Ontology highlight
ABSTRACT:
PROVIDER: PRJNA684935 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13261842_1.fastq.gz | Fastqsanger.gz | |||
| SRR13261842_2.fastq.gz | Fastqsanger.gz | |||
| SRR13261843_1.fastq.gz | Fastqsanger.gz | |||
| SRR13261843_2.fastq.gz | Fastqsanger.gz | |||
| SRR13261844_1.fastq.gz | Fastqsanger.gz |
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Project description:Channel catfish, Ictalurus punctatus, are the primary cultured species of the catfish industry. Significant losses in production are attributed to bacterial diseases which are challenging to control and new interventions need to be developed. To gain insight into the in situ catfish immune system, we used single-nuclei RNAseq. We produced two single-nuclei atlases from three individual catfish using flow cytometry sorted IgM+ splenic cells. Libraries were prepared using the 10X Genomics system and sequenced on an Illumina sequencer. The reads were aligned to the reference genome (Ip Coco_2.0) using Cell Ranger (v8.0.0).
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Project description:Background: Farm exposures in early life reduce the risks for childhood allergic diseases and asthma. There is less information about how farm exposures relate to respiratory illnesses and mucosal immune development. Objective: We hypothesized that children raised in farm environments have a lower incidence of viral illnesses over the first two years of life than non-farm children. We also analyzed between farm exposures or respiratory illnesses were related to patterns of nasal cell gene expression. Methods: The Wisconsin Infant Study Cohort (WISC) birth cohort enrolled farm and non-farm pregnant women from central Wisconsin. Parents reported prenatal farm and other environmental exposures. Illness frequency and severity were assessed using illness diaries and periodic surveys. Nasopharyngeal cell gene expression at age two years was compared to farm exposure and respiratory illness history. Results: There was a higher rate of respiratory illnesses in the non-farm vs. farm group (rate ratio 0.82 [0.69,0.97], p=0.020), but no significant differences in wheezing illnesses. There was a stepwise reduction in rates of respiratory illnesses in children exposed at least weekly to 0, 1, or ≥2 animals (p=0.006). In analyzing nasal cell gene expression, farm exposures and preceding respiratory illnesses were positively related to gene signatures for mononuclear cells and innate and antimicrobial responses. Conclusions: Children exposed to farms and farm animals had lower rates of respiratory illnesses over the first two years of life. Both farm exposures and preceding respiratory illnesses were associated with increased innate immune responses, suggesting that these exposures stimulate mucosal immune responses to reduce subsequent illness frequency.
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Project description:Diversity clinical phenotypes of autism spectrum disorders (ASD), caused by heterogeneity of genetic and environmental factors, hampered the investigation in uncovering pathological mechanisms. Here we generated ASD patient-cerebral organoids from induced pluripotent stem cells (iPSCs) that reprogramed from the early-onset ASD individuals at around 2 years old with common clinical diagnosis in a prospective birth cohort, which was excluded typical autistic mutations and environmental exposures.
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Project description:The acute phase response (APR) is a set of metabolic and physiological reactions occurring in the host in response to tissue infection or injury and is a crucial component of the larger innate immune response. The APR is best characterized by dramatic changes in the concentration of a group of plasma proteins known as acute phase proteins (APP) which are synthesized in the liver and which function in a wide range of immunity-related activities. Utilizing a second generation high-density in situ oligonucleotide microarray for catfish, we have surveyed for the first time the APR in channel catfish liver following infection with Edwardsiella ictaluri, a fast-acting bacterial pathogen that causes enteric septicemia of catfish. Our catfish microarray design (28K) builds upon a previous 19K channel catfish array by adding recently sequenced immune transcripts from channel catfish along with 7159 unique sequences from closely-related blue catfish. Analysis of microarray results using a traditional two-fold change in gene expression cutoff and a 10% false discovery rate revealed a well-developed APR in catfish, with particularly high up-regulation (>50-fold) of genes involved in iron homeostasis (i.e. intelectin, hemopexin, haptoglobin, ferritin, and transferrin). Other classical APP upregulated greater than two-fold included coagulation factors, proteinase inhibitors, transport proteins, and complement components. Up-regulation of the majority of the complement cascade including the membrane attack complex components and complement inhibitors was observed. A number of pathogen recognition receptors (PRRs) and chemokines were also differentially expressed in the liver following infection. Validation with real-time PCR confirmed microarray results. Keywords: Disease state analysis
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