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accession-icon SRP002416
mRNA-seq with Agnostic Splice Site Discovery for CNS Transcriptomics Tested in Chronic Pain
  • organism-icon Rattus norvegicus
  • sample-icon 24 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer II

Description

The study pursued dual goals: To advance mRNA-seq bioinformatics towards unbiased transcriptome capture and to demonstrate its potential for discovery in neuroscience by applying the approach to an in vivo model of neurological disease. We found that 12.4% of known genes were induced and 7% were suppressed in the dysfunctional (but anatomically intact) L4 dorsal root ganglion (DRG) 2 weeks after L5 spinal Nerve Ligation (SNL). A new algorithm for agnostic mapping of pre-mRNA splice junctions (SJ) achieved a precision of 97%. Overall design: mRNA-seq of L4 DRG 2 weeks and 2 months after L5 spinal nerve ligation. CONTROL and SNL were used to identify differential gene expression between chronic pain and standard conditions in Rattus norvegicus. CONTROL and SNL and PILOT were used to perform 'agnostic splice site discovery' in the nervous system transcriptome in Rattus norvegicus

Publication Title

mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE24598
The human nose harbours a niche of olfactory ecto-mesenchymal stem cells displaying neurogenic and osteogenic properties
  • organism-icon Homo sapiens
  • sample-icon 28 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a), Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

We previously identified multipotent stem cells within the lamina propria of the human olfactory mucosa, located in the nasal cavity. We also demonstrated that this cell type differentiates into neural cells and improves locomotor behavior after transplantation in a rat model of Parkinsons disease. Yet, next to nothing is known about their specific stemness characteristics. We therefore devised a study aiming to compare olfactory lamina propria stem cells from 4 individuals to bone marrow mesenchymal stem cells from 4 age- and gendermatched individuals. Using pangenomic microarrays and immunostaining with 34 cell surface marker antibodies, we show here that olfactory stem cells are closely related to bone marrow stem cells. However, olfactory stem cells exhibit also singular traits. By means of techniques such as proliferation assay, cDNA microarrays, RT-PCR, in vitro and in vivo differentiation, we report that, when compared to bone marrow stem cells, olfactory stem cells display i) a high proliferation rate; ii) a propensity to differentiate into osseous cells and iii) a disinclination to give rise to chondrocytes and adipocytes. Since peripheral olfactory stem cells originate from a neural crest-derived tissue and, as shown here, exhibit an increased expression of neural cellrelated genes, we propose to name them olfactory ecto-mesenchymal stem cells (OE-MSC). Further studies are now required to corroborate the therapeutic potential of OE-MSCs in animal models of bone and brain diseases.

Publication Title

The human nose harbors a niche of olfactory ectomesenchymal stem cells displaying neurogenic and osteogenic properties.

Sample Metadata Fields

Sex, Age, Specimen part, Treatment

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accession-icon SRP017294
Genomewide analysis of U1C-dependent alternative splicing
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer II

Description

To investigate whether U1C plays a role in splicing regulation in human system, we performed siRNA-mediated knockdown of U1C in HeLa cells and analyzed alternative splicing patterns by high-throughput RNA sequencing (RNAseq) Overall design: RNAseq performed with poly(A)+ selected total RNA from U1C-knockdown and control-treated HeLa cells

Publication Title

A novel intra-U1 snRNP cross-regulation mechanism: alternative splicing switch links U1C and U1-70K expression.

Sample Metadata Fields

Cell line, Treatment, Subject

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accession-icon SRP047124
Analysis of allele-specific gene expression in total RNA from blood lymphocytes
  • organism-icon Homo sapiens
  • sample-icon 1 Downloadable Sample
  • Technology Badge IconIlluminaGenomeAnalyzerII

Description

Recently a genome of Russian individual (somatic DNA from blood) was sequenced (Skryabin et al. 2009). That study was continued to find a linkage between genetic differences in parental alleles and bias in biallelic expression of genes.

Publication Title

Individual genome sequencing identified a novel enhancer element in exon 7 of the CSFR1 gene by shift of expressed allele ratios.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE37562
hnRNP L-RNA in HeLa
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L.

Sample Metadata Fields

Cell line, Treatment

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accession-icon GSE37561
Expression data from HeLa cells after hnRNP L knockdown (versus luciferase control), including cycloheximide treatment
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)

Description

Transient siRNA-mediated knockdown of hnRNP L, followed by cycloheximide treatment to eliminate NMD.

Publication Title

Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L.

Sample Metadata Fields

Cell line, Treatment

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accession-icon SRP145098
Differentially regulated genes in Esr2-mutant rat granulosa cells.
  • organism-icon Rattus norvegicus
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 4000

Description

RNA seq analyses were performed in granulosa cells (GCs) collected from gonadotropin treated ESR2 mutant rats. Data obtained from a null mutant with Esr2 exon 3 deletion (?3) and another DNA binding domain (DBD) mutant with exon 4 deletion (?4) were compared to that of wildtype (WT) rats. The raw data were analyzed using CLC genomics workbench. High quality RNA-sequencing reads were aligned to the Rattus norvegicus genome. Differentially expressed genes in ?3 or ?4 Esr2-mutant GCs were identified based on the following criteria: FDR p-Value =0.05 and an absolute fold change of 2. Fewer differentially expressed genes were identified in ?3 compared to the ?4 mutant group. As both of the mutant groups demonstrated a common phenotype of ovulation failure, differentially expressed genes common to both in ?3 and ?4 mutant rats were emphasized and further analyzed in the companion article “ESR2 regulates granulosa cell genes essential for follicle maturation and ovulation” (Khristi et al., 2018).

Publication Title

ESR2 regulates granulosa cell genes essential for follicle maturation and ovulation.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE36598
Global transcriptional role of CtBP in breast cancer cells
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Genome-wide profiles of CtBP link metabolism with genome stability and epithelial reprogramming in breast cancer.

Sample Metadata Fields

Specimen part, Cell line, Treatment

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accession-icon GSE36529
Expression data from CtBP knockdown MCF-7 cells
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

CtBP is a global co-repressor by serving as transcriptional factor in multiple pathways. CtBP functioned as transcriptional factor by recruiting other cofactors such as G9a, HDAC1 and PcG proteins. CtBP is found to be over enriched in several type of tumor samples. To dipict the role of CtBP in globally regulating gene expression, we applied gene microarray technology to find out what subgroups of genes are mainly affected.

Publication Title

Genome-wide profiles of CtBP link metabolism with genome stability and epithelial reprogramming in breast cancer.

Sample Metadata Fields

Cell line, Treatment

View Samples
accession-icon GSE87109
Conserved and species-specific molecular denominators in mammalian skeletal muscle aging
  • organism-icon Macaca mulatta, Mus musculus, Homo sapiens, Rattus norvegicus
  • sample-icon 46 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip, Illumina ratRef-12 v1.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Conserved and species-specific molecular denominators in mammalian skeletal muscle aging.

Sample Metadata Fields

Sex, Specimen part

View Samples

refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Developed by the Childhood Cancer Data Lab

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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