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accession-icon GSE30172
Expression data from Porcine alveolar macrophages infection with Haemophilus parasuis (HPS)
  • organism-icon Sus scrofa
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Porcine Genome Array (porcine)

Description

Porcine alveolar macrophages (PAMs) play impoartant role in innate immunity. Haemophilus parasuis is the etiological agent of Glassers disease in pigs.

Publication Title

Transcription analysis on response of porcine alveolar macrophages to Haemophilus parasuis.

Sample Metadata Fields

Specimen part, Disease, Disease stage

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accession-icon SRP189243
RNA sequencing data of human prostate cancer cells treated with androgen
  • organism-icon Homo sapiens
  • sample-icon 11 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

To analyse and understand the differentially expressed genes following treatment with synthetic androgen (R1881) Overall design: LNCaP or LAPC4 cells were plated in RPMI 1640 media with no phenol red and with 5% charcoal stripped serum, sodium pyruvate, penicillin and streptomycin. After 48h (to allow adnrogen deprivation), fresh media was added, with 96% ethanol or the synthetic androgen R1881 (10nM concentration). 24h later, cells were harvested for RNA purification using the QIAGEN RNeasy plus purification kit. RNA was then enriched for mRNA and then sequenced.

Publication Title

RNA sequencing data of human prostate cancer cells treated with androgens.

Sample Metadata Fields

Treatment, Subject

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accession-icon SRP059586
Genome-wide analysis of embryonic gene epression in the absence of Prox1 compared to wild type
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Overview: We report here that gene expression in E13.5 wild type (WT) mouse lenses differs from the lenses of mice that conditionally lack the Prox1 transcription factor in the lens of their eyes (Prox1 cKO) as assayed by high throughput RNA sequencing (RNAseq). The methodology outlined herein is similar to a previous RNAseq experiment from our lab (Manthey et al., 2014a)(Geo ascension: GSE 49949), and the filtering and processing criteria for this experiment was published as well.(Manthey et al., 2014b). The mammalian lens is notable for its biased gene expression, where 90% of the observed protein is expressed by just 50 genes. RNAseq was employed to sequence past these highly expressed lens structural genes and report the relative abundance of both high and low expression genes. In this study we demonstrated that 642 genes were differentially expressed in the lenses of Prox1 cKOs as compared to WT lenses. These data were analyzed using the DAVID biostatical analysis package and we found that the expression of lens specific proteins, as well as cytoskeletal genes and genes that regulated the cytoskeleton were expressed at lower levels in Prox1 cKOs. This analysis showed that the expression of genes encoding extracellular matrix components and their regulators, as well as cell adhesion increased in Prox1 cKO lenses when compared to WTs. Description of Filtering Criteria: Our initial analysis identified 5,492 genes that were differentially expressed in Prox1 cKO lenses as compared to WTs as computed by Pair-wise qCML method exact tests with a Benjamini Hochberg false discovery rate correction greater than the threshold of P < 0.05. As we described previously, there is significant variation in gene expression between inbred C57Bl/6 <har> and mice with a mixed background below a threshold of 2.5 fold. For this reason we filtered out all genes whose differential expression was less than 2.5 fold. We also wanted to filter out genes that were expressed at such low levels that they were unlikely to impact cellular function. We restricted our list to those genes that were expressed at greater than 2 Reads per Kilobase per million reads (RPKM) in either WT or Prox1 cKO samples, a value which corresponds to approximately 1 mRNA molecule per cell. The application of these filtering criteria resulted in narrowing our list to 642 genes that were likely to impact the Prox1 cKO lens phenotype. Manthey, A. L., Lachke, S. A., FitzGerald, P. G., Mason, R. W., Scheiblin, D. A., McDonald, J. H. and Duncan, M. K. (2014a) ''Loss of Sip1 leads to migration defects and retention of ectodermal markers during lens development'', Mech Dev 131: 86-110. Manthey, A. L., Terrell, A. M., Lachke, S. A., Polson, S. W. and Duncan, M. K. (2014b) ''Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis'', Genom Data 2: 369-374. Overall design: RNA-Seq comparison of C57Bl/6 <har> wild type controls and Prox1 conditional knockout lenses at E13.5

Publication Title

Prox1 and fibroblast growth factor receptors form a novel regulatory loop controlling lens fiber differentiation and gene expression.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP188242
RNA-seq analyses of human prostate cancer cells
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

To study the transcriptome of human prostate cancer cells, RNA-seq experiments were performed. Overall design: RNA was harvested after 72h of steroid deprivation to study the basal transcriptome of LNCaP and 22rv1 cells, two human AR-positive prostate cancer cell lines,

Publication Title

Reprogramming of Isocitrate Dehydrogenases Expression and Activity by the Androgen Receptor in Prostate Cancer.

