A Hidradenitis Suppurativa molecular disease signature derived from patient samples by high-throughput RNA sequencing and re-analysis of previously reported transcriptomic data sets
Johannes FreudenbergZ. LiuJaswant SinghE ThomasChristopher TrainiDeepak K. RajpalChristopher J. Sayed
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Hidradenitis Suppurativa
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Fenneropenaeus chinensis is an important fishery species in China.Hatchery-reared seeds have been released into the wild for improvement of shrimp productivity.Jinzhou bay is the major natural habitat and we used this location to temporally monitor the genetic effects of release of hatchery stocks on local F. chinensis populations across five years.A set of 13 microsatellite markers were used to evaluate genetic patterns across 2015, 2016 and 2019.We observed a significant Hardy-Weinberg disequilibrium across all stocks.The inbreeding coefficient (F is ) was positive (0.121-0.131) for all stocks.A loss of genetic diversity was detected in the 2019 stock and significant differences were observed for number of different alleles, number of effective alleles, allelic richness and unbiased expected heterozygosity in the 2019 stock (P < 0.05).The highest pairwise relatedness and the lowest observed heterozygosity were also observed in 2019 stock.Moreover, a small but significant genetic differentiation was detected between the 2019 stock and the stocks of the previous two years.Given the continuously large scale of artificial enhancements in this area, these data may indicate that releases of hatchery-reared F. chinensis individuals may be associated with inbreeding and potentially the reduction in genetic diversity of the F. chinensis population.
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The rat is used extensively by the pharmaceutical, regulatory, and academic communities for safety assessment of drugs and chemicals and for studying human diseases; however, its transcriptome has not been well studied. As part of the SEQC (i.e., MAQC-III) consortium efforts, a comprehensive RNA-Seq data set was constructed using 320 RNA samples isolated from 10 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four ages (2-, 6-, 21-, and 104-week-old) with four biological replicates for each of the 80 sample groups (organ-sex-age). With the Ribo-Zero rRNA removal and Illumina RNA-Seq protocols, 41 million 50 bp single-end reads were generated per sample, yielding a total of 13.4 billion reads. This data set could be used to identify and validate new rat genes and transcripts, develop a more comprehensive rat transcriptome annotation system, identify novel gene regulatory networks related to tissue specific gene expression and development, and discover genes responsible for disease and drug toxicity and efficacy.
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Supplementary Table 9 from Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq
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Supplementary Figure 1 from Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq
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