiles of NCI-H209 and Lu139 cell lines electroporated with control and TTF-1 siRNAs.
Publication Title
An integrative transcriptome analysis reveals a functional role for thyroid transcription factor-1 in small cell lung cancer.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
Sequencing of 5' and 3'ends and RNA-seq of PROMPT and mRNA molecules from control and exosome-depleted cells. Overall design: CAGE, 3'TAG and RNAseq library construction from RNA extracted from control and exosome-depleted cells.
Publication Title
Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 18 Downloadable Samples
- Illumina HiSeq 2000
Description
The PLZF transcription factor is essential for osteogenic differentiation of hMSCs, however, its regulation and molecular function during this process is not fully understood. Here we revealed that the ZBTB16 locus encoding PLZF, is repressed by Polycomb (PcG) and H3K27me3 in naïve hMSCs. At the pre-osteoblast stage of differentiation, the locus lost PcG binding and H3K27me3, gained JMJD3 recruitment, and H3K27ac resulting in high expression of PLZF. Subsequently, PLZF was recruited to osteogenic enhancers, influencing H3K27 acetylation and expression of nearby genes important for osteogenic function. Furthermore, we identified a latent enhancer within the ZBTB16/PLZF locus itself that became active, gained PLZF, p300 and Mediator binding and looped to the promoter of the nicotinamide N-methyltransferase (NNMT) gene. The increased expression of NNMT correlated with a decline in SAM levels, which is dependent on PLZF and is required for osteogenic differentiation. Overall design: Effect of PLZF knockdown on osteogenic differentiation of hMSC (RNAseq)
Publication Title
PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
Pigment regeneration is critical for the function of cone photoreceptors in bright and rapidly-changing light conditions. This process is facilitated by the recently-characterized retina visual cycle, in which Müller cells recycle spent all-trans-retinol visual chromophore back to 11-cis-retinol. This 11-cis-retinol is oxidized selectively in cones to the 11-cis-retinal used for pigment regeneration. However, the enzyme responsible for the oxidation of 11-cis-retinol remains unknown. Here, we sought to determine whether retinol dehydrogenase 10 (RDH10), upregulated in rod/cone hybrid retinas and expressed abundantly in Müller cells, is the enzyme that drives this reaction. We created mice lacking RDH10 either in cone photoreceptors, Müller cells, or the entire retina. In vivo electroretinography and transretinal recordings revealed normal cone photoresponses in all RDH10-deficient mouse lines. Notably, their cone-driven dark adaptation both in vivo and in isolated retina was unaffected, indicating that RDH10 is not required for the function of the retina visual cycle. We also generated transgenic mice expressing RDH10 ectopically in rod cells. However, rod dark adaptation was unaffected by the expression of RDH10 and transgenic rods were unable to use cis-retinol for pigment regeneration. We conclude that RDH10 is not the dominant retina 11-cis-RDH, leaving its primary function in the retina unknown. Overall design: Retinas from rd7 and wild-type (C57BL/6J) mice at age 21 days were harvested. Two biological replicates per strain were collected. Each replicate consisted of 8 retinas total from two female and two male mice. RNA was extracted with Trizol, polyA-selected, and processed for mRNA-seq. All four samples were sequenced on a single lane of Illumina HiSeq 2000 (1x50 bp). Note that Nr2e3 transcript levels are higher in the rd7 mutant, as previously reported (Chen et al 2006 Hum Mol Genet 15(13):2146-56).
Publication Title
The role of retinol dehydrogenase 10 in the cone visual cycle.
Sample Metadata Fields
Age, Cell line, Subject
View Samples- Mus musculus
- 67 Downloadable Samples
- Illumina HiSeq 2000
Description
Mutations in the mitochondrial DNA (mtDNA) have been proposed to be essential for metabolic adaptation, and because metabolism is intrinsically associated with multiple disease states, including obesity, we hypothesized that changes in the mtDNA would significantly influence adiposity and gene expression in response to diet. To test these predictions we used Mitochondrial-Nuclear eXchange mice, which have nuclear and mitochondrial genomes that have been exchanged from different M. musculus strains. Overall design: Purpose: Mutations in the mitochondrial DNA (mtDNA) have been proposed to be essential for metabolic adaptation, and because metabolism is intrinsically associated with multiple disease states, including obesity, we hypothesized that changes in the mtDNA would significantly influence adiposity and gene expression in response to diet. To test these predictions we used Mitochondrial-Nuclear eXchange mice, which have nuclear and mitochondrial genomes that have been exchanged from different M. musculus strains. Methods: Wild type (C57BL6/J – C57n:C57mt and C3H/HeN - C3Hn:C3Hmt) and MNX (C57n:C3Hmt and C3Hn:C57mt) mouse were weaned with Chor diet and continued with Chow or changed to high-fat diet from 6 to 12-13 weeks of age. RNA samples were isolated from white adipose tissues collected from epididymal (eWAT) and inguinal (iWAT) fat, representing visceral and subcutaneous fat depots, respectively with RNeasy kit (Qiagen). Reverse transcribed cDNA libraries were sequenced with an Illumina HiSeq 2000. Read mapping was conducted with a proprietary algorithm by Expression Analysis (www.q2labsolutions.com), and read counts were used as input for differential expression analysis in DESeq2 version 1.10.1, using default settings. Results: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the mouse genome (build mm9). Transcriptional changes were interrogated for 961 genes previously reported to be associated with fat metabolism and 29,209 genes representing the entire mouse transcriptome. These results show that the C57 mtDNA increased the number of DE genes in response to high fat diet in mice harboring the C3H nuclear genome (209% increase; C3Hn:C57mt versus C3Hn:C3Hmt, 165/79) and the C3H mtDNA decreased response in animals carrying the C57 nucleus (46% decrease; C57n:C3Hmt versus C57n:C57mt, 112/206) in eWAT (Figure 2B). Similarly, the high fat diet resulted in 25 and 231 DE genes in the C3Hn:C3Hmt and C3Hn:C57mt iWAT, respectively, and 344 and 143 DE genes in C57n:C57mt and C57n:C3Hmt iWAT. This corresponded to a 924% increase in the number of DE genes responding to high fat diet C3Hn:C57mt versus C3Hn:C3Hmt, and a decreased response (58% decrease) in C57n:C3Hmt relative to C57n:C57mt iWAT. Further analysis showed that each MNX and corresponding wild-type shared and had distinct DE genes in eWAT and iWAT. Conclusions: Results also show that the degree of transcriptional response influenced by the mtDNA can vary based upon the type of adipose tissue, suggesting that mtDNA background can have varying effects on the number of nuclear genes differentially responding to stimuli, depending upon tissue and location.
Publication Title
Mitochondrial - nuclear genetic interaction modulates whole body metabolism, adiposity and gene expression in vivo.
Sample Metadata Fields
Specimen part, Subject
View Samples