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Arabidopsis thaliana
83 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The organs of multicellular species are comprised of cell types that must function together to perform specific tasks. One critical organ function is responding to internal or external change but little is known about how responses are tailored to specific cell types or coordinated among them on a global level. Here we use cellular profiling of five Arabidopsis root cell types in response to a limiting resource, nitrogen, to uncover a vast and predominantly cell-specific response that was largely undetectable using traditional methods. These methods reveal a new class of cell-specific nitrogen responses. As a proof-of-principle, we dissected one cell-specific response circuit that mediates nitrogen-induced changes in root branching from pericycle cells. Thus, cellular response profiling links gene modules to discrete functions in specific cell types.
Publication Title
Cell-specific nitrogen responses mediate developmental plasticity.
Sample Metadata Fields
Specimen part
View Samples- Bos taurus
- 18 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Sexual dimorphism in mammals is mostly attributable to sex-related hormonal differences in fetal and adult tissues; however, this may not be the sole determinant. Though genetically-identical for autosomal chromosomes, male and female preimplantation embryos could display sex-specific transcriptional regulation which can only be attributted to the differences in sexual chromosome dosage.
Publication Title
Sex determines the expression level of one third of the actively expressed genes in bovine blastocysts.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 24 Downloadable Samples
Illumina HiSeq 2500
Description
Induction of dnFGFR2bfor 3 partially overlapping intervals at the early stages of otocyst morphogenesis revealed expected and novel up and downregulated genes that were validated by in situ hybridization analysis. Cell cyle genes were enriched in the downregulated datasets and human hearingloss genes were enriched in the upregulated datasets. Overall design: Differential mRNA expression analysis of pooled Rosa26rtTA/+ (control) and pooled Rosa26rtTA/+;Tg(tetO-s(dn)Fgfr2b)/+ (experimental) embryos induced with doxycycline for the indicated intervals. N=4 biological replicates per treatment (i.e. 4 pregnant females)
Publication Title
Spatial and temporal inhibition of FGFR2b ligands reveals continuous requirements and novel targets in mouse inner ear morphogenesis.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 20 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Ovarian cancer is the fifth most common form of cancer in women in the United States. Epithelial ovarian cancer is the most common and is highly lethal. In 2014, there will be an estimated 21,980 new cases and 14,270 deaths from ovarian cancer in the United States. No major strides have been made to improve survival over the past decade. Ovarian cancer is notable for initial chemotherapy sensitivity (>75% response rates) using combination platinum and taxane chemotherapy following debulking surgery. However, eventually, the vast majority of these women (>75-80%) will have their cancer recur within 12 to 24 months after diagnosis and will die of progressively chemotherapy-resistant diseases. Transcription factors act as master switches of various biochemical pathways by regulating gene transcription. Large number of studies demonstrated the role of transcription factors in cancer development and progression. However, transcription factors involved in the pathogenesis of ovarian cancer have not been explored thoroughly. Therefore, we propose to using transcriptome profiling to generate a transcription factor gene signature for high-grade serous ovarian cancer.
Publication Title
ELF3 is a negative regulator of epithelial-mesenchymal transition in ovarian cancer cells.
Sample Metadata Fields
Specimen part, Disease
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
The lipocalin Apolipoprotein D (ApoD), known to protect the nervous system against oxidative stress (OS) in model organisms, is up-regulated early in the mouse brain in response to the ROS generator paraquat (PQ). However, the processes triggered by this up-regulation have not been explored.
Publication Title
Apolipoprotein D alters the early transcriptional response to oxidative stress in the adult cerebellum.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
How chromatin controls transcription elongation and splicing is an open question. Here we determine the transcriptomic changes of cells partially depleted of core histones. For that we construct a cell line with Doxycycline-controlled levels of the histone regulatory protein SLBP (HCT-shSLBP). HCT-shSLBP is derived from the human colon cancer cell line HCT116.
Publication Title
Defective histone supply causes changes in RNA polymerase II elongation rate and cotranscriptional pre-mRNA splicing.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Bos taurus
- 12 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Temporal changes in the embryo transcriptome between the blastocyst stage (Day 7) and initiation of elongation (Day 13) differ between in vivo- and in vitro-derived embryos and are reflective of subsequent developmental fate.
Publication Title
Transcriptome changes at the initiation of elongation in the bovine conceptus.
Sample Metadata Fields
Specimen part
View Samples
GSE22529- Homo sapiens
- 104 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Evaluation of differential expression between CLL patients in a chemoimmunotherapy trial with age-matched controls
Publication Title
LEF-1 is a prosurvival factor in chronic lymphocytic leukemia and is expressed in the preleukemic state of monoclonal B-cell lymphocytosis.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Bos taurus
- 15 Downloadable Samples
- Bovine Gene 1.0 ST Array (bovgene10st)
Description
The aim of this study was to compare the transcriptome of the different regions of the oviduct between pregnant and cyclic heifers. After synchronizing crossbred beef heifers, those in standing oestrus (=Day 0) were randomly assigned to cyclic (non bred, n=6), or pregnant (artificially inseminated, n=11) groups. They were slaughtered on Day 3 and both oviducts from each animal were isolated and cut in half to separate ampulla and isthmus. Each portion was flushed to confirm the presence of an oocyte/embryo and was then opened longitudinally and scraped to obtain epithelial cells which were snap-frozen. Oocytes and embryos were located in the isthmus of the oviduct ipsilateral to the corpus luteum. Microarray analysis of oviductal cells revealed that proximity to the corpus luteum did not affect the transcriptome of the isthmus, irrespective of pregnancy status. However, 2287 genes were differentially expressed (P<0.01) between the ampulla and isthmus of the oviduct ipsilateral to the corpus luteum. Gene ontology revealed that the main biological processes overrepresented in the isthmus were synthesis of nitrogen, lipids, nucleotides, steroids and cholesterol as well as vesicle-mediated transport, cell cycle, apoptosis, endocytosis and exocytosis, whereas cell motion, motility and migration, DNA repair, calcium ion homeostasis, carbohydrate biosynthesis and regulation of cilium movement and beat frequency were overrepresented in the ampulla. In conclusion, large differences in gene expression were observed between the isthmus and ampulla that reflect morphological and functional characteristics of each segment.
Publication Title
Spatial differences in gene expression in the bovine oviduct.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 15 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA sequencing of T-ALL tumors derived from genetically modified mouse models: CIC loss-of-function, HRASG12V driven from the Kras promoter and Trp53 KO. Results provide insight into the role of the RAS/CIC axis in T-ALL development. Overall design: RNA-Sequencing of 5 CIC LOF, 3 K:HrasG12V and 4 Trp53 KO T-ALL murine tumor samples.
Publication Title
Inactivation of Capicua in adult mice causes T-cell lymphoblastic lymphoma.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples