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GSE45255
Homo sapiens
123 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
To facilitate a better understanding of the molecular heterogeneity of breast cancer and to uncover gene-survival associations that segregate with distinct molecular subtypes, we recently compiled a meta-analytical database of over 2,000 human breast tumor expression profiles variously annotated for clinical and pathological variables and derived from various institutions worldwide. This database was utilized for the breast tumor study cited below: Nagalla, et. al., Genome Biology, 2013. While the majority of the tumor expression profiles included in this database derived from publicly accessible microarray repositories, a number of the samples had not been previously published. Here, we describe the origin of these samples and provide their associated clinical and pathological annotations with the hope that other investigators will be able to utilize these data in their own research.
Publication Title
Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis.
Sample Metadata Fields
Age, Disease stage
View Samples- Homo sapiens
- 153 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Racial differences in the pathophysiology of atherothrombosis are poorly understood. We explored the function and transcriptome of platelets in healthy black (n=70) and white (n=84) subjects.
Publication Title
Racial differences in human platelet PAR4 reactivity reflect expression of PCTP and miR-376c.
Sample Metadata Fields
Specimen part, Race
View Samples- Mus musculus
- 9 Downloadable Samples
Ion Torrent Proton
Description
Analysis of murine cardiomyocyte cell line HL-1 treated with Ivermectin or Importazole. Results provide insight into the pathways regulated by the treatments. Overall design: RNA-seq of mouse HL-1 cardiomyocytes treated with vehicle (DMSO), Ivermectin, or Importazole for 24 hours, in triplicate, using Ion Proton System.
Publication Title
Antihypertrophic Effects of Small Molecules that Maintain Mitochondrial ATP Levels Under Hypoxia.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Homo sapiens
- 10 Downloadable Samples
- Illumina HiSeq 2000
Description
Purpose: RNA-Seq analysis can help identify large set of differentially expressed genes at a time. We performed RNA-Seq analysis to identify differentially expressed genes in the PBMCs of war veterans suffering from PTSD. Methods: Total RNA from PBMCs from PTSD +ve and -ve individuals were used for RNA-Seq analysis. Results: We obtained, on average, ~60 millions reads per sample. More than 70% of the reads were mapped to human genome. Functional analysis of the differentially expressed genes (362) revealed dysregulation in immune system network. Conclusions: Our present study provides further proof that immune system related genes and pathways are dysregulated in PTSD PBMCs. Overall design: RNA-Seq was performed with RNA from 5 each control and PTSD individuals. PBMCs collected within one hour of blood draw were used for RNA isolation. 1 ug of total RNA was used for library synthesis and sequenced in a HighSeq 2000 illumina instrument at Tufts University.
Publication Title
Decreased AGO2 and DCR1 in PBMCs from War Veterans with PTSD leads to diminished miRNA resulting in elevated inflammation.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
G-CSF treatment targets CXCL12-abundant reticular (CAR) cells to suppress their production of a number of B trophic factors, including CXCL12, IL-6, IL-7, IGF-1, and Flt3 ligand.
Publication Title
Granulocyte colony-stimulating factor reprograms bone marrow stromal cells to actively suppress B lymphopoiesis in mice.
Sample Metadata Fields
Treatment
View Samples- Homo sapiens
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
We performed RNA-Seq on PHF21A-deficient patient-dervied lymphoblasts as well as two unaffected individuals. Overall design: We performed RNA-Seq from patient-derived lymphoblast cells. Libraries were polyA-selected and strand-specific according to the protocol described in PMID: 25607527
Publication Title
Transcriptome Analysis Revealed Impaired cAMP Responsiveness in PHF21A-Deficient Human Cells.
Sample Metadata Fields
Sex, Specimen part, Disease stage, Subject
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We explored the functional role of YAP in SCLC cells (SBC3 and SBC5) by YAP knockdown.
Publication Title
YAP and TAZ modulate cell phenotype in a subset of small cell lung cancer.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms.
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We recently identified recurrent mutations of cohesin complex in myeloid neoplasms through whole-exome sequencing analysis. RAD21 is one of the main components of the cohesin complex.
Publication Title
Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms.
Sample Metadata Fields
Cell line
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis thaliana wild-type and ire1a/ire1b double mutant plants were treated with tunicamycin. RNA was extracted and subjected to microarray analysis.
Publication Title
Arabidopsis IRE1 catalyses unconventional splicing of bZIP60 mRNA to produce the active transcription factor.
Sample Metadata Fields
No sample metadata fields
View Samples