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accession-icon GSE40730
Genome-wide analysis of RNAs translationally regulated upon BRCA1 depletion in human mammary epithelial cells
  • organism-icon Homo sapiens
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Loss of function of the tumor suppressor BRCA1 (Breast Cancer 1) protein is responsible for numerous familial and sporadic breast cancers. We previously identified PABP1 as a novel BRCA1 partner and showed that BRCA1 modulates translation through its interaction with PABP1. We showed that the global translation was diminished in BRCA1-depleted cells and increased in BRCA1-overexpressing cells. Our findings raised the question whether BRCA1 affects translation of all cytoplasmic cellular mRNAs or whether it specifically targets a subset of mRNAs.

Publication Title

BRCA1-Dependent Translational Regulation in Breast Cancer Cells.

Sample Metadata Fields

Cell line

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accession-icon GSE46518
Transcriptional and post-transcriptional analysis of CD4+ T cell clones deriving from HTLV-1 infected individuals
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

T-cell clones were obtained by limiting dilution culture of PBMC of HTLV-1 carriers. Exon expression profiling was performed using Affymetrix exon array (Affymetrix Human Exon 1.0 ST Array) according to the manufacturer's instructions.

Publication Title

HTLV-1 bZIP factor HBZ promotes cell proliferation and genetic instability by activating OncomiRs.

Sample Metadata Fields

Specimen part

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accession-icon GSE54207
Expression data from mouse limb tendon cells during development.
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

We have undertaken a screen of mouse limb tendon cells in order to identify molecular pathways involved in tendon development. Mouse limb tendon cells were isolated based on Scleraxis (Scx) expression at different stages of development: E11.5, E12.5 and E14.5

Publication Title

Transcriptomic analysis of mouse limb tendon cells during development.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE2394
Neuromuscular Junction
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)

Description

NMJ Junction various time points normal C57BL10 LCM mRNA

Publication Title

Intracellular expression profiling by laser capture microdissection: three novel components of the neuromuscular junction.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP130944
Transcriptional profiles of lung macrophage subsets in Mycobacterium Tuberculosis infection
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

We investigated transcriptional responses of different lung macrophage lineages during M.tuberculosis infection by RNAseq. Our data revealed that different lineages of macrophages respond differentially to M.Tuberculosis infection. Overall design: Alveolar macrophage (AM) and interstitial macrophages (IM) with or without Mtb were FACS-sorted from Mtb infected mice for RNAseq.

Publication Title

Growth of <i>Mycobacterium tuberculosis</i> in vivo segregates with host macrophage metabolism and ontogeny.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE34297
Expression data from skin of mice treated subcutaneously with TGF-beta, IL-13 or TSLP for 7 days
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)

Description

Gene expression in mice skin stimulated with 3 different cytokines

Publication Title

Thymic stromal lymphopoietin is up-regulated in the skin of patients with systemic sclerosis and induces profibrotic genes and intracellular signaling that overlap with those induced by interleukin-13 and transforming growth factor β.

Sample Metadata Fields

Specimen part

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accession-icon GSE84788
Compared performance of Affymetrix HTA arrays and Illumina RNAseq for the analysis of tumours
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000, Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples.

Sample Metadata Fields

Specimen part

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accession-icon GSE41764
Correlated alterations in genome organization, histone methylation, and DNA-lamina interactions in Hutchinson-Gilford progeria syndrome
  • organism-icon Homo sapiens
  • sample-icon 6 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

Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome.

Sample Metadata Fields

Sex, Specimen part, Disease, Cell line

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accession-icon GSE84784
Compared performance of Affymetrix HTA arrays and Illumina RNAseq for the analysis of tumours [Affymetrix]
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000, Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

Here we compared the performance of Affymetrix HTA 2.0 microarray and Illumina 2000 RNA-sequencing techniques on the clinical samples collected from patients with lung squamous cell carcinoma.

Publication Title

RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples.

Sample Metadata Fields

Specimen part

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accession-icon GSE41751
Correlated alterations in genome organization, histone methylation, and DNA-lamina interactions in Hutchinson-Gilford progeria syndrome (expression)
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging disease that is frequently caused by a de novo point mutation at position 1824 in LMNA. This mutation activates a cryptic splice donor site in exon 11, and leads to an in-frame deletion within the prelamin A mRNA and the production of a dominant negative lamin A protein, known as progerin. Here we show that HGPS cells experience genome-wide alterations in patterns of H3K27me3 deposition, changes in the associations of genomic loci with nuclear lamin A/C, and, at late passages, genome-wide loss of spatial compartmentalization of active and inactive chromatin domains that characterizes chromosome folding in normal cells. We further demonstrate that the H3K27me3 changes associate with gene expression alterations in HGPS cells. Our results support a model that the accumulation of progerin in the nuclear lamina leads to altered H3K27me3 marks in heterochromatin, possibly through the down-regulation of EZH2, and disrupts heterochromatin-lamina interactions. These changes may then lead to the genomic disorganization and changes in transcriptional regulation we observe in HGPS fibroblasts.

Publication Title

Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome.

Sample Metadata Fields

Sex, Specimen part, Disease, Cell line

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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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