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accession-icon SRP051702
mRNA profiling of wildtype, germline depleted, NMD mutant C. elegans whole worms and wildtype dissected gonads
  • organism-icon Caenorhabditis elegans
  • sample-icon 5 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Adjacent alternative 3’ splice sites, those separated by =18nt, provide a unique problem in the study of alternative splicing regulation; there is overlap of the cis-elements that define the adjacent sites. Identification of the intron''s 3'' end depends upon sequence elements that define the branchpoint, polypyrimidine tract and terminal AG dinucleotide. Starting with RNA-seq data from germline-enriched and somatic cell-enriched C. elegans samples, we identify hundreds of introns with adjacent alternative 3’ splice sites. We identify 203 events that undergo tissue-specific alternative splicing. For these, the regulation is mono-directional, with somatic cells preferring to splice at the distal 3'' splice site and germline cells showing a distinct shift towards usage of the adjacent proximal 3'' splice site. Splicing patterns in somatic cells follow consensus rules of 3’ splice site definition, using sites with a short stretch of pyrimidines and an AG dinucleotide. Splicing in germline cells occurs at proximal 3'' splice sites that frequently lack a polypyrimidine tract or, occasionally, the AG dinucleotide. We provide evidence that use of germline-specific proximal 3'' splice sites is conserved across Caenorhabditis species. We propose that divergent mechanisms exist between germline and somatic cells in determining an intron terminus at adjacent alternative 3’ splice sites. Overall design: Examination of alternative splicing changes between germline- and somatic-cell enriched samples as well as nonsense-mediated decay mutants.

Publication Title

Coordinated tissue-specific regulation of adjacent alternative 3' splice sites in C. elegans.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE146556
Global DNA hypomethylation in ovarian cancer
  • organism-icon Homo sapiens
  • sample-icon 55 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Global DNA Hypomethylation in Epithelial Ovarian Cancer: Passive Demethylation and Association with Genomic Instability.

Sample Metadata Fields

Sex, Age, Specimen part, Disease stage

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accession-icon GSE146553
Global DNA hypomethylation in ovarian cancer (Affymetrix_expression_data)
  • organism-icon Homo sapiens
  • sample-icon 55 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Comparison of DNA methylome, mRNA transcriptome, and copy number variation in tumors with global loss of DNA methylation to tumors with normal global methylation.

Publication Title

Global DNA Hypomethylation in Epithelial Ovarian Cancer: Passive Demethylation and Association with Genomic Instability.

Sample Metadata Fields

Sex, Age, Specimen part, Disease stage

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accession-icon GSE10685
Human skeletal muscle biopsies from a 3h IL-6 infusion
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Skeletal muscle has been identified as a secretory organ. We hypothesized that IL-6, a cytokine secreted from skeletal muscle during exercise, could induce production of other secreted factors in skeletal muscle.

Publication Title

Calprotectin is released from human skeletal muscle tissue during exercise.

Sample Metadata Fields

Sex, Subject, Time

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accession-icon GSE60184
UCSD GBM Data Set
  • organism-icon Homo sapiens
  • sample-icon 21 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Total RNA microarray data from Fresh-Frozen Glioblastoma tumor samples.

Publication Title

Epigenetic suppression of EGFR signaling in G-CIMP+ glioblastomas.

Sample Metadata Fields

Specimen part, Disease stage

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accession-icon SRP040292
Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors
  • organism-icon Homo sapiens
  • sample-icon 1 Downloadable Sample
  • Technology Badge IconIlluminaHiSeq2000

Description

We performed mRNA-seq of a PRKACA-mutant adrenal tumor and demonstrated that the mutation is expressed at the mRNA level. Overall design: Total RNA obtained from a cortisol-producing adrenal tumor with a PRKACA p.Leu206Arg mutation.

Publication Title

Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP064433
RNA sequencing of e15.5 pancreas from Wild Type, Blinc1-/- and Blinc+/- mice.
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

We report the transcriptome changes that result of the genomic deletion of one or two alleles of an islet-specific long non-coding RNA (Blinc1) in isolated pancreas from e15.5 mouse embryos. Overall design: Pancreas from e15.5 embryos were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq.

Publication Title

βlinc1 encodes a long noncoding RNA that regulates islet β-cell formation and function.

Sample Metadata Fields

Specimen part, Subject

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accession-icon SRP027383
Whole transcriptome sequencing in 274 glioma patients reveals gene fusion profiling and novel candidate fusion genes
  • organism-icon Homo sapiens
  • sample-icon 270 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

We detected fusion genes in 274 fresh surgical samples of gliomas using whole transcriptome sequencing. Using this approach we screened a panel of glioma samples and identified a number of activating novel fusion transcripts. Overall design: Fusion detection in 274 glioma patients

Publication Title

RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas.

Sample Metadata Fields

Subject

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accession-icon GSE55487
Isolation and genomic characterization of cancer stem cells in head and neck cancer
  • organism-icon Homo sapiens
  • sample-icon 30 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

This study investigated the use of three different established cell sorting strategies to isolate and characterize stem cells from head and neck cancer cell lines.

Publication Title

Isolation and genomic characterization of stem cells in head and neck cancer.

Sample Metadata Fields

Cell line

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accession-icon GSE18583
Baseline skeletal muscle gene expression
  • organism-icon Homo sapiens
  • sample-icon 40 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Muscle biopsy samples were obtained from two groups of male subjects prior to endurance training. The samples were used to predict training responses.

Publication Title

Using molecular classification to predict gains in maximal aerobic capacity following endurance exercise training in humans.

Sample Metadata Fields

Sex

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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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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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