run_metadata: 40831
This data as json
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| 40831 | SRR3381829 | SRX1704275 | SRS1396348 | SRP073272 | PRJNA318414 | Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] | GSE80260 | Transcriptome Analysis | Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. | parent bioproject:PRJNA318502 | pubmed:27444789 | Control 1 blood | GSM2122866 | source name:whole blood DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO | Control 1 blood | Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. | whole blood DMSO control | DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. | RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. | AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. | strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO | GSM2122866 | GSM2122866: Control 1 blood; Danio rerio; RNA Seq | GSM2122866 | 1 | RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. | GEO Accession:GSM2122866 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP073272 | C8DKGANXX_s8_1_GSLv3-7_33_SL139790.fastq.gz C8DKGANXX_s8_2_GSLv3-7_33_SL139790.fastq.gz | fastq fastq | 1596331500.0 | 15963315.0 | GSM2122866 r5 | 0:50 1:50 | A:444854958;C:353331559;G:354367449;T:442888766;N:888768 | 50 | 50 | 444854958 | 353331559 | 354367449 | 442888766 | 888768 | SRX1704275 | SRS1396348 | SRA411416 | GEO | Molecular and Biomedical Sciences, University of Maine | 2 | 0.90554 | 0.91175 | 0.17327 | 0.17968 | 0.73669 | 0.73728 | 0.55044 | 0.5651 | 50 | 50 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2016-04-13 | Adult | Adult | Blood | Hematopoietic System |