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GSE52309
Homo sapiens
11 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Generation of human fibroblast-derived hepatocytes capable of extensive proliferation, as evidenced by significant liver repopulation of mice. Unlike current protocols for deriving hepatocytes from human fibroblasts, ours did not generate iPSCs, but shortcut reprogramming to pluripotency to generate an induced multipotent progenitor cell (iMPC) stage from which endoderm progenitor cells (iMPC-EPCs) and subsequently hepatocytes (iMPC-Heps) could be efficiently differentiated. After transplantation into an immune-deficient mouse model of human liver failure, iMPC-Heps were able to engraft and proliferate, and acquired levels of hepatocyte function similar to adult hepatocytes.
Publication Title
Mouse liver repopulation with hepatocytes generated from human fibroblasts.
Sample Metadata Fields
Specimen part
View Samples- Pseudomonas aeruginosa
- 8 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
Pseudomonas aeruginosa (P. aeruginosa) lung infection is a significant cause of mortality in patients with cystic fibrosis (CF). Existing experimental data in our lab showed significantly different levels of virulence of "early" and "late" P. aeruginosa infection isolates in a C. elegans slow killing model. We wished to examine the expression profile of these isolates in order to explore genes that may be responsible for the observed differences. The expression profiles of two pairs of isolates (four isolates in total) were compared to each other using the Affymetrix P. aeruginosa PAO1 genome array, to gain insight into properties mediating virulence in these isolates. Data analysis was carried out using BIOCONDUCTOR software.
Publication Title
Modulation of gene expression by Pseudomonas aeruginosa during chronic infection in the adult cystic fibrosis lung.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Plant drought stress response and resistance are complex biological processes that merit systems-level analyses to dissect drought stress encountered by crops in the field. We have used gene expression profiling of Arabidopsis plants subjected to a controlled, sublethal, moderate drought (mDr) treatment to characterize early and late response to drought. We have also compared these profiles to those from plants treated with soil water deficit (progressive) drought (pDr) to reveal acclimation responses in plants.
Publication Title
Molecular and physiological analysis of drought stress in Arabidopsis reveals early responses leading to acclimation in plant growth.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 8 Downloadable Samples
NextSeq 500
Description
The X-linked DDX3X gene encodes an ATP-dependent DEAD-box RNA helicase frequently altered in various human cancers including melanomas. Despite its important roles in translation and splicing, how DDX3X dysfunction specifically rewires gene expression in melanoma remains completely unknown. Here we uncover a DDX3X-driven post-transcriptional program that dictates melanoma phenotype and poor disease prognosis. Through an unbiased analysis of translating ribosomes we identified the microphtalmia-associated transcription factor, MITF, as a key DDX3X translational target that directs a proliferative-to-metastatic phenotypic switch in melanoma cells. Mechanistically, DDX3X controls MITF mRNA translation via an internal ribosome entry site (IRES) embedded within the 5' untranslated region. Through this exquisite translation-based regulatory mechanism, DDX3X steers MITF protein levels dictating melanoma metastatic potential in vivo and response to targeted therapy. Together these findings unravel a post-transcriptional layer of gene regulation that may provide a unique therapeutic vulnerability in aggressive male melanomas. Overall design: We sequenced transcripts associated with translationally active ribosomes (polysomes) isolated by sucrose gradient fractionation from DDX3X and control siRNA-transduced HT144 cells. Experiments were performed in duplicates.
Publication Title
The X-Linked DDX3X RNA Helicase Dictates Translation Reprogramming and Metastasis in Melanoma.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 7 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We aim to identify genes differentially expressed between mouse WT and COUP-TFI_Nex-Cre mutant cortices.
Publication Title
Postmitotic control of sensory area specification during neocortical development.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 136 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Classification of tamixifen-treated breast cancer patients into high and low risk groups using the 76-gene signature
Publication Title
The 76-gene signature defines high-risk patients that benefit from adjuvant tamoxifen therapy.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
We report the transcriptome profile of one sequenced sample of mRNA isolated from pooled (20 from each genotype) abdomen fly extracts enriched in fat body content of fat body-specific Sdc RNAi knockdown and control flies Overall design: Abdominal fat body mRNA profiles of 4-6-day old control and fat body-specific Sdc RNAi knockdown were generated by deep sequencing using Illumina HiSeq 2500
Publication Title
Knockdown expression of Syndecan in the fat body impacts nutrient metabolism and the organismal response to environmental stresses in Drosophila melanogaster.
Sample Metadata Fields
Subject
View Samples- Drosophila melanogaster
- 396 Downloadable Samples
- Illumina HiSeq 2000
Description
In order to understand the effect of genetic background on the response to gene dose perturbation, we performed mRNA transcriptional profiling on 99 hemizygotic lines (Df/+) from the DrosDel project, which have hybrid genetic background of OregonR/w1118. Overall design: We performed RNA-Seq analysis of 417 single adult flies in duplicate or triplicate. Flies are from 73 different genotypes. Differential gene expression was analyzed separately for each sex, gene expression from each genotype was compared to normalized mean of gene expression remaining 72 genotypes.
Publication Title
Dosage-Dependent Expression Variation Suppressed on the <i>Drosophila</i> Male <i>X</i> Chromosome.
Sample Metadata Fields
Sex, Subject
View Samples- Drosophila melanogaster
- 343 Downloadable Samples
- Illumina HiSeq 2000
Description
We performed mRNA transcriptional profiling on 99 hemizygotic lines (Df/+) from the DrosDel project covering 68% of chromosome 2L, in order to understand how changes in gene copy number affect overall transcriptome. Overall design: We performed RNA-Seq analysis on 396 pools of 15-25 adult flies each. Samples include males or females from 99 different genotypes in duplicate. Differential gene expression was analyzed separately for each sex, by comparing each genotype with the remaining 98.
Publication Title
Dosage-Dependent Expression Variation Suppressed on the <i>Drosophila</i> Male <i>X</i> Chromosome.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Drosophila melanogaster
- 247 Downloadable Samples
- Illumina HiSeq 2000
Description
To measure the response to gene dose, we performed mRNA-Seq of fly heads with molecularly defined deletions constructed from DrosDel deficiency lines (Ryder et al. Genetics 2007, 177(1):615-29) on the Illumina HiSeq 2000 platform. Overall design: We performed single-end next-generation sequencing (RNA-Seq) on poly-A+ RNA extracted from adult female and male heads in biological triplicate. Besides wildtype females (XX) and males (XY) that were heterozygous for deletions, we also sequenced females that were transformed into males (XX males) by using mutations in the sex determination gene transformer-2 (tra2). The original lines with deletions, including 22 deletions on the chromosome X and 12 deletions on the chromosome 3L, were from the DrosDel project. The diploid controls without DrosDel deletions were derived from w1118 (the parental line of DrosDel stocks) or Oregon-R Strain. We sequenced a total of 249 samples.
Publication Title
Dosage-Dependent Expression Variation Suppressed on the <i>Drosophila</i> Male <i>X</i> Chromosome.
Sample Metadata Fields
Sex, Subject
View Samples