refine.bio
  • Search
      • Normalized Compendia
      • RNA-seq Sample Compendia
  • Docs
  • About
  • My Dataset
github link
Showing
of 43 results
Sort by

Filters

Organism

Technology

Platform

accession-icon GSE60249
PPAR controls alveolar macrophage identity
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.1 ST Array (mogene11st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Induction of the nuclear receptor PPAR-γ by the cytokine GM-CSF is critical for the differentiation of fetal monocytes into alveolar macrophages.

Alternate Accession IDs

E-GEOD-60249

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE60247
PPAR controls alveolar macrophage identity [part1]
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.1 ST Array (mogene11st)

Description

Tissue-resident macrophages comprise heterogeneous populations with unique functions and distinct gene expression signatures. While it has been established that they mostly originate from embryonic progenitors, the signals inducing a characteristic tissue-specific differentiation program remain unknown. Here we identify PPAR as the crucial transcription factor determining perinatal alveolar macrophage (AM) development and identity. Development of the fetal monocyte derived AM precursor was largely abrogated in CD11c-Cre/Ppargfl/fl mice. To reveal the underlying changes in gene expression, we performed microarray analysis of sorted WT and KO AM and pre-AM from 3 different timepoints.

Publication Title

Induction of the nuclear receptor PPAR-γ by the cytokine GM-CSF is critical for the differentiation of fetal monocytes into alveolar macrophages.

Alternate Accession IDs

E-GEOD-60247

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE60248
PPAR controls alveolar macrophage identity [part2]
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.1 ST Array (mogene11st)

Description

Tissue-resident macrophages comprise heterogeneous populations with unique functions and distinct gene expression signatures. While it has been established that they mostly originate from embryonic progenitors, the signals inducing a characteristic tissue-specific differentiation program remain unknown. Here we identify PPAR as the crucial transcription factor determining perinatal alveolar macrophage (AM) development and identity. Development of the fetal monocyte derived AM precursor was largely abrogated in CD11c-Cre/Ppargfl/fl mice. To reveal the underlying changes in gene expression, we performed microarray analysis of sorted WT and KO AM and pre-AM from 3 different timepoints.

Publication Title

Induction of the nuclear receptor PPAR-γ by the cytokine GM-CSF is critical for the differentiation of fetal monocytes into alveolar macrophages.

Alternate Accession IDs

E-GEOD-60248

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP041461
A new dataset of spermatogenic vs oogenic transcriptomes in the nematode C. elegans
  • organism-icon Caenorhabditis elegans
  • sample-icon 57 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The nematode Caenorhabditis elegans is an important model for studies of germ cell biology, including specification as sperm or oocyte, the meiotic cell cycle and gamete differentiation. Fundamental to those studies is a genome-level knowledge of the germline transcriptome. Here we use RNA-Seq to identify genes expressed in isolated XX gonads, which are roughly 95% germline and 5% somatic gonadal tissue. We generate data from mutants making either sperm [fem-3(q96)] or oocytes (fog-2), both grown at 22°C. Our dataset identifies a total of 10,754 mRNAs in the polyadenylated transcriptome of XX gonads, with 1,723 enriched in spermatogenic gonads, 2,869 enriched in oogenic gonads and the remaining 6,274 not enriched in either. These spermatogenic, oogenic and gender-neutral gene datasets compare well with those of earlier studies, but double the number of genes identified. We also query our RNA-Seq data for differential exon usage and find 351 mRNAs with sex-specific isoforms. We suggest that this new dataset will prove useful for studies focusing on C. elegans germ cell biology. Overall design: Comparison of spermatogenic vs oogenic transcriptomes

Publication Title

A new dataset of spermatogenic vs. oogenic transcriptomes in the nematode Caenorhabditis elegans.

Alternate Accession IDs

GSE57109

Sample Metadata Fields

Specimen part, Cell line, Subject

View Samples
accession-icon GSE13982
Effect of CORM-2 on E. coli transcriptome
  • organism-icon Escherichia coli str. k-12 substr. mg1655
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix E. coli Genome 2.0 Array (ecoli2)

Description

We recently reported that carbon monoxide (CO) has bactericidal activity. To understand its mode of action we analysed the gene expression changes occurring when Escherichia coli, grown aerobically and anaerobically, is treated with the carbon monoxide releasing molecule, CORM-2. The E. coli microarray analysis shows that E. coli CORM-2 response is multifaceted with a high number of differentially regulated genes spread through several functional categories, namely genes involved in inorganic ion transport and metabolism, regulators, and genes implicated in posttranslational modification, such as chaperones. CORM-2 has higher impact in E. coli cells grown anaerobically, as judged by the existence of repressed genes belonging to eight functional classes which are absent in aerobically CORM-2 treated cells. In spite of the relatively stable nature of the CO molecule, our results show that CO is able to trigger a significant alteration in the transcriptome of E. coli which necessarily has effects in several key metabolic pathways.

