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SRP091722
Mus musculus
24 Downloadable Samples
Illumina HiSeq 2500
Description
We analysed the transcriptional signature in endothelial cells extracted from the bone marrow of mice engrafted with human AML and compared it to the one of mice engrafted with human normal hematopoietic cells Overall design: Immunodeficient mice were transplanted with human AML cells derived from patients, or with normal human hematopoietic cells derived from cord blood. Mice were sacrificed once assessed the bone marrow engraftment, and the bones were processed to isolate endothelial cells using the CD31 marker. RNA was extracted, sequencing libraries were prepared and sequenced.
Publication Title
Increased Vascular Permeability in the Bone Marrow Microenvironment Contributes to Disease Progression and Drug Response in Acute Myeloid Leukemia.
Sample Metadata Fields
Specimen part, Disease, Subject
View Samples- Homo sapiens
- 24 Downloadable Samples
Illumina humanRef-8 v2.0 expression beadchip
Description
At least six histone H1 variants exist in mammalian somatic cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be involved in the active regulation of gene expression. It is not well known whether the different variants have specific roles or regulate specific promoters. We have explored this by inducible shRNA-mediated knock-down of each of the H1 variants in a human breast cancer cell line. A different subset of genes is altered in each H1 knock-down.
Publication Title
Depletion of human histone H1 variants uncovers specific roles in gene expression and cell growth.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The Wnt/beta-catenin pathway is required for the development of leukemia stem cells in MLL-AF9 AML.
Publication Title
KRas(G12D)-evoked leukemogenesis does not require β-catenin.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 12 Downloadable Samples
- Drosophila Gene 1.1 ST Array (drogene11st)
Description
Coupling immunity and development is essential to ensure survival despite changing internal conditions in the organism. The metamorphosis of the fruit fly represents a striking example of drastic and systemic physiological changes that need to be integrated with the innate immune system. However, the mechanisms that coordinate development and immune cell activity in the transition from larva to adult in Drosophila remain to elucidate. The steroid hormone ecdysone is known to act as a key coordinator of metamorphosis. This hormone activates a nuclear receptor, the Ecdysone Receptor (EcR), which acts as a heterodimer with its partner Ultraspiracle (USP). Together, they activate the transcription of primary response genes, which in turn activate the transcription of a battery of late response genes. We have revealed that regulation of macrophage-like cells (hemocytes) by the steroid hormone ecdysone is essential for an effective innate immune response over metamorphosis. We have shown that in response to ecdysone signalling, hemocytes rapidly up regulate actin dynamics, motility and phagocytosis of apoptotic corpses, and acquire the ability to chemotax to damaged epithelia. Most importantly, individuals lacking ecdysone-activated hemocytes are defective in bacterial phagocytosis and are fatally susceptible to infection by bacteria ingested at larval stages, despite the normal systemic production of antimicrobial peptides. This decrease in survival is comparable to the one observed in pupae lacking immune cells altogether, indicating that ecdysone-regulation is essential to hemocyte immune functions and survival after infection.
Publication Title
Steroid hormone signaling is essential to regulate innate immune cells and fight bacterial infection in Drosophila.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
Aim: Transcriptional analysis of the duodenum of adult Nkx2.2flox/SD;Villin-Cre (SDint) mice versus control Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq. Results: 206 genes with a p-value <0.05 were significantly changed. Among these are some enteroendocrine hormones. Conclusion: The SD domain of Nkx2.2 regulates specification of some enteroendocrine cells Overall design: mRNA profiles of the duodenum of 6 week old control and SDint mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.
Publication Title
The novel enterochromaffin marker Lmx1a regulates serotonin biosynthesis in enteroendocrine cell lineages downstream of Nkx2.2.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
Aim: Transcriptional analysis of the colon of adult Nkx2.2flox/flox;Villin-Cre (Nkx2.2int) mice versus control Methods: 2 cm of the colon (as measured after the caecum) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq. Results: 53 genes with a p-value <0.05 were down-regulated and 36 were up-regulated. Among the changed genes are enteroendocrine hormones. Conclusion: Nkx2.2 regulates enteroendocrine cell specification Overall design: mRNA profiles of the colon of 6 week old control and Nkx2.2int mice were generated by deep sequencing, using Illumina HiSeq2000.
