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SRP052057
Homo sapiens
6 Downloadable Samples
IlluminaHiSeq2000
Description
Expression from CD133+ cells isolated from adult human exocrine tissue was compared to a CD133-depleted cell population Overall design: Islet-depleted exocrine tissue from three independent adult human cadaveric pancreata were cultured for four days in Miami media 1A. Following trypsinization, cells were isolated using anti-CD133 immunomagnetic beads to >95% CD133+. CD133-negative cells were further depleted of CD133+ cells to <1% CD133+.
Publication Title
Neurogenin 3 is regulated by neurotrophic tyrosine kinase receptor type 2 (TRKB) signaling in the adult human exocrine pancreas.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 110 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Analysis of 104 breast cancer biopsies (removed prior to any treatment with tamoxifen or chemotherapeutic agents) from patients aged between 31 years and 89 years at the time of diagnosis (mean age = 58 years). Twenty were less than 50 years and seventy-seven women were 50 years, or older, at diagnosis. The size of the tumours ranged between 0.6 cm and 8.0 cm (mean = 2.79 cm). Eighteen tumours were T1 (<2 cm) in maximal dimension; 83 were T2 (25 cm) and 3 tumours were T3 (>5 cm). Eighty-two were invasive ductal carcinoma, 17 were invasive lobular and five were tumours of special type (two tubular and three mucinous). Eleven tumours were grade 1; 40 were grade 2; and 53 were grade 3. Sixty-seven tumours were oestrogen receptor (ER) positive and 34 were ER negative (ER status was determined by Enzyme Immuno-Assay (EIA); a positive result was defined as more than 200 fmol/g protein). ER status was not available for 3 patients. Forty-five tumours had no axillary metastases and 59 tumours had metastasised to axillary lymph nodes. Sixty-nine women were treated with post-operative tamoxifen; 26 did not receive tamoxifen. Fifty patients were treated with adjuvant systemic chemotherapy (CMF +/ adriamycin); 45 patients did not receive chemotherapy. Details regarding tamoxifen and systemic chemotherapy were not available for 9 patients. Maximal follow-up was 3,026 days with a mean follow-up of 1,887 days.
Publication Title
Correlating transcriptional networks to breast cancer survival: a large-scale coexpression analysis.
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Disease stage
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Objective: To quantify changes in adipogenic gene expression in the presence of ritonavir (RTV) or tenofovir (TDF), and determine whether conjugated linoleic acid (CLA) isomers (cis9,trans11 or trans10,cis12) can mitigate detrimental effects of antiretoviral drugs.
Publication Title
Microarray Analysis Reveals Altered Lipid and Glucose Metabolism Genes in Differentiated, Ritonavir-Treated 3T3-L1 Adipocytes.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Drosophila melanogaster
- 14 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Study of gene expression patterns of Drosophila melanogaster Sesb1 mutants compared to wild type
Publication Title
Phenotypic rescue of a Drosophila model of mitochondrial ANT1 disease.
Alternate Accession IDs
Sample Metadata Fields
Sex
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
This study was aimed at elucidating the mechanisms underlying activity-dependent gene regulation during LTP of mouse hippocampal CA3-CA1 synapses. Deep sequencing of the 3' end of transcripts allowed to identify changes in APA induced 1 hour and 3 hours after LTP induction. We detected APA changes that only affected the 3''UTR (3''UTR-APA events) and APA changes that also affected the coding sequence (CDS-APA events). Overall design: We performed 3' region extraction and deep sequencing (3''READS) of acute hippocampal slices 1 hour and 3 hours after LTP induction, and of time-matched control slices. Hippocampal slices were prepared from 2-3 month old C57BL/6 wild-type mice, the dentate gyrus was trimmed, and the slices were placed in interface chambers to recover for 2 hours with continuous ACSF perfusion. From the same animal, half of the mini-slices were used for LTP induction (using a pharmacological protocol, cLTP) and the remaining slices were treated with a DMSO vehicle solution as controls. We sequenced triplicates (samples 1-3) of controls and cLTP treated slices for the 1 hour and 3 hours time-point.
Publication Title
Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long-Term Potentiation.
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later. To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.
Publication Title
Identification of candidate surface antigens for non-invasive prenatal diagnosis by comparative global gene expression on human fetal mesenchymal stem cells.
Alternate Accession IDs
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens, Rattus norvegicus
- 22 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
[Hela cells]: We performed cdr2 knockdown with a pool of 4 cdr2-specific siRNAs to test whether cdr2 may regulate c-myc target genes as cells passage through mitosis.
Publication Title
The onconeural antigen cdr2 is a novel APC/C target that acts in mitosis to regulate c-myc target genes in mammalian tumor cells.
Alternate Accession IDs
Sample Metadata Fields
Cell line
View Samples- Saccharomyces cerevisiae
- 6 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Reactive oxygen species, generated in vivo or exogenously encountered, constantly challenge living organisms. Oxidation of polyunsaturated fatty acids (PUFA), which are susceptible to oxidant attack, can lead to initiation of lipid peroxidation and in turn rapid production of toxic lipid hydroperoxides. Eukaryotic microorganisms such as Saccharomyces cerevisiae can survive harsh industrial conditions that contain high levels of the PUFA linoleic acid and its oxidised derivative, linoleic acid hydroperoxide (LoaOOH). The precise signalling and response mechanisms induced by yeast to overcome lipid hydroperoxide stress are ill understood.
Publication Title
Transcriptomic insights into the molecular response of Saccharomyces cerevisiae to linoleic acid hydroperoxide.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 2 Downloadable Samples
- IlluminaHiSeq2000
Description
We''ve developed a new Method to Analyze RNA following Intracellular Sorting (MARIS) allowing us to carry out gene expression studies on cells sorted based on intracellular immunoflourescence. The purpose of this study is to determine the degree of bias that MARIS introduces on gene expression. We report RNA-seq gene expression data from human embryonic stem cells differentiated to a stage in which insulin-expressing cells are present. Gene expression data using RNA isolated from live cells is compared to gene expression data using RNA isolated from MARIS processed cells (fixed, permeabilized, antibody stained and mock sorted) to determine the degree of correlation in gene expression between these two biologically identical samples. Overall design: Human embryonic stem cells are differentiated to a stage in which insulin-expressing cells are present and split into two biologically identical samples. RNA is immediately isolated from one sample using the RNeasy protocol (live sample). RNA is isolated from the second sample following MARIS (processed sample) with all cells collected after the sort in order to keep the cell type composition between the live and processed samples the same.
Publication Title
MARIS: method for analyzing RNA following intracellular sorting.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus, Homo sapiens
- 38 Downloadable Samples
- Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Transcriptomic signature of fasting in human adipose tissue.
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Subject
View Samples