refine.bio
  • Search
      • Normalized Compendia
      • RNA-seq Sample Compendia
  • Docs
  • About
  • My Dataset
github link
Showing
of 250 results
Sort by

Filters

Organism

Technology

Platform

accession-icon GSE153391
Expression data from adipocyte differentiation from diabetic adipose-derived stem cells (dADSC) treated with squalene (Sq) and its derivative (HH-Sq)
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U219 Array (hgu219)

Description

Gene expression profiling reveals functional difference between Sq and HH-Sq on differentiation, metabolism, and lipid droplot formation of dADSC

Publication Title

New Amphiphilic Squalene Derivative Improves Metabolism of Adipocytes Differentiated From Diabetic Adipose-Derived Stem Cells and Prevents Excessive Lipogenesis.

Alternate Accession IDs

E-GEOD-153391

Sample Metadata Fields

Specimen part, Disease, Disease stage

View Samples
accession-icon SRP001893
Regulation of alternative splicing by histone modifications
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIlluminaGenomeAnalyzer

Description

Alternative splicing of pre-mRNA is a prominent mechanism to generate protein diversity, yet its regulation is poorly understood. Here, we demonstrate a direct role for histone modifications in alternative splicing. We find distinctive histone modification signatures which correlate with splicing outcome in a set of human genes. Modulation of histone modifications causes splice site switching. The mechanism for histone-mediated splice site selection involves a histone mark which is read by a chromatin protein, which in turn recruits a splicing regulator. These results outline an adaptor system for reading of histone marks by the pre-mRNA splicing machinery. Overall design: To obtain an estimate of how many PTB-dependent alternative splicing events are regulated by SET2/MRG15-mediated recruitment of PTB, we carried out a genomewide comparative analysis of alternative splicing in hMSC cells depleted of either SETD2, MRG15 or PTB using specific siRNAs, or mock-depleted using a control siRNA.

Publication Title

Regulation of alternative splicing by histone modifications.

Alternate Accession IDs

GSE19373

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE19251
KKTa_isolated glomeruli
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

High dietary fat intake is a major risk factor for the development of obesity, which is frequently associated with diabetes. To identify genes involved in diabetic nephropathy, GeneChip Expression Analysis was employed to survey the glomerular gene expression profile in diabetic KK/Ta mice fed with a high-fat diet (HFD).

Publication Title

Mindin: a novel marker for podocyte injury in diabetic nephropathy.

Alternate Accession IDs

E-GEOD-19251

Sample Metadata Fields

Sex, Age

View Samples
accession-icon GSE148775
Expression data from water extracted olive leaf (WOL)-treated CD34+ cells
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U219 Array (hgu219)

Description

Gene expression profiling reveals a potential role of WOL in differentiation of CD34+ cells towards erythropoiesis

Publication Title

Comprehensive transcriptome analysis of erythroid differentiation potential of olive leaf in haematopoietic stem cells.

Alternate Accession IDs

E-GEOD-148775

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE137998
Expression profiling of cervical cancer cells with IGF2R knock down
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

From comprehensive expression analysis of RNAseq data, IGF2R was found to correlate with poor prognosis in cervical cancer. Gene knockdown of IGF2R lead to cell death in cervical cancer. To reveal its biological function, we performed microarray analysis using IGF2R knockdown cervical cancer cells.

Publication Title

Upregulation of IGF2R evades lysosomal dysfunction-induced apoptosis of cervical cancer cells via transport of cathepsins.

Alternate Accession IDs

E-GEOD-137998

Sample Metadata Fields

Cell line

View Samples
accession-icon SRP047155
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Jmjd6-/- Thymic stromal Transcriptomes
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The goals of this study are to comprehensively identify genes controlled by Jmjd6 in the thymic stroma, and to identify a novel alternative splicing mechanism. Methods: Samples were WT and Jmjd6-/- fetal thymus organ culture with (2 samples for each category) or without (1 sample for each category) RANKL stimulation for 4 days under 2-DG. One µg of total RNA was used for library construction with TruSeq RNA Sample Prep Kit v2. THe ligated products were amplified using 8 cycles of PCR to generate RNA-seq library. Library integrity was verified by Bioanalyzer DNA1000 assay. Sequencing was performed in 101-bp paired-end mode using an Illumina HiSeq.Technical duplicate has done. Results: A total of 177,060,020 reads were obtained for 6 samples. Filtered reads were mapped to the UCSC mm10 using the TopHat program(v2.0.10) with the default parameters. The Cufflinks program (v2.1.1) was then used to assemble 22,448 transcripts and to calculate the fragments per kilobase of exon per million mapped fragments(FPKM) values, which are normalized measurement of gene expression levels(= genes-FPKM file).To identify differentially expressed genes, the ratio of the maximum FPKM to the minimum FPKM was compared among 6 samples. When the ratio was more than 3, the gene was regarded as being significantly altered in expression level. We added 0.1 to the FPKM value to avoid division by zero. This led us to identify 3212 genes with differential expression. Among these, the expression levels of 2536 genes were significantly associated with the RANKL treatment or Jmjd6 expression ( P value <0.05). Analysis for intron retention was performed as follows. According to the current gene annotation ("known genes" in UCSC mm10), there are 188,208 introns in total. As intron retention events should be observed in the genes with relatively high expression, we only focused on the genes with the maximum FPKM value more than 10 at least in one of the six samples. As a result, we obtained 84,708 introns. The reads mapped to these intronic regions were counted by the intersectBed program in the BEDTools utilities with -c option, and the counts are converted into the FPKM values for each intron (intronic FPKM). There are 1051 introns with intronic FPKM more than 10 in at last on of the six samples, and the degree of intron retention was calculated by dividing intronic FPKM value by conventional FPKM value for each gene (intron-FPKM file). Overall design: Samples were WT and Jmjd6-/- fetal thymus organ culture with (2 samples for each category) or without (1 sample for each category) RANKL stimulation for 4 days under 2-DG. One µg of total RNA was used for library construction with TruSeq RNA Sample Prep Kit v2. THe ligated products were amplified using 8 cycles of PCR to generate RNA-seq library. Library integrity was verified by Bioanalyzer DNA1000 assay. Sequencing was performed in 101-bp paired-end mode using an Illumina HiSeq.Technical duplicate has done.

Publication Title

Intronic regulation of Aire expression by Jmjd6 for self-tolerance induction in the thymus.

Alternate Accession IDs

GSE61444

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE42904
Reduced adult neurogenesis and neuronal abnormalities in the hippocampus underlie cognitive deficiency following prenatal administration of the anti-epileptic drug valproic acid
  • organism-icon Mus musculus
  • sample-icon 59 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Prenatal exposure to valproic acid, an established anti-epileptic drug, has been reported to impair postnatal cognitive function of children from epileptic mothers. Nevertheless, its pathology and proper treatment to minimize the effects remain unknown. In mice, we found that the postnatal cognitive function impairment was mainly caused by a reduction of adult neurogenesis and abnormal neuronal features in the hippocampus, which could be ameliorated by voluntary running.

Publication Title

Reduced Adult Hippocampal Neurogenesis and Cognitive Impairments following Prenatal Treatment of the Antiepileptic Drug Valproic Acid.

Alternate Accession IDs

E-GEOD-42904

Sample Metadata Fields

Sex, Specimen part, Treatment

View Samples
accession-icon GSE17043
Molecular and functional characterization of FD-iPSC derived neural crest precursor cells
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge IconIllumina human-6 v2.0 expression beadchip

Description

Global gene expression analysis of FD-iPSC and deribved neural crest cells

Publication Title

Modelling pathogenesis and treatment of familial dysautonomia using patient-specific iPSCs.

Alternate Accession IDs

E-GEOD-17043

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE19735
Comparison of human embroynic stem cell derived vascular cells to mature human vascular and hematopoietic cells
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

The pathways involved in hierarchical differentiation of human embryonic stem cells (hESC) into abundant and durable endothelial cells (EC) are unknown. We employed an EC-specific VE-cadherin promoter driving GFP (hVPr-GFP) to screen for factors that augmented yields of vascular-committed ECs from hESCs. In phase 1 of our approach, inhibition of TGFb, precisely at day 7 of hESC differentiation, enhanced emergence of hVPr-GFP+ ECs by 10-fold. In the second phase, TGFb-inhibition preserved proliferation and vascular identity of purified ECs, resulting in net 36-fold expansion of homogenous EC-monolayers, and allowing transcriptional profiling that revealed a unique angiogenic signature defined by the VEGFR2highId1highVE-cadherin+EphrinB2+CD133+HoxA9- phenotype. Using an Id1-YFP hESC reporter line, we showed that TGFb-inhibition sustained Id1 expression in hESC-derived ECs, which was required for increased proliferation and preservation of EC commitment. These data provide a multiphasic method for serum-free differentiation and long-term maintenance of authentic hESC-derived ECs, establishing clinical-scale generation of transplantable human ECs.

Publication Title

Expansion and maintenance of human embryonic stem cell-derived endothelial cells by TGFbeta inhibition is Id1 dependent.

Alternate Accession IDs

E-GEOD-19735

Sample Metadata Fields

Specimen part

View Samples
accession-icon E-MEXP-515
Transcription profiling of diabetic neuropathy in dorsal root ganglia from streptozotocin-diabetic male wistar rats over the first 8 weeks of diabetes
  • organism-icon Rattus norvegicus
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302), UNKNOWN

Description

A study of diabetic neuropathy in dorsal root ganglia from streptozotocin-diabetic male wistar rats over the first 8 weeks of diabetes

Publication Title

Identification of changes in gene expression in dorsal root ganglia in diabetic neuropathy: correlation with functional deficits.

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Disease stage, Time

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)

fund-icon Fund the CCDL

Developed by the Childhood Cancer Data Lab

Powered by Alex's Lemonade Stand Foundation

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.

BSD 3-Clause LicensePrivacyTerms of UseContact
Version 1.42.67-hotfix - .0.0