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Saccharomyces cerevisiae
27 Downloadable Samples
Illumina HiSeq 2000
Description
Engineering microbes with novel metabolic properties is a critical step for production of biofuels and biochemicals. Synthetic biology enables identification and engineering of metabolic pathways into microbes; however, knowledge of how to reroute cellular regulatory signals and metabolic flux remains lacking. Here we used network analysis of multi-omic data to dissect the mechanism of anaerobic xylose fermentation, a trait important for biochemical production from plant lignocellulose. We compared transcriptomic, proteomic, and phosphoproteomic differences across a series of strains evolved to ferment xylose under various conditions. Overall design: RNA-seq and transcriptome analysis of three evolved S. cerevisiae strains (Y22-3, Y127, Y128) grown aerobically or anaerobically in rich lab media with glucose, xylose, galactose, or sorbitol. Duplicates were collected on different days.
Publication Title
Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast.
Sample Metadata Fields
Subject
View Samples- Saccharomyces cerevisiae
- 16 Downloadable Samples
- Illumina HiSeq 2500
Description
Engineering microbes with novel metabolic properties is a critical step for production of biofuels and biochemicals. Synthetic biology enables identification and engineering of metabolic pathways into microbes; however, knowledge of how to reroute cellular regulatory signals and metabolic flux remains lacking. Here we used network analysis of multi-omic data to dissect the mechanism of anaerobic xylose fermentation, a trait important for biochemical production from plant lignocellulose. We compared transcriptomic, proteomic, and phosphoproteomic differences across a series of strains evolved to ferment xylose under various conditions. Overall design: RNA-seq and transcriptome analysis of Azf1 deletion and over-expression (via MoBY 2.0 plasmid) in YPX -O2. Duplicate samples were collected on different days.
Publication Title
Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
CK1-alpha-LS was knocked down in human coronary artery smooth muscle cells. Gene level and exon level changes in expression were assessed.
Publication Title
Protein kinase CK1alphaLS promotes vascular cell proliferation and intimal hyperplasia.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 38 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302), Affymetrix Mouse Expression 430A Array (moe430a)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Novel subtype-specific genes identify distinct subpopulations of callosal projection neurons.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 34 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Myocardial infarction (MI) often results in left ventricular (LV) remodeling followed by heart failure (HF). It is of great clinical importance to understand the molecular mechanisms that trigger transition from compensated LV injury to HF and to identify relevant diagnostic biomarkers. In this study, we performed transcriptional profiling of LVs in rats with a wide range of experimentally induced infarct sizes and of peripheral blood mononuclear cells (PBMCs) in animals that developed HF.
Publication Title
Transcriptional profiling of left ventricle and peripheral blood mononuclear cells in a rat model of postinfarction heart failure.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 19 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a), Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
3 subtypes of cortical projection neurons were purified by fluorescence-activated cell sorting (FACS) at 4 different stages of development from mouse cortex. A detailed description of the data set is described in Arlotta, P et al (2005) and Molyneaux, BJ et al (2009). The hybridization cocktails used here were originally applied to the Affymetrix mouse 430A arrays and submitted as GEO accession number GSE2039. The same hybridization cocktails were then applied to the Affymetrix mouse 430 2.0 arrays, and those data are contained in this series.
Publication Title
Novel subtype-specific genes identify distinct subpopulations of callosal projection neurons.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 33 Downloadable Samples
- Illumina HumanRef-8 v3.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Expression profiling of human basophils: modulation by cytokines and secretagogues.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 33 Downloadable Samples
- Illumina HumanRef-8 v3.0 expression beadchip
Description
Human basophils were examined in vitro for changes in their mRNA expression profiles during stimulation under a variety of conditions. Basophils were obtained from two sources prior to purification, residual cell packs from leukapheresis procedures (which represent the 80% of the sample results) or by venipuncture. For cells obtained by leukapheress, purification included application of elutration, 2-step Percoll gradients and negative selection on Miltenyi columns using StemSep basophil isolation antibodies (see J. Immunol. Methods, 385:51, 2012). For cells obtained by venipuncture, purification included application of 2-step Percoll gradients following by negative selection on Miltenyi columns using StemSep basophil isolation antibodies. The time from subject donation to the start of an in vitro study (first lysis for mRNA) ranged from 6-7 hours for leukapheresis packs to 4-5 hours for venipuncture. Basophil purities averaged 99% for these studies.
Publication Title
Expression profiling of human basophils: modulation by cytokines and secretagogues.
Sample Metadata Fields
Specimen part, Treatment
View Samples
GSE138610- Homo sapiens
- 25 Downloadable Samples
- Affymetrix Clariom S Human array (clariomshuman), Illumina HumanRef-8 v3.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Identifying regulatory pathways of spleen tyrosine kinase expression in human basophils.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 21 Downloadable Samples
- Illumina HumanRef-8 v3.0 expression beadchip
Description
CD34+ progenitor cells were cultured for 0 or 21 days in StemPro medium + supplement + IL-3 at 5 ng/ml
Publication Title
Identifying regulatory pathways of spleen tyrosine kinase expression in human basophils.
Sample Metadata Fields
Specimen part
View Samples