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accession-icon GSE60324
Effect of knock down of LASP-1 on human breast cancer cells
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 2.0 ST Array (hugene20st), Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

LASP-1: a nuclear hub for the UHRF1-DNMT1-G9a-Snail1 complex.

Alternate Accession IDs

E-GEOD-60324

Sample Metadata Fields

Specimen part, Cell line

View Samples
accession-icon GSE60322
Effect of knock down of LASP-1 on luminal breast cancer cells (MCF7)
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Nuclear LASP-1 has a direct correlation with the overall survival of breast cancer patients. Gene expression analysis of MCF7 human breast cancer cells cultured in 3D-Matrigel was performed.

Publication Title

LASP-1: a nuclear hub for the UHRF1-DNMT1-G9a-Snail1 complex.

Alternate Accession IDs

E-GEOD-60322

Sample Metadata Fields

Specimen part, Cell line

View Samples
accession-icon GSE1062
Extraocular, masticatory, and hindlimb muscles, comparison of putative muscle allotypes (Porter lab)
  • organism-icon Mus musculus
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Array (mgu74a)

Description

Extraocular Muscle is Defined by a Fundamentally Distinct Gene Expression Profile. Adult mouse extraocular, masticatory, and hindlimb (gastrocnemius/soleus) muscles of adult mice were compared using Affymetrix microarrays. Data form part of publication: Proceedings of the National Academy of Sciences USA 98:12062-12067, 2001.

Publication Title

Extraocular muscle is defined by a fundamentally distinct gene expression profile.

Alternate Accession IDs

E-GEOD-1062

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE1472
Extraocular and hindlimb muscle, comparison of wild type and mdx mice, 56 days (Porter lab)
  • organism-icon Mus musculus
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Array (mgu74a)

Description

Determination of gene expression changes in extraocular and hindlimb (gastrocnemius/soleus) of mdx (dystrophin-deficient) mice at postnatal day 56. 5 independent replicates/muscle group/strain.

Publication Title

A chronic inflammatory response dominates the skeletal muscle molecular signature in dystrophin-deficient mdx mice.

Alternate Accession IDs

E-GEOD-1472

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE109471
Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Here we describe a method for fabricating a primary human Small Intestine-on-a-Chip (Intestine Chip) containing epithelial cells isolated from healthy regions of intestinal biopsies. The primary epithelial cells are expanded as 3D organoids, dissociated, and cultured on a porous membrane within a microfluidic device with human intestinal microvascular endothelium cultured in a parallel microchannel under flow and cyclic deformation. In the Intestine Chip, the epithelium forms villi-like projections lined by polarized epithelial cells that undergo multi-lineage differentiation similar to that of intestinal organoids, however, these cells expose their apical surfaces to an open lumen and interface with endothelium. Transcriptomic analysis also indicates that the Intestine Chip more closely mimics whole human duodenum in vivo when compared to the duodenal organoids used to create the chips. Because fluids flowing through the lumen of the Intestine Chip can be collected continuously, sequential analysis of fluid samples can be used to quantify nutrient digestion, mucus secretion and establishment of intestinal barrier function over a period of multiple days in vitro. The Intestine Chip therefore may be useful as a research tool for applications where normal intestinal function is crucial, including studies of metabolism, nutrition, infection, and drug pharmacokinetics, as well as personalized medicine.

Publication Title

Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids.

Alternate Accession IDs

E-GEOD-109471

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE53148
Gene expression profiles in vitiligo lesional skin
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina MouseWG-6 v2.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

CXCL10 is critical for the progression and maintenance of depigmentation in a mouse model of vitiligo.

Alternate Accession IDs

E-GEOD-53148

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE53147
Genome-wide analysis of gene expression within vitiligo mouse skin
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina MouseWG-6 v2.0 expression beadchip

Description

Skin samples from mice in a model of vitiligo were selected for gene expression profiling in order to identify active inflammatory pathways.

Publication Title

CXCL10 is critical for the progression and maintenance of depigmentation in a mouse model of vitiligo.

Alternate Accession IDs

E-GEOD-53147

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE25263
Pneumococcal conjugate vaccination at birth induces robust recall responses at 9 months of age.
  • organism-icon Homo sapiens
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

The objective of this study was to compare recall responses to vaccine antigens at 3 months and 9 months of age in infants who were vaccinated at birth or at 1 month.

Publication Title

Pneumococcal conjugate vaccination at birth in a high-risk setting: no evidence for neonatal T-cell tolerance.

Alternate Accession IDs

E-GEOD-25263

Sample Metadata Fields

Age, Specimen part, Treatment

View Samples
accession-icon SRP010139
Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq)
  • organism-icon Zea mays
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer IIx

Description

Bulked segregant analysis (BSA) is an efficient method to rapidly and efficiently map genes responsible for mutant phenotypes. This procedure, however, requires access to quantitative genetic markers that are polymorphic in the mapping population. We have developed a modification of BSA (BSR-Seq) that makes use of RNA-Seq reads to efficiently map genes even in populations for which no polymorphic markers have been previously identified. Because of the digital nature of next-generation sequencing (NGS) data, it is possible to conduct de novo SNP discovery and quantitatively genotype BSA samples using the same RNA-Seq data. In addition, analysis of the RNA-Seq data provides information on the effects of the mutant on global patterns of gene expression at no extra cost. In combination these results greatly simplify gene cloning experiments. To demonstrate the utility of this strategy BSR-Seq was used to clone the glossy3 (gl3) gene of maize. Mutants of the glossy loci exhibit altered accumulation of epicuticular waxes on juvenile leaves. We previously generated a large collection of glossy mutants using the Mu transposon system. By subjected a reference allele to BSR-Seq, we were able to map the gl3 locus to a ~2.3Mb interval that is consistent with the results of prior mapping experiments. The single gene located in the 2.3Mb mapping interval that contained a Mu insertion and whose expression was down-regulated in the mutant pool was subsequently demonstrated to be the gl3 gene via the analysis of multiple independently Mu transposon induced mutant alleles. The gl3 gene encodes a putative myb transcription factor, which directly or indirectly affects the expression of a number of genes involved in the biosynthesis of very-long-chain fatty acids.

Publication Title

Changes in genome content generated via segregation of non-allelic homologs.

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE41821
A role for Prenylated rab acceptor 1 in vertebrate photoreceptor development
  • organism-icon Mus musculus
  • sample-icon 32 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Expression 430A Array (moe430a)

Description

The rd1 mouse retina is a well-studied model of retinal degeneration where rod photoreceptors undergo cell death beginning at postnatal day P10 until P21. This period coincides with photoreceptor terminal differentiation in a normal retina. We have used the rd1 retina as a model to investigate early molecular defects in developing rod photoreceptors prior to the onset of degeneration. Using a microarray approach, we performed gene profiling comparing rd1 and wild type retinas at four time points starting at P2, prior to any obvious biochemical or morphological differences, and concluding at P8, prior to the initiation of cell death. We have identified genes that are differentially regulated in the rd1 retina at early time points, which may give insights into developmental defects that precede photoreceptor cell death. This is the first report of PRA1 expression in the retina. Our data support the hypothesis that PRA1 plays an important role in vesicular trafficking between the Golgi and cilia in differentiating and mature rod photoreceptors.

Publication Title

A role for prenylated rab acceptor 1 in vertebrate photoreceptor development.

Alternate Accession IDs

E-GEOD-41821

Sample Metadata Fields

Specimen part

View Samples
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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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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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