Publication Title
The novel enterochromaffin marker Lmx1a regulates serotonin biosynthesis in enteroendocrine cell lineages downstream of Nkx2.2.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 163 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
We have performed a genome-wide analysis of common genetic variation controlling differential expression of transcript isoforms in the CEU HapMap population using a comprehensive exon tiling microarray covering 17,897 genes. We detected 324 genes with significant associations between flanking SNPs and transcript levels. Of these, 39% reflected changes in whole gene expression and 55% reflected transcript isoform changes such as splicing variants (exon skipping, alternate splice site usage, intron retention), differential 5 UTR (initiation of transcription) usage, and differential 3 UTR (alternative polyadenylation) usage.
Publication Title
Genome-wide analysis of transcript isoform variation in humans.
Sample Metadata Fields
Sex
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
A subpopulation of pericytes expressing the Glast-CreERT2 transgene (Type A pericytes) has recently been identified as the main source of stromal scar tissue that forms after SCI. Identification of molecules associated with pericyte-derived scarring may offer new therapeutic targets to facilitate axon regeneration following central nervous system (CNS) injury. We conducted genome-wide RNA sequencing of (i) uninjured spinal cord segments and (ii) lesion sites presenting full or attenuated pericyte-derived scarring 14 days after SCI. Overall design: Adult Glast-Rasless-YFP (Glast-CreERT2 x R26R-YFP x Rasless) mice receiving vehicle (Veh) or tamoxifen (Tam) underwent dorsal hemisection at high thoracic level. Fourteen days after SCI, injury sites were dissected out, homogenized and total RNA was isolated from lesions presenting (i) dense (Veh, n=4) and (ii) attenuated (Tam, n=4) pericyte-derived scarring. Age-matched Glast-Rasless-YFP mice served as uninjured controls (n=4).
Publication Title
Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury.
Sample Metadata Fields
Specimen part, Treatment, Subject, Time
View Samples- Homo sapiens
- 15 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Bisphenol A (BPA) is a xenobiotic endocrine disrupting chemical. In vitro and in vivo studies indicated that BPA alters endocrine-metabolic pathways in adipose tissue increasing the risk of developing metabolic disorders. BPA effects on human adipocytes, specifically in children, are poorly investigated. To investigate in childhood the effect of exposure to BPA on metabolic disorders we analyzed in vitro the effects of environmentally relevant doses of BPA on gene expression of mature human adipocytes from pre-pubertal lean patients and on related physiological outcomes. Adipocytes from children were treated in vitro with BPA and gene expression was evaluated by qRT-PCR. Genome wide analyses were performed using GeneChip Human Gene 1.0 ST array. Lipid content in adipocytes was estimated by ORO staining and Triglyceride Quantification Kit. Secreted IL-1, in adipocytes culture medium, and insulin, in PANC-1 culture medium, were performed using ELISA assays. BPA was found to promote up-regulation of ER and ERR, and down-regulation of GPR30 expression modulating estrogen signaling and following a non-linear dose-response. Microarray data analysis demonstrated that BPA increases the gene expression of pro-inflammatory cytokines and lipid metabolism-related FABP4 and CD36 in adipocytes. PCSK1 resulted the most interesting gene being down-regulated by BPA thus impairing insulin production in pancreas. BPA promotes inflammation and lipid metabolism dysregulation in adipocytes from lean children. Moreover, PCSK1 can be a key gene in BPA action modulating insulin production. Exposure to BPA in childhood may be an important risk factor in developing obesity and metabolic disorders.
Publication Title
Bisphenol A effects on gene expression in adipocytes from children: association with metabolic disorders.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 25 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
The goal was to identify the differently expressed genes between laryngeal tumor and nonmalignant surrounding mucosa
Publication Title
Transcriptome Analysis Identifies ALCAM Overexpression as a Prognosis Biomarker in Laryngeal Squamous Cell Carcinoma.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject
View Samples