Publication Title

Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli.

Alternate Accession IDs

E-GEOD-13982

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE73070
RIP-Chip analysis of the C. elegans FOG-1 and FOG-3 proteins
  • organism-icon Caenorhabditis elegans
  • sample-icon 40 Downloadable Samples
  • Technology Badge Icon Affymetrix C. elegans Genome Array (celegans)

Description

FOG-1/CPEB and FOG-3/Tob are the terminal regulators of the sex determination in C. elegans germ cells. CPEB and Tob proteins are both translational regulators. To investigate how FOG-1 and FOG-3 regulate germ cell sex determination we sought to identify the target mRNAs. We used transgenic epitope tagged animals (3xMyc::FOG-1 and FOG-3::3xFLAG). To identify the mRNA targets of FOG-1/CPEB and FOG-3/Tob on a genome wide scale we used RNA immunoprecipitation followed by microarray analysis. We found 81 putative mRNA targets of FOG-1 and 722 putative targets of FOG-3. 76 target mRNAs were common to both FOG-1 and FOG-3.

Publication Title

Genomic Analyses of Sperm Fate Regulator Targets Reveal a Common Set of Oogenic mRNAs in Caenorhabditis elegans.

Alternate Accession IDs

E-GEOD-73070

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE18854
Time course analysis of dedifferentiation in porcine follicular granulosa cells
  • organism-icon Sus scrofa
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Porcine Genome Array (porcine)

Description

Cellular dedifferentiation signifies the withdrawal of cells from a specific differentiated state into a stem cell-like undifferentiated state. However, the mechanism of dedifferentiation remains obscure. We showed that follicular granulosa cells (GC), which have distinct functions in vivo, can dedifferentiate during culture in vitro and acquire multipotency.

Publication Title

Dedifferentiated follicular granulosa cells derived from pig ovary can transdifferentiate into osteoblasts.

Alternate Accession IDs

E-GEOD-18854

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE27642
MiRNA-127 Inhibits IgG Immune Complex-induced Lung Inflammation by Targeting IgG Fc Receptor I
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

The molecular mechanisms of acute lung injury are incompletely understood. MicroRNAs (miRNAs) are crucial biological regulators that act by suppressing their target genes and are involved in a variety of pathophysiologic processes. MiR-127 appeared to be down-regulated during lung injury. We set out to investigate the role of miR-127 in lung injury and inflammation. Expression of miR-127 significantly reduced cytokine release by macrophages. Looking into the mechanisms of the regulation of inflammation by miR-127, we found that IgG Fc Receptor I (FcRI/CD64) was a target of miR-127, as evidenced by reduced CD64 protein expression in macrophages over-expressing miR-127. Furthermore, miR-127 significantly reduced the luciferase activity with a reporter construct containing the native 3-UTR of CD64. Importantly, we demonstrated that miR-127 attenuated lung inflammation in an IgG immune complex (IgG IC) model in vivo. Collectively, these data show that miR-127 targets macrophage CD64 expression and promotes the reduction of lung inflammation. Understanding how miRNAs regulate lung inflammation may represent an attractive way to control inflammation induced by infectious or non-infectious lung injury.

Publication Title

MicroRNA-127 inhibits lung inflammation by targeting IgG Fcγ receptor I.

Alternate Accession IDs

E-GEOD-27642

Sample Metadata Fields

Cell line

View Samples
accession-icon GSE97198
RNA expression across 6 strains of mice in relation to prepulse inhibition testing, as described in: Pdxdc1 (pyridoxal-dependent decarboxylase domain containing 1) modulates pre-pulse inhibition of acoustic startle in the mouse
  • organism-icon Mus musculus
  • sample-icon 54 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

C3H/HeJ, BalbC/J, C57BL/6J, C57BL10/J, C57BLKS/J, C57L/J strains were tested for variability in gene expression in hippocampus, striatal, and brainstem tissues to affiliate findings with behavioural prepulse inhibition scores

Publication Title

Pdxdc1 modulates prepulse inhibition of acoustic startle in the mouse.

Alternate Accession IDs

E-GEOD-97198

Sample Metadata Fields

Sex, Specimen part

View Samples
accession-icon GSE64809
Gene Expressoin Profile in the Hypothalamus and Liver of Male Bgn_KO, FMOD_KO and WT Mice at 13 Weeks Old, With and Without DHA (omega-3) Treatment
  • organism-icon Mus musculus
  • sample-icon 15 Downloadable Samples
  • Technology Badge IconIllumina MouseRef-8 v2.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Biglycan gene connects metabolic dysfunction with brain disorder.

Alternate Accession IDs

E-GEOD-64809

Sample Metadata Fields

Sex, Age, 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)

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