A GFP-expressing recombinant A/Puerto Rico/8/1934 influenza virus was used to infect C57BL/6 wild type mice and on day 3 post infection, lung alveolar epithelial cells (AEC) were isolated and sorted based on GFP expression. GFP+ AEC represent the infected AEC and GFP- AEC represent the bystander AEC. AEC were also sorted from uninfected mice to serve as controls. Overall design: AEC from infected mice were pooled to make three (3) infected GFP+ AEC replicates for sequencing. Five (5) bystander GFP- replicates and five (5) uninfected AEC replicates were also isolated for sequencing
Transcriptome Analysis of Infected and Bystander Type 2 Alveolar Epithelial Cells during Influenza A Virus Infection Reveals <i>In Vivo</i> Wnt Pathway Downregulation.
Specimen part, Subject, Time
View SamplesTo begin to identify genes involved in the transdifferentiation process we analyzed Barretts esophagus (with no dysplasia), normal esophagus and small intestine biopsy samples by Affymetrix microarray.
Cdx1 and c-Myc foster the initiation of transdifferentiation of the normal esophageal squamous epithelium toward Barrett's esophagus.
No sample metadata fields
View SamplesA comparison of gene expression in the mammary gland of lactating mice at day 9 after parturition between Akt -/- and wildtype individuals.
Isoform-specific requirement for Akt1 in the developmental regulation of cellular metabolism during lactation.
Sex, Age, Specimen part, Subject
View SamplesLoss of p120ctn results in dysplasia and invasive cancer in the mouse esophagus and squamous forestomach.
Deletion of p120-catenin results in a tumor microenvironment with inflammation and cancer that establishes it as a tumor suppressor gene.
Specimen part
View SamplesThe vertebrate embryo undergoes a series of dramatic morphological changes as the body extends to form the complete anterior-posterior axis during the somite-forming stages. The molecular mechanisms regulating these complex processes are still largely unknown. We show that the Hippo pathway transcriptional coactivators Yap1 and Wwtr1 are specifically localized to the ectoderm and notochord, and play a critical and unexpected role in posterior body extension by regulating the assembly of Fibronectin underneath the ectoderm and surrounding the notochord. We also find that Yap1/Wwtr1, also acting through Fibronectin, have an essential role in the ectodermal morphogenesis necessary to form the initial dorsal and ventral fins, a process that had been thought to involve bending of an epithelial sheet, but which we now show involves active cell migration. Our results reveal how the Hippo pathway transcriptional program, localized to two specific tissues, acts to control essential morphological events in the vertebrate embryo. Overall design: two biological replicates of tails of yap1/wwtr1 double homozygous mutants and siblings (24 each at 16-18 somite stage) were collected for RNAseq. Tails are tissues of the posterior end until the third newest somite (S-III).
Regulation of posterior body and epidermal morphogenesis in zebrafish by localized Yap1 and Wwtr1.
Specimen part, Subject
View SamplesThe goal of this study is to determine gene expression changes in the adult zebrafish spinal cord at 2 weeks after complete transection. Overall design: 2 samples were analyzed in duplicates: sham injured spinal cord and transected spinal cord at 2 weeks post-injury
Injury-induced ctgfa directs glial bridging and spinal cord regeneration in zebrafish.
No sample metadata fields
View SamplesWe Report the genome-wide RNA expression levels in control and schizophrenia hiPSC dervied NPC treated with neuronal media for 2 days. In total about 15,000 gene expression were detected in all samples, of which 1349 were dysregualted. Overall design: Examination, identification and comparision of mRNA expression profliles in control and schizophrenia npc
Common developmental genome deprogramming in schizophrenia - Role of Integrative Nuclear FGFR1 Signaling (INFS).
Specimen part, Subject
View SamplesSarcoidosis + Follow-up 6 month after
Functional genomics and prognosis in sarcoidosis--the critical role of antigen presentation.
No sample metadata fields
View SamplesSamples collected from human subjects in clinical trials possess a level of complexity, arising from multiple cell types, that can obfuscate the analysis of data derived from them. Blood, for example, contains many different cell types that are derived from a distinct lineage and carry out a different immunological purpose. Failure to identify, quantify, and incorporate sources of heterogeneity into an analysis can have widespread and detrimental effects on subsequent statistical studies.
Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples.
Sex, Specimen part
View SamplesA LysM Receptor-like Kinase Mediates Chitin Perception and Fungal Resistance in Arabidopsis
A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis.
No sample metadata fields
View Samples