RNA-seq of E17.5 WT and Emb-/- mouse placentas and lungs
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Mus musculus
SUBMITTER: Jyrki Heino
PROVIDER: E-MTAB-10641 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To compare gene expression profiling of EMB+ cells and EMB- cells whin CD45-Ter119-CD31--Thy1-6C3-CD200+CD105- population across long bone and vertebrae, we isolated related cells form long bone or vertebrae of zic1 -cre mtmg mice by FACS.
2023-04-30 | GSE230724 | GEO
Project description:This study investigates the baseline or inducible differences in between populations of Atlantic salmon lice Lepeophtheirus salmonis with differing levels of resistance to the parasiticidal drug emamectin benzoate (EMB), as well as the induced effects of EMB exposure to Pacific salmon lice. F1 generation lice were exposed in bioassays to a dilution series of emamectin benzoate. Two separate experiments were conducted, one for Atlantic and one for Pacific salmon lice (to be analyzed separately). Atlantic pre-adult salmon lice, separated into male and female, and sensitive or resistant to EMB populations, and exposed to a dilution series: 0 (control), 0.1, 25, 300, and 1000 parts per billion EMB. For each combination four biological replicates were included, except male resistant 25 (n = 3) and female resistant 300 (n = 2). Pacific pre-adult lice of both sexes were exposed to a dilution series: 0 (control), 25, 50 parts per billion EMB.
2014-11-17 | E-GEOD-56024 | biostudies-arrayexpress
Project description:Timepoint 12 wild type adult with emb 3 vs mixed stage reference Keywords: other
2003-12-31 | GSE737 | GEO
Project description:Timepoint 11 wild type adult with emb 2 vs mixed stage reference Keywords: other
2003-12-31 | GSE736 | GEO
Project description:Aims. Serial invasive endomyocardial biopsies (EMB) remain the gold standard for acute cellular rejection (ACR) diagnosis. However histological grading has several limitations. We aimed to explore the value of myocardial Gene Expression Profiling (GEP) for diagnosing and identifying predictive biomarkers of ACR. Methods. A case-control study nested within a retrospective heart transplant patients cohort included 126 patients with median (IQR) age 50 (41-57) years and 111 (88%) males. Among 1157 EMB performed, 467 were eligible (i.e, corresponding to either ISHLT grade 0 or â¥3A), among which 36 were selected for GEP according to the grading: 0 (CISHLT, n= 13); rejection â¥3A (RISHLT, n=13); 0 one month before ACR (BRISHLT, n=10). Results. We found 294 genes differentially expressed between CISHLT and RISHLT, mainly involved in immune activation, and inflammation. Hierarchical clustering showed a clear segregation of CISHLT and RISHLT groups and heterogeneity of GEP within RISHLT. All EMB presented immune activation, but some RISHLT EMB were strongly subject to inflammation, whereas others, closer to CISHLT, were characterized by structural modifications with lower inflammation level. We identified 15 probes significantly different between BRISHLT and CISHLT, including the gene of the muscular protein TTN. This result suggests that structural alterations precede inflammation in ACR. Linear Discriminant Analysis based on these 15 probes was able to identify the histological status of every 36 samples. Conclusion. Myocardial GEP is a helpful method to accurately diagnose ACR, and predicts rejection one month before its histological occurrence. These results should be considered in cardiac allograft recipientsâ care.
2017-03-07 | E-MTAB-5136 | biostudies-arrayexpress
Project description:Caligid copepods, also called sea lice, are common ectoparasites of wild and farmed marine fish. The salmon louse Lepeophtheirus salmonis (KrM-xyer, 1837) has emerged as a serious problem for salmon farming in the Northern hemisphere. The annual cost of sea lice to the global salmon mariculture industry has been estimated at M-^@300 million, of which the majority accounts for the cost of chemically treating the farmed salmon. The treatments available for salmonids with sea lice infestation have been limited with a large scale reliance on single products and the use of antiparasitics with similar modes of action, which when used over a long period of time can enhance the selection pressure for reduced sensitivity. The aim of the present study was to identify transcripts whose expression correlated to emamectin benzoate (EMB) susceptibility, or those genes regulated in response to EMB exposure. Two L. salmonis laboratory strains, established from field isolates and differing in susceptibility to EMB were studied using a custom sea louse 15K oligonucleotide microarray and RT-qPCR. Adult male sea lice were sampled from both strains after 1 and 3 hours of aqueous exposure to 0.2 M-5g mL-1 emamectin benzoate, 0.01% PEG300 or sea water. Bioinformatic analysis identified that in the absence of drug treatment, a large number of genes were significantly down regulated in the louse strain hyposensitive to EMB. EMB exposure had marked effects on gene expression in the EMB susceptible strain, but caused little changes in EMB hyposensitive lice. We therefore suggest that transcriptional responses induced by EMB exposure may not be responsible for reduced susceptibility to this antiparasitic compound, but may involve genes that are constitutively expressed in EMB tolerant salmon louse strains.