Sample Metadata Fields

Subject

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accession-icon GSE60762
Expression data of osteoarthritic and healthy human labrum cells
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Osteoarthritic cartilage has largely been investigated, however supporting structures as the acetabular labrum are less investigated. In this studies we aimed to identify differences in gene expression between healthy and osteoarthritic labrum cells

Publication Title

Distinct dysregulation of the small leucine-rich repeat protein family in osteoarthritic acetabular labrum compared to articular cartilage.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE97477
Calcium-mediated shaping of naive CD4 T cell phenotype and function
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

Continuous contact with self-major histocompatibility complex ligands is essential for the survival of naive CD4 T cells. We have previously shown that the resulting tonic TCR signaling also influences their fate upon activation by increasing their ability to differentiate into induced regulatory T cells. To decipher the molecular mechanisms governing this process, microarray data comparing highly (Ly-6C-) and lowly (Ly-6C+) Self-reactive naive CD4 T cells were obtained.

Publication Title

Calcium-mediated shaping of naive CD4 T-cell phenotype and function.

Sample Metadata Fields

Specimen part

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accession-icon GSE43946
Human induced pluripotent stem cells reveal early developmental molecular correlates with a probable Leber congenital amaurosis type I
  • organism-icon Homo sapiens
  • sample-icon 34 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Human induced pluripotent stem cells as a tool to model a form of Leber congenital amaurosis.

Sample Metadata Fields

Sex, Specimen part, Cell line

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accession-icon GSE43924
Global gene expression analysis of human iPSC-derived Neural Stem Cells (NSC) from LCA patients and unaffected persons
  • organism-icon Homo sapiens
  • sample-icon 21 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

Our purpose was to investigate genes and molecular mechanisms involved in patients with Leber congenital amaurosis (LCA). Fibroblasts from two unrelated clinically-identified patients (Coriell) were reprogrammed to pluripotency by retroviral transduction. These human induced Pluripotent Stem Cells (hiPSCs) were differentiated into neural stem cells (NSC) that mimicked the neural tube stage and retinal pigmented epithelial (RPE) cells that could be targeted by the disease. A genome wide transcriptome analysis was performed with Affymetrix Exon Array GeneChip, comparing LCA-hiPSCs derivatives to controls. The aim was to identify differentially expressed genes which may be associated with early developmental defect before the establishment of mature retinal circuitry.

Publication Title

Human induced pluripotent stem cells as a tool to model a form of Leber congenital amaurosis.

Sample Metadata Fields

Sex, Specimen part, Cell line

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accession-icon GSE43926
Global gene expression analysis of human iPSC-derived Retinal Pigmented Epithelial (RPE) cells from LCA patients and unaffected persons
  • organism-icon Homo sapiens
  • sample-icon 13 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

Our purpose was to investigate genes and molecular mechanisms involved in patients with Leber congenital amaurosis (LCA). Fibroblasts from two unrelated clinically-identified patients (Coriell) were reprogrammed to pluripotency by retroviral transduction. These human induced Pluripotent Stem Cells (hiPSCs) were differentiated into neural stem cells (NSC) that mimicked the neural tube stage and retinal pigmented epithelial (RPE) cells that could be targeted by the disease. A genome wide transcriptome analysis was performed with Affymetrix Exon Array GeneChip, comparing LCA-hiPSCs derivatives to controls. The aim was to identify differentially expressed genes which may be associated with early developmental defect before the establishment of mature retinal circuitry.

Publication Title

Human induced pluripotent stem cells as a tool to model a form of Leber congenital amaurosis.

Sample Metadata Fields

Sex, Specimen part, Cell line

View Samples
accession-icon GSE75877
The PGC-1/ERR Axis Represses One-Carbon Metabolism and Promotes Sensitivity to Anti-Folate Therapy in Breast Cancer
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

The PGC-1α/ERRα Axis Represses One-Carbon Metabolism and Promotes Sensitivity to Anti-folate Therapy in Breast Cancer.

Sample Metadata Fields

Specimen part, Cell line

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)

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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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