run_metadata: 76318

This data as json

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76318	SRR24827621	SRX20592546	SRS17893038	SRP441132	PRJNA980117	Sex blind: bridging the gap between drug exposure and sex related gene expression in Danio rerio using next generation sequencing NGS data and a literature review to find the missing links in pharmaceutical and environmental toxicology studies	GSE234104	Transcriptome Analysis	Abstract: The sex of both humans and Danio rerio has previously been shown to affect the way individuals respond to drug exposure. Genes which allow identification of sex in juvenile zebrafish show potential to reveal these confounding variables between sex in toxicological and preclinical trials but the link between these is so far missing. These sex specific early expressed genes where expression is not altered by drug exposure must be carefully selected for this purpose. We aimed to discover genes which can be used in pharmaceutical trials and environmental toxicology studies to uncover sex related variations in gene expression with drug application using the model organism Danio rerio. Previously published early sex determining genes from King et al. were evaluated as well as additional genes selected from our zebrafish Next generation sequencing NGS data which are known from previously published works not to be susceptible to changes in expression with drug exposure. NGS revealed a further ten female specific genes vtg1 cyp17a1 cyp19a1a igf3 ftz f1 gdf9 foxl2a Nr0b1 ipo4 lhcgr and five male related candidate genes FKBP5 apobb1 hbaa1 dmrt1 spata6 which are also expressed in juvenile zebrafish 28 dpf dpf. Following this a literature review was performed to classify which of these early expressed sex specific genes are already known to be affected by drug exposure in order to determine candidate genes to be used in pharmaceutical trials or environmental toxicology testing studies. Discovery of these early sex determining genes in Danio rerio will allow identification of sex related responses to drug testing to improve sex specific healthcare and the medical treatment of human patients. Overall design: NGS RNA sequences were produced from two 28 dpf zebrafish which we classified as juvenile in this paper two adult male and two adult female zebrafish using whole body tissue samples. Juveniles were tested to indicate whether sex was genetically visible at this stage of development. RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF Basel according to Illumina's standard protocol for RNA sequencing Illumina Inc. San Diego USA Cat. # RS 100 0801. The NGS transcript data of the sampled zebrafish were compared to identify possible genes that contribute to sex determination as well as those which are expressed early in juvenile development 28dpf King et al. 2020. All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al. 2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al. 2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al. 2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2 the NGS data was normalised and differential gene expression analysis of juvenile male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al. 2014; King et al. 2020. Normalisation was based on the 'median of ratios' the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Four male Sox9a Gapdhs atp1b1a and cyp26b1 and nine female genes gyg1a rdh10b pdia KPNA2 ccnb1 ctsla Chr4 bmp15 and zbp3 which were previously identified as an early sex determining marker in zebrafish King et al. 2020 were used within a literature search to access previous information as to whether their level of expression was known to be influenced by certain drugs. In this study a further ten female and five male genes which could be used in early sex determination were selected from NGS data. A literature search was also carried out on these genes to discover if they were known to be affected by drug usage. Based on published literature from ScienceDirect in early 2021 we obtained information previous studies from the past twenty years by searching for the key terms; including the gene name drug or pharmaceutