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GSE14420
Arabidopsis thaliana
17 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Global gene expression was compared between Arabidopsis lines with altered expression of ANAC102 (over-expressed and knocked-out) and wild-type. ANAC102 is a putative NAC domain transcription factor. Gene expression was compared between an ANAC102 over-expressing line and parental ecotype C24 under ambient atmosphere to determine which genes ANAC102 is capable of regulating. Gene expression was also compared between three week old plants of an ANAC102 knock-out line and parental ecotype Col-0 under 0.1% Oxygen and ambient atmosphere conditions to determine which genes may require ANAC102 for appropriate expression under these conditions. Gene expression was also compared between imbibed seeds of an ANAC102 knock-out line and parental ecotype Col-0 following a 0.1% Oxygen treatment.
Publication Title
The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment.
Sample Metadata Fields
No sample metadata fields
View Samples- Gossypium hirsutum
- 8 Downloadable Samples
- Affymetrix Cotton Genome Array (cotton)
Description
Global gene expression was compared between roots of cotton plants (variety Sicot 71) flooded for 4 hours and roots of unflooded cotton plants. Global gene expression was also compared between leaves of cotton plants (variety Sicot 71) flooded for 24 hours and leaves of unflooded cotton plants.
Publication Title
Global gene expression responses to waterlogging in roots and leaves of cotton (Gossypium hirsutum L.).
Sample Metadata Fields
Specimen part, Time
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Global gene expression was compared between root RNA samples from three-week-old Arabidopsis Col-0 plants subjected to 0.1% oxygen (balance nitrogen) or ambient atmospheric conditions.
Publication Title
Comparisons of early transcriptome responses to low-oxygen environments in three dicotyledonous plant species.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Gossypium barbadense, Gossypium hirsutum
- 2 Downloadable Samples
- Affymetrix Cotton Genome Array (cotton)
Description
affy_cotton_2011_12 - affy_cotton_2011_12 - In this study we characterized the fiber transcriptomes of the two species, Gossypium hirsutum and Gossypium barbadense that were parental genotypes of a RIL mapping population used previously for phenotypic QTL and expression QTL mapping., We used 454 deep pyrosequencing to characterize cDNAs from developing fibers at two key developmental time-points; 10 and 22 days post anthesis. A unigene set was assembled and annotated, and differential digital gene expression was assessed from the different time-point and genotype representations of the reads within assembled contigs. As a complementary approach, we conducted microarray-based hybridization profiling using the cotton Affymetrix gene chip and labeled cDNAs from fibers at 11 dpa and for the same two genotypes and compared differentially expressed genes identified by the two platforms. The 454 unigenes were also mined for the presence of microsatellite repeats and SNPs that will be useful markers for mapping and marker-assisted selection in cotton improvement.-Total RNA was extracted from 11 dpa-old fibers from the two genotypes, Guazuncho 2 (Gossypium hirsutum) and VH8-4602 (G. barbadense), and included two replicates of each. RNA was checked for quality and quantity using an Agilent Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA, http://www.home.agilent.com) following the manufacturers recommendations. The RNA was sent to the Australian Genome Research Facility Ltd. (http://www.agrf.org.au, Melbourne, Victoria, Australia) for labeling and hybridization to the Affymetrix Genechip Cotton Genome Array (21,854 genes) (Affymetrix, http://www.affymetrix.com/). -
Publication Title
Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 477 Downloadable Samples
- Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)
Description
Microarray Analysis of Human Whole Blood and Intestinal Biopsy Samples from a Phase 2b, Multicenter, Randomized, Double-blind, Placebo-controlled, Parallel-group Study of Ustekinumab in Crohns Disease
Publication Title
A functional genomics predictive network model identifies regulators of inflammatory bowel disease.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Treatment
View Samples- Homo sapiens
- 125 Downloadable Samples
Illumina HiSeq 2500
Description
This study focuses on inflammatory bowel disease gene expression profiling. Surgical specimens from 134 patients undergoing bowel resection for inflammatory bowel disease (IBD) and non IBD controls at Mount Sinai Medical Center were collected as the source of tissue. Control samples (CLs) were harvested from normal non inflamed bowel located more than 10 cm away from the tumor from patients undergoing bowel resection for sporadic colon cancer. Ulcerative colitis (UC) and Crohn’s (CD) patient samples were all isolated from areas containing moderate to severe inflammation. The diagnostic pathology report for each specimen was provided by the Mount Sinai Hospital Pathology Department. Patients with UC and patients with CD shared common medications including corticosteroids, infliximab, azathioprine, and mesalamine. Overall design: Surgical specimens from 134 patients undergoing bowel resection for inflammatory bowel disease (IBD) and non IBD controls at Mount Sinai Medical Center were collected as the source of tissue. Control samples (CLs) were harvested from normal non inflamed bowel located more than 10 cm away from the tumor from patients undergoing bowel resection for sporadic colon cancer. Ulcerative colitis (UC) and Crohn’s (CD) patient samples were all isolated from areas containing moderate to severe inflammation. The diagnostic pathology report for each specimen was provided by the Mount Sinai Hospital Pathology Department. Patients with UC and patients with CD shared common medications including corticosteroids, infliximab, azathioprine, and mesalamine. The samples were collected fresh and the tissue was further processed for isolation. A representative 0.5 cm tissue fragment was isolated from the collected surgical specimen samples, flash frozen and stored at -80C. Tissue was homogenized in Trizol following the manufacturer''s protocol (Life Technologies) and RNA extraction was performed. RIN scores >7 were used for Poly A RNA-seq.
Publication Title
A functional genomics predictive network model identifies regulators of inflammatory bowel disease.
Sample Metadata Fields
Sex, Subject
View Samples- Gallus gallus
- 10 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
Few families of signaling factors have been implicated in the control of development. Here we identify the neuropeptides nociceptin and somatostatin, a neurotransmitter and neuroendocrine hormone, as a class of developmental signals in chick and zebrafish. We show that signals from the anterior mesendoderm are required for the formation of anterior placode progenitors with one of the signals being somatostatin. Somatostatin controls ectodermal expression of nociceptin and both peptides regulate Pax6 in lens and olfactory progenitors. Consequently, loss of somatostatin and nociceptin signaling leads to severe reduction of lens formation. Our findings not only uncover these neuropeptides as developmental signals, but also identify a long-sought-after mechanism that initiates Pax6 in placode progenitors and may explain the ancient evolutionary origin of neuropeptides, pre-dating a complex nervous system.
Publication Title
Neuropeptides: developmental signals in placode progenitor formation.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
A nxnl2 knockout mouse model was created and the transcriptome used to demonstrate that the retina is compromised by the absence of nxnl2.
Publication Title
Nxnl2 splicing results in dual functions in neuronal cell survival and maintenance of cell integrity.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus, Homo sapiens
- 28 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip, Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 28 Downloadable Samples
Illumina MouseWG-6 v2.0 expression beadchip
Description
Microarray analysis of murine microglia from different stages of development was performed. Results showed that different phases of microglia development had different group of genes up-regulated for specific functions.
Publication Title
Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner.
Sample Metadata Fields
Specimen part
View Samples