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Homo sapiens
46 Downloadable Samples
IlluminaHiSeq2000
Description
Genome-wide mapping and characterization of novel Notch-regulated long non-coding RNAs in acute leukemia Overall design: Total RNA was extracted from samples using the RNeasy Plus mini kit (Life Technologies, Carlsbad, CA). Samples were then subject to PolyA selection (Figures 1E, 5F and 5G only) using oligo-dT beads (Life Technologies, Carlsbad, CA) or rRNA removal (all other samples) using the Ribo-Zero kit (Epicentre, Madison, WI) according to the manufacturers instructions. The resulting RNA samples were then used as input for library construction using the dUTP method as described by Parkhomchuck et al, 2009. RNA libraries were then sequenced on the Illumina HiSeq 2000 or 2500 using 50bp paired-end reads.
Publication Title
Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
We used RNA sequencing to characterize gene expression of CD4+ CD8a+ double positive (DP), Foxp3+ Treg (TR) and CD4+ single positive (SP) cells in the lamina propria (LP) and intraepithelial compartment (IEL) that had differentiante from the same clonal transnuclear (TN) precursor. Overall design: We adoptively transferred CD4+ CD8a- Foxp3-GFP- isolated from pTregTN/RKO/Foxp3-GFP mice into TCRaßKO hosts. After 6 weeks, we sorted transferred CD4+ CD8a+, Foxp3+ pTreg as well as unconverted CD4+ CD8a- Foxp3-GFP- from the small intestine LP and IEL compartments for whole transcriptome analysis by mRNA sequencing.
Publication Title
Tissue-specific emergence of regulatory and intraepithelial T cells from a clonal T cell precursor.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 146 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This dataset encompassing the profiles of 150 lung cancer tumors was developed to serve as test dataset in the SBV IMPROVER Diagnostic Signature Challenge (sbvimprover.com). The aim of this subchallenge was to verify that it is possible to extract a robust diagnostic signature from gene expression data that can identify stages of different types of lung cancer. Participants were asked to develop and submit a classifier that can stratify lung cancer patients in one of four groups Stage 1 of Adenocarcinoma (AC Stage 1), Stage 2 of Adenocarcinoma (AC Stage 2), Stage 1 of Squamous cell carcinoma (SCC Stage 1) or Stage 2 of Squamous cell carcinoma (SCC Stage 2). The classifier could be built by using any publicly available gene expression data with related histopathological information and was tested on the independent dataset described here.
Publication Title
Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge.
Sample Metadata Fields
Sex, Specimen part, Disease stage, Race
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
In order to determine the imprinted transcription factor Zac1 targets, we overexpressed Zac1 in a mouse insulinoma cell line and measured the regulated expressed genes by RNA-seq. We have shown that Zac1 regulates many genes belonging to the Imprinted Gene Network, including genes coding for the extra-cellular matrix. Overall design: Determination of Zac1 target genes in transfected Min6 cells (4 biological replicates) using RNA-seq, .
Publication Title
Identification of Plagl1/Zac1 binding sites and target genes establishes its role in the regulation of extracellular matrix genes and the imprinted gene network.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 16 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Findings suggest that PPARalpha plays a decisive role in the development of hypertrophy, affecting the functional outcome of the heart. Unfortunately, information on the nature of PPARalpha-dependent processes in cardiac hypertrophy is fragmentary and incomplete.
Publication Title
Transcriptomic analysis of PPARalpha-dependent alterations during cardiac hypertrophy.
Sample Metadata Fields
No sample metadata fields
View Samples
GSE40488- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Neuropilin 1 is expressed on thymus-derived natural regulatory T cells, but not mucosa-generated induced Foxp3+ T reg cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 5 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
iTreg cells from Tbmc mLN mice treated with one week of 1% Oral Ova were compared to Total Treg from WT mice.
Publication Title
Neuropilin 1 is expressed on thymus-derived natural regulatory T cells, but not mucosa-generated induced Foxp3+ T reg cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 3 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
To compare subpopulations of Treg cells in wild type mice based upon Nrp1 Expression, differentiating nTreg and iTreg
Publication Title
Neuropilin 1 is expressed on thymus-derived natural regulatory T cells, but not mucosa-generated induced Foxp3+ T reg cells.
Sample Metadata Fields
Specimen part
View Samples- Hordeum vulgare, Triticum aestivum
- 36 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
We utilized the Barley1 Affymetrix GeneChip for comparative transcript analysis of Betzes barley, Chinese Spring wheat, and Chinese SpringBetzes ditelosomic chromosome addition lines to physically map barley genes to their respective chromosome arm locations. We mapped barley genes to chromosome arms (1HS, 2HS, 2HL, 3HS, 3HL, 4HS, 4HL, 5HS, 5HL, 7HS, and 7HL) based on their transcript levels in the ditelosomic addition lines. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Hatice Bilgic. The equivalent experiment is BB55 at PLEXdb.]
Publication Title
Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
STEAP4 is a plasma membrane metallo-reductase involved in the transport of iron and copper. Recently, STEAP4 was implicated in promoting insulin sensitivity by acting in white adipose tissue (WAT) to control the production of inflammatory cytokines such as IL-6. Indeed, the loss of STEAP4 expression in mice leads to increased production of inflammatory cytokines in visceral WAT and systemic insulin resistance. In this report, we demonstrate that in mouse liver STEAP4 is produced at significant levels and that STEAP4 transcription is induced by IL-6. We further demonstrate that the STEAP4 gene is a direct target of phosphorylated STAT3 in mouse liver. In addition, hepatic STEAP4 expression is regulated by feeding and fasting, and obesity leads to the induction of STEAP4 expression in the liver. Interestingly, the regulation of STEAP4 in both feeding and fasting and the obese state appears to require the transcription factor C/EBPalpha that may act in concert with STAT3 as they both bind to the proximal STEAP4 promoter in vivo. Taken together these data suggest the transcriptional regulation of hepatic STEAP4 may play a critical role in the response to nutritional and inflammatory stress and contribute to the protective effect of STEAP4 in vivo.
Publication Title
Regulation of hepatic six transmembrane epithelial antigen of prostate 4 (STEAP4) expression by STAT3 and CCAAT/enhancer-binding protein alpha.
Sample Metadata Fields
Sex, Specimen part
View Samples