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accession-icon GSE27149
Expression data from murine vaginal samples following adjuvant treatment
  • organism-icon Mus musculus
  • sample-icon 47 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Vaccine research today is focused on using safer, highly purified or recombinant antigens with poor immunogenicity, which has created a need for potent adjuvants. Rational design of effective and safe mucosal adjuvants for human use necessitates a thorough understanding of the mode of action of successful candidate adjuvants.

Publication Title

Unraveling molecular signatures of immunostimulatory adjuvants in the female genital tract through systems biology.

Sample Metadata Fields

Sex, Treatment

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accession-icon SRP149798
Genome wide analysis of upper spinal cords with training after spinal cord hemisection injury
  • organism-icon Rattus norvegicus
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 1500

Description

The goal of this study is to elucidate the influence of treadmill training on transcriptome of the upper lumbar spinal cord after thoracic spinal cord hemisection. mRNA profiles of spinal cords at 23 days-post injury with/without treadmill training were generated. The expression levels of 650 genes in the trained animal were increased ( > 2-fold) compared to untrained animals. Our study represents the detailed analysis of transcriptomes of spinal cord distal to the hemisected lesion after treadmill training, with biologic replicates, generated by RNA-seq technology. Overall design: The effect of training after spinal cord injury (T9) on the transcriptome of intact upper spinal cord was investigated.

Publication Title

Locomotor Training Increases Synaptic Structure With High NGL-2 Expression After Spinal Cord Hemisection.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE12404
Expression data from Arabidopsis Seed Compartments at 5 discrete stages of development
  • organism-icon Arabidopsis thaliana
  • sample-icon 87 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

Sample Metadata Fields

Specimen part

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accession-icon GSE11262
Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
  • organism-icon Arabidopsis thaliana
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We collected globular stage seed compartments from 5 or 7-micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments of an Arabidopsis seed containing a globular stage embryo. For the purposes of this study we broke down the seed into 8 capturable compartments: embyro proper, suspensor, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat, general seed coat, and whole seeds.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE15160
Expression data from Arabidopsis seed compartments at the heart stage.
  • organism-icon Arabidopsis thaliana
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We collected heart stage seed compartments from 7 micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments from seeds containing heart stage embryos. For the purposes of this study we captured 6 compartments: embryo proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat and seed coat, as well sets of serial sections encompassing the entire heart stage seed.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE12403
Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
  • organism-icon Arabidopsis thaliana
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We collected linear-cotyledon stage seed compartments from 5 to 7 micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments from seeds containing linear-coyledon-stage embryos. For the purposes of this study we captured 7 compartments: embyro proper, cellularized endosperm, chalazal endosperm, chalazal seed coat, general seed coat, whole seeds and micropylar endosperm.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE15165
Expression data from Arabidopsis seed compartments at the mature green stage.
  • organism-icon Arabidopsis thaliana
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We collected mature green seed compartments from 7 micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments from seeds containing mature green-stage embryos. For the purposes of this study we captured 6 compartments: embryo proper, micropylar endosperm, cellularized peripherial endosperm, chalazal endosperm, chalazal seed coat and seed coat, as well sets of serial sections encompassing the entire mature green stage seed.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE12402
Expression data from Arabidopsis seed compartments at the pre-globular stage
  • organism-icon Arabidopsis thaliana
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We collected pre-globular stage seed compartments from 7-micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments of seeds containing pre-globular-stage embryos was identified as those seeds containing embryo propers made up of between 2 and 8 cells. For the purposes of this study we captured 6 compartments: embyro proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat and general seed coat. Serial sections of entire seeds were also captured for comparison.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE20039
Expression data from Arabidopsis seed compartments at the bending coyledon stage
  • organism-icon Arabidopsis thaliana
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We collected bending-cotyledon seed compartments from 7 micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments from seeds containing bending cotyledon stage embryos. For the purposes of this study we captured 6 compartments: embryo proper, mycropylar endosperm, cellularized peripherial endosperm, chalazal endosperm, chalazal seed coat and seed coat, in addition to serial sections encompasing the entire bending-cotyledon stage seed.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE33352
Gene regulation following MIF stimulation.
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)

Description

Lasting B-cell persistence depends on survival signals that are transduced by cell surface receptors. Here, we describe a novel biological mechanism essential for survival and homeostasis of normal peripheral mature B cells and chronic lymphocytic leukemia (CLL) cells, regulated by the heparin-binding cytokine, midkine (MK), and its proteoglycan receptor, the receptor-type tyrosine phosphatase zeta (RPTP). We demonstrate that MK initiates a signaling cascade leading to B cell survival, by binding to RPTP. In mice lacking PTPRZ, the proportion and number of the mature B cell population is reduced. Our results emphasize a unique and critical function for MK signaling in the previously described MIF/CD74 induced survival pathway. Stimulation of CD74 with MIF leads to c-Met activation, resulting in elevation of MK expression in both normal mouse splenic B and CLL cells. Our results indicate that MK and RPTP are important regulators of the B cell repertoire. These findings could pave the way towards understanding the mechanisms shaping B cell survival, and suggest novel therapeutic strategies based on the blockade of the midkine/RPTP-dependent survival pathway.

Publication Title

The cytokine midkine and its receptor RPTPζ regulate B cell survival in a pathway induced by CD74.

Sample Metadata Fields

Age

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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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