2013-11-06 | E-MTAB-1478 | biostudies-arrayexpress
Project description:Caligid copepods, also called sea lice, are common ectoparasites of wild and farmed marine fish. The salmon louse Lepeophtheirus salmonis (KrM-xyer, 1837) has emerged as a serious problem for salmon farming in the Northern hemisphere. The annual cost of sea lice to the global salmon mariculture industry has been estimated at M-^@300 million, of which the majority accounts for the cost of chemically treating the farmed salmon. The treatments available for salmonids with sea lice infestation have been limited with a large scale reliance on single products and the use of antiparasitics with similar modes of action, which when used over a long period of time can enhance the selection pressure for reduced sensitivity. Two L. salmonis laboratory strains, established from field isolates and differing in susceptibility to emamectin benzoate (EMB) were studied using a custom sea louse 15K oligonucleotide microarray and RT-qPCR. The aim of the present study was to identify differential expression of transcripts between these two strains to identify potential constitutive gene expression changes associated with reduced susceptibility to EMB. Adult male salmon lice were sampled without exposure to antiparasitic agents for the purpose of studying gene expression from unchallenged individuals. In this study changes in expression of Glutamate-gated Chloride channel (GluCl) subunits, considered the major target site for avermectin (AVM) drugs in invertebrates, was not observed, but expression changes were seen for alternative ligand-gated ion channel (LGIC) subunits that form an ion channels shown to interact with AVMs in vertebrates, but which is not traditionally considered to be a target site for AVMs in invertebrates. We hypothesise that these LGIC subunits represent additional EMB target sites in salmon lice, and that the down-regulation of these channel subunits in this EMB-resistant strain is related to the resistance phenotype.
2013-11-06 | E-MTAB-1484 | biostudies-arrayexpress
Project description:Proper regulation of the germline transcriptome is essential for the maintenance of fertility and survival of a species. In C. elegans, germline transcriptome homeostasis hinges on a complex repertoire of small RNA pathways that act in both activating and silencing capacities. Our understanding of how fundamental RNA processing steps intersect with these small RNA machineries in the germline remains relatively limited. Here, we link the conserved intron binding protein and splicing factor, EMB-4/AQR/IBP160 to two key 22G-RNA pathways in the C. elegans germline. EMB-4 associates with the Argonautes CSR-1 and HRDE-1, and is enriched at the genomic loci of CSR-1 and HRDE-1 target genes. Loss of emb-4 leads to distinct alterations in CSR-1 vs. HRDE-1 small RNA and mRNA transcriptomes. Our transcriptome-wide analysis shows that EMB-4 is enriched along pre-mRNAs of nearly 10,000 transcripts. For a subset of these genes, including mostly CSR-1 pathway targets, EMB-4 enriches for intronic, but not exonic, sequences. Together these data point to EMB-4 as a factor that may help to distinguish the targets of these two germline small RNA pathways.
2017-11-01 | GSE94455 | GEO
Project description:The proteomes of placentas corresponding to EpoR+/+ and EpoR-/- mice were analyzed by label-free LC-MS/MS.
2022-09-28 | PXD008368 | Pride
Project description:IUGR (Intra-Uterine Growth Restriction) refers to a condition where the foetus does not reach its growth potential in utero. It is supposed to be often linked with placental dysfunction, especially of vascular origin. In this study, 4 pools of three placentas from human normal pregnancies and 4 pools of three placentas from IUGR human pregnancies, obtained after caesarean section near normal term , were used to prepare RNA. The cDNAs prepared from these RNA were hybridized to a Nimblegen expression array in order to detect differences in gene expression between normal and pathological placentas.
2014-01-14 | E-MTAB-1956 | biostudies-arrayexpress