refine.bio
  • Search
      • Normalized Compendia
      • RNA-seq Sample Compendia
  • Docs
  • About
  • My Dataset
github link
Showing
of 112 results
Sort by

Filters

Organism

Technology

Platform

accession-icon GSE23724
Genes differentially regulated by the glucocorticoid receptor in developing skin of the GR knock out and wt embryos.
  • organism-icon Mus musculus
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

To understand the transcriptional program by which GR regulates skin development, we performed a microarray analysis using the skin of E18.5 GR-/- and GR+/+ mouse embryos.

Publication Title

Glucocorticoid receptor regulates overlapping and differential gene subsets in developing and adult skin.

Alternate Accession IDs

E-GEOD-23724

Sample Metadata Fields

Specimen part

View Samples
accession-icon SRP100615
RNA-seq transcriptomics of the Atp7b-/- mouse liver at six weeks of age
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer IIx, Illumina HiSeq 2000

Description

We report liver transcript profiling by RNA sequencing of Atp7b-/- and wild type mice at six weeks of age. Transcriptional network analysis of RNA-seq data reveals a highly interconnected network of transcriptional activators with over-representation of zinc-dependent and zinc-responsive transcription factors. Overall design: Wild type and Atp7b-/- Mice were maintained on strain C57BL x 129S6/SvEv. Housing was in shoebox cages and fed Mazuri Rodent diet (PMI Nutrition, Inc., Richmond, Indiana), containing 16 ppm Cu, 100 ppm Zn, and 235 ppm Fe and water ad libitum, with a 12-hour light/dark cycle. Six-week-old mice of both sexes were used for transcriptomic studies. Animals were sacrificed by carbon dioxide asphyxiation and liver tissue was harvested for RNA isolation. RNA sequencing was performed at the National Center for Genome Resources (NCGR) using the GAIIx platform. Average read quality was 38. An initial dataset was generated using two wild type and two Atp7b-/- samples with singleton 1x54 runs with 15,823,058; 8,149,631; 22,931,967 and 9,538,147 reads. A second paired end (2x54) dataset was generated to augment the initial singleton dataset with one wild type and one Atp7b-/- run resulting in 36,360,686 and 38,366,743 reads, respectively.

Publication Title

Altered zinc balance in the Atp7b<sup>-/-</sup> mouse reveals a mechanism of copper toxicity in Wilson disease.

Alternate Accession IDs

GSE95260

Sample Metadata Fields

Sex, Specimen part, Cell line, Subject

View Samples
accession-icon SRP066440
Simultaneous pathway activity inference and global gene expression analysis using RNA-sequencing [myd88]
  • organism-icon Mus musculus
  • sample-icon 383 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

Two 96-well plates per genotype wild type and Myd88 knockout, 4 hour time series in 0.5 hr increments Overall design: Myd88 BMDM transcriptional profiling to complement TF-seq data

Publication Title

Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.

Alternate Accession IDs

GSE75210

Sample Metadata Fields

Sex, Age, Specimen part, Cell line, Treatment, Subject, Time

View Samples
accession-icon SRP066443
Simultaneous pathway activity inference and global gene expression analysis using RNA-sequencing [halofuginone]
  • organism-icon Mus musculus
  • sample-icon 120 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

Bone marrow derived macrophages treated with small molecules and stimulated with LPS Overall design: Wild-type BMDMs pretreated with small molecules for 30 minutes prior to stimulation with LPS

Publication Title

Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.

Alternate Accession IDs

GSE75209

Sample Metadata Fields

Sex, Age, Specimen part, Cell line, Treatment, Subject, Time

View Samples
accession-icon SRP066437
Simultaneous pathway activity inference and global gene expression analysis using RNA-sequencing [SM screen]
  • organism-icon Mus musculus
  • sample-icon 96 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

Bone marrow derived macrophages treated with small molecules and stimulated with LPS Overall design: Wild-type BMDMs pretreated with small molecules for 30 minutes prior to stimulation with LPS

Publication Title

Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.

Alternate Accession IDs

GSE75211

Sample Metadata Fields

Sex, Age, Specimen part, Cell line, Treatment, Subject

View Samples
accession-icon GSE61643
PGC-1 Promotes Enterocyte Lifespan and Tumorigenesis in the Intestine
  • organism-icon Mus musculus
  • sample-icon 17 Downloadable Samples
  • Technology Badge IconIllumina MouseRef-8 v2.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

PGC-1β promotes enterocyte lifespan and tumorigenesis in the intestine.

Alternate Accession IDs

E-GEOD-61643

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE61642
Genome-wide analysis expression of ileum tumor samples from FVBN/APCmin and iPGC-1/APCmin
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina MouseRef-8 v2.0 expression beadchip

Description

Analysis of metabolic pathway gene expression. The hypothesis tested in the present study is to assess mRNA level changes in metabolic genes in intestinal tumors from APCmin mice overexpressing PGC-1 specifically in the intestine.

Publication Title

PGC-1β promotes enterocyte lifespan and tumorigenesis in the intestine.

Alternate Accession IDs

E-GEOD-61642

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE61640
Genome-wide analysis expression of ileum samples from PGC-1 fl/? and iKOPGC-1
  • organism-icon Mus musculus
  • sample-icon 5 Downloadable Samples
  • Technology Badge IconIllumina MouseRef-8 v2.0 expression beadchip

Description

Analysis of metabolic pathway gene expression. The hypothesis tested in the present study is to assess mRNA level changes in metabolic genes in enterocytes from intestine specific PGC-1 konckout mice.

Publication Title

PGC-1β promotes enterocyte lifespan and tumorigenesis in the intestine.

Alternate Accession IDs

E-GEOD-61640

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE15072
Mitochondrial dysregulation and oxidative stress in patients with chronic kidney disease
  • organism-icon Homo sapiens
  • sample-icon 34 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

Several reports have focused on the identification of biological elements involved in the development of abnormal systemic biochemical alterations in chronic kidney disease, but this abundant literature results most of the time fragmented. To better define the cellular machinery associated to this condition, we employed an innovative high-throughput approach based on a whole transcriptomic analysis and classical biomolecular methodologies. The genomic screening of peripheral blood mononuclear cells revealed that 44 genes were up-regulated in both chronic kidney disease patients in conservative treatment (CKD, n=9) and hemodialysis (HD, n=17) compared to healthy subjects (NORM) (p<0.001, FDR=1%). Functional analysis demonstrated that 11/44 genes were involved in the oxidative phosphorylation system (OXPHOS). Western blotting for COXI and COXIV, key constituents of the complex IV of OXPHOS, performed on an independent testing-group (12 NORM, 10 CKD and 14 HD) confirmed the elevated synthesis of these subunits in CKD/HD patients. However, complex IV activity was significantly reduced in CKD/HD patients compared to NORM (p<0.01). Finally, CKD/HD patients presented higher reactive oxygen species and 8-hydroxydeoxyguanosine levels compared to NORM. Taken together these results suggest, for the first time, that CKD/HD patients may have an impaired mitochondrial respiratory system and this condition may be both the consequence and the cause of an enhanced oxidative stress.

Publication Title

Mitochondrial dysregulation and oxidative stress in patients with chronic kidney disease.

Alternate Accession IDs

E-GEOD-15072

Sample Metadata Fields

Disease, Treatment, Subject

View Samples
accession-icon SRP183811
Spatial and Temporal Mapping of Human Innate Lymphoid Cells Reveals Elements of Tissue Specificity
  • organism-icon Homo sapiens
  • sample-icon 95 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

We provide a map of human ILC heterogeneity across multiple anatomical sites. Tissue-specific distinctions are particularly apparent for ILC1 populations, whose distribution was markedly altered in obesity or aging. Furthermore, the degree of ILC1 population hetero- geneity differed substantially in lymphoid versus mucosal sites. Together, these analyses comprise a comprehensive characterization of the spatial and temporal dynamics regulating the anatomical distri- bution, subset heterogeneity, and functional poten- tial of ILCs in non-diseased human tissues. Overall design: We present a quantitative analysis of ILC distribution and heterogeneity in lymphoid, mucosal, and metabolic tissues obtained from a diverse cohort of 44 previously non-diseased organ donors over a wide range of ages and body mass indexes (BMIs).

Publication Title

Spatial and Temporal Mapping of Human Innate Lymphoid Cells Reveals Elements of Tissue Specificity.

Alternate Accession IDs

GSE126107

Sample Metadata Fields

Specimen part, Subject

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