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accession-icon GSE6300
Expression data from eye antennal imaginal disc expressing either activated Ras or secreted Spitz
  • organism-icon Drosophila melanogaster
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome Array (drosgenome1)

Description

We have used microarrays to identify genes expressed and required for the second mitotic wave (SMW) during eye development. Eye discs expressing Spitz under the control of GMR Gal4 have no SMW as Spitz promotes G1 arrest, ectopic differentiation also occures. To control for the ectopic differentiation, Spi expressing eye antennal discs were compared to eye antennal discs expressing activated RasV12. In discs expresseding RasV12 under the control of GMRGal4 the SMW takes place normally prior to any ectopic differentiation.

Publication Title

Spitz from the retina regulates genes transcribed in the second mitotic wave, peripodial epithelium, glia and plasmatocytes of the Drosophila eye imaginal disc.

Alternate Accession IDs

E-GEOD-6300

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP103000
A memory of early life physical activity is retained in bone marrow of adult rats but does not prevent reversal to obese phenotype
  • organism-icon Rattus norvegicus
  • sample-icon 39 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 4000

Description

Studies have reported opposing effects of high-fat diet and mechanical stimulation on lineage commitment of the bone marrow stem cells. Yet, how the bone marrow modulates its gene expression in response to the combined effects of mechanical loading and a high-fat diet has not yet been addressed. We investigated whether early-life voluntary physical activity can modulate the effects of a high-fat diet on body composition, bone phenotype and bone marrow gene expression in male Sprague Dawley rats. We show that early-life high-fat diet positively affected body weight, total fat percentage and bone mass indices. In the bone marrow, early-life high-fat diet resulted in adipocyte hypertrophy and a pro-inflammatory and pro-adipogenic gene expression profile. Crucially, the bone marrow of the rats that undertook wheel exercise while on a high-fat diet retained a memory of the early-life exercise. This memory lasted at least 60 days after the cessation of the voluntary exercise and was manifest by: 1) the bone marrow adipocyte size of the exercised rats not exhibiting hypertrophy; and 2) genes associated with mature adipocyte function being down-regulated. Our results are consistent with the marrow adipose tissue having a unique and long-lasting response to high-fat feeding in the presence or absence of exercise. Overall design: Eighty male SD rats were randomised at weaning into : chow-fed group (C-SED) or a high-fat fed group. The high-fat fed group was further divided into three sub-groups: the high-fat sedentary (HF-SED) group, the high-fat late-exercise (HF-LEX) group, and the high-fat early-exercise (HF-EEX) group. At day 120-123, the animals were culled and total RNA was extracted from the bone marrow of the femur. The RNA was sequenced using Illumina Hiseq4000 technology. Differential gene expression analysis was carried out using Tuxedo suite of bioinformatic tools.

Publication Title

A Memory of Early Life Physical Activity Is Retained in Bone Marrow of Male Rats Fed a High-Fat Diet.

Alternate Accession IDs

GSE97376

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE14908
Global expression profiling of CD4 T-cell responses to house dust mite allergens in human atopics and nonatopics.
  • organism-icon Homo sapiens
  • sample-icon 88 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

The aim of this study was to employ a systems-level analysis to elucidate gene expression networks operating in the CD4 T-cell responses which underpin human atopic disease.

Publication Title

A network modeling approach to analysis of the Th2 memory responses underlying human atopic disease.

Alternate Accession IDs

E-GEOD-14908

Sample Metadata Fields

Time

View Samples
accession-icon E-TABM-255
Transcription profiling of bone marrow from children with T-cell acute lymphoblastic leukamia comparing those who remained in continuous complete remission with those that relapsed
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

We compared the gene expression profile from a group of children with T-cell acute lymphoblastic leukamia who remained in continuous complete remission (CCR) (n = 7) with that from a group who relapsed (n = 5), using Affymetrix HG-U133A arrays. Using the decision-tree based supervised learning algorithm Random Forest (RF), genes were ranked with respect to their ability to discriminate between patients who remained in CCR and those who relapsed. From the 300 top-ranked probe sets 9 genes were selected for further investigation and validation in an independent cohort of 25 T-ALL patients using quantitative real time polymerase chain reaction.

Publication Title

Identification of novel molecular prognostic markers for paediatric T-cell acute lymphoblastic leukaemia.

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Subject

View Samples
accession-icon GSE33923
2C::tomato ES cells, 2-cell embryos and wild type oocytes
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Embryonic stem cell potency fluctuates with endogenous retrovirus activity.

Alternate Accession IDs

E-GEOD-33923

Sample Metadata Fields

Specimen part, Cell line, Treatment

View Samples
accession-icon GSE33763
Expression data from 2C::tomato+ vs 2C::tomato - ES cells
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

We compared gene expression from 2C::tomato+/- ES cells from Kdm1a wt and mutant ES cultures

Publication Title

Embryonic stem cell potency fluctuates with endogenous retrovirus activity.

Alternate Accession IDs

E-GEOD-33763

Sample Metadata Fields

Cell line

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accession-icon SRP009468
RNA-Seq from two-cell (2C) stage embryos
  • organism-icon Mus musculus
  • sample-icon 3 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

To determine gene expression in 2 cell stage embryos Overall design: 3 Replicates of litters of wild type 2 cell stage embryos

Publication Title

Embryonic stem cell potency fluctuates with endogenous retrovirus activity.

Alternate Accession IDs

GSE33921

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon SRP011988
RNA-Seq from wt and G9A knockout ES cells
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

To measure gene expression difference between wt and g9A knockout ES cells Overall design: G9A TT2 ES cells (Yokochi et al) were treated with Veh. Or 4OHT (to delete G9A)

Publication Title

Embryonic stem cell potency fluctuates with endogenous retrovirus activity.

Alternate Accession IDs

GSE36896

Sample Metadata Fields

Specimen part, Treatment, Subject

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accession-icon SRP009467
mRNA-Seq of 2C::tomato+ vs. - ES cells
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer II

Description

We identified/quantified genes and repeat elements enriched within 2C::tomato+ cells vs. 2C::tomato - cells Overall design: 2C::tomato + and - cells were collected by FACS for RNA-Seq analysis

Publication Title

Embryonic stem cell potency fluctuates with endogenous retrovirus activity.

Alternate Accession IDs

GSE33920

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon GSE18876
Transcriptional Profile of Aging in Healthy Human Skin
  • organism-icon Homo sapiens
  • sample-icon 98 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

Gene expression changes were assessed from the non sun-exposed skin of the lower back of 98 healthy males aged 19-86. We show that contrary to previous thought, genome wide transcriptional activity does not display an exclusively linear correlation with ageing, but rather, in human skin, undergoes a period of significant transient change between 30 and 45 years of age. The identified transient transcriptional changes suggest a period of heightened metabolic activity and cellular damage mediated primarily through the actions of TP53 (tumour protein 53) and TNF (tumour necrosis factor). We also identified a subgroup of the population characterised by increased expression of a large group of hair follicle genes that correlates strongly with a younger age of onset and increasing severity of androgenetic alopecia.

Publication Title

Transcriptome analysis of human ageing in male skin shows mid-life period of variability and central role of NF-κB.

Alternate Accession IDs

E-GEOD-18876

Sample Metadata Fields

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)

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Developed by the Childhood Cancer Data Lab

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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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