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accession-icon SRP049716
RNA sequencing of the developing zebrafish head
  • organism-icon Danio rerio
  • sample-icon 3 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

We sequenced strand-specific mRNA from the heads of 3 groups of wild type zebrafish (Danio rerio) 5 days post fertilization. Overall design: Examination of the relative expression of genes in the developing zebrafish brain

Publication Title

BRF1 mutations alter RNA polymerase III-dependent transcription and cause neurodevelopmental anomalies.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE14363
Expression data from adipocytes and white adipose tissue of mice maintained on normal chow or high fat diet
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)

Description

We studied the role of the cAMP responsive factor CREB in promoting insulin resistance following its activation in adipose under obese conditions

Publication Title

Adipocyte CREB promotes insulin resistance in obesity.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE104403
Expression data in Ucp2+/+ (WT) and Ucp2-/- (KO) colon tumors from AOM/DSS-treated mice
  • organism-icon Mus musculus
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

The objective of the study was to evalute the changes in gene expression associated to UCP2 invalidation in colon tumors from AOM/DSS-treated mice

Publication Title

UCP2 Deficiency Increases Colon Tumorigenesis by Promoting Lipid Synthesis and Depleting NADPH for Antioxidant Defenses.

Sample Metadata Fields

Specimen part

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accession-icon GSE58460
Rheumatoid Arthritis Rat Model Treated with Acupuncture
  • organism-icon Rattus norvegicus
  • sample-icon 38 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Systemic Wound Healing Associated with local sub-Cutaneous Mechanical Stimulation.

Sample Metadata Fields

Sex, Specimen part

View Samples
accession-icon GSE48025
Affymetrix Chip Data of the Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture (Affymetrix, mRNA, batch1)
  • organism-icon Rattus norvegicus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

We report the application of Affymetrix technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA), with acupuncture, Methotrexate, Isofluorane anesthetic and placebo treatments, as well as the healthy control.

Publication Title

Systemic Wound Healing Associated with local sub-Cutaneous Mechanical Stimulation.

Sample Metadata Fields

Sex, Specimen part

View Samples
accession-icon SRP043193
Short Read Sequencing Data of the Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture (HiSeq 2000, miRNA, batch 1)
  • organism-icon Rattus norvegicus
  • sample-icon 19 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

We report the application of Illumina Hiseq2000 sequencing technology for high-throughput miRNA profiling of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA), with acupuncture and placebo treatments. Overall design: The experiment is designed as 2 arms: epidermal needle manipulation (AP/MEC) and placebo (PLA, used as control) on CIA induced rheumatoid arthritis (RA) rats. Muscle tissue samples sampling was carried out before any therapy in RA rats (RA_T0), and after at 1 hour and 34 days of therapeutic treatments for both AP and PLA. From all the 10 blood collected samples (2 replicates for each group, for each timepoint), total RNA were extracted. Finally, purified RNA were analyzed using illumina hiseq 2000).

Publication Title

Systemic Wound Healing Associated with local sub-Cutaneous Mechanical Stimulation.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE58456
Affymetrix Chip Data of the Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture (Affymetrix, mRNA, batch 2)
  • organism-icon Rattus norvegicus
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

We report the application of Affymetrix technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA), with acupuncture and Methotrexate+acupuncture treatment, as well as epidermal needle manipulation on healthy rat model.

Publication Title

Systemic Wound Healing Associated with local sub-Cutaneous Mechanical Stimulation.

Sample Metadata Fields

Sex, Specimen part

View Samples
accession-icon SRP043707
Short Read Sequencing Data of the Transcriptome of the Rheumatoid Arthritis and Treated with Acupuncture or not
  • organism-icon Rattus norvegicus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

We report the application of Illumina Hiseq2000 sequencing technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA) and treated with acupuncture or not. Overall design: 2 rats in total, i.e., 2 replicates RA rat model before treatment (RA1, 2) for 3 in vitro culture conditions (standard serum FBS, blood serum from animals acupuncture treated AP+, blood serum from animals acupuncture untreated AP-).

Publication Title

Systemic Wound Healing Associated with local sub-Cutaneous Mechanical Stimulation.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE8868
Comparison of splenic and small intestine lamina propria macrophages
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

The intestinal immune system must elicit robust immunity against harmful pathogens but restrain immune responses directed against commensal microbes and dietary antigens. The mechanisms that maintain this dichotomy are poorly understood. Here we describe a population of CD11b+F4/80+CD11c macrophages in the lamina propria (LP) that express several anti-inflammatory molecules including interleukin 10 (IL-10), but little or no pro-inflammatory cytokines, even upon stimulation with Toll-like receptor (TLR) ligands. These macrophages induced, in a manner dependent on IL-10, retinoic acid and exogenous transforming growth factor-, differentiation of FoxP3+ regulatory T cells. In contrast, LP CD11b+ dendritic cells elicited IL-17 production. This IL-17 production was suppressed by LP macrophages, indicating that a dynamic interplay between these subsets may influence the balance between immune activation and tolerance.

Publication Title

Lamina propria macrophages and dendritic cells differentially induce regulatory and interleukin 17-producing T cell responses.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE18897
Whole blood expression profiling of obese diet-sensitive, obese diet-resistant and lean human subjects
  • organism-icon Homo sapiens
  • sample-icon 77 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

We have carried out whole-genome expression profiling of whole blood from obese subjects, defined as obese diet-sensitive and obese diet-resistant, and well matched lean individuals. The diet-sensitive or diet-resistant status refers to the different rates of weight loss observed in the two groups on a low-calorie diet regimen. Bioinformatic analysis revealed alterations in transcription in key pathways that are consistent with impaired capacity for fatty acid oxidation driven mitochondrial ATP synthesis in obese subjects who are resistant to weight loss.

Publication Title

Gene expression profiling in whole blood identifies distinct biological pathways associated with obesity.

Sample Metadata Fields

Sex, Subject, Time

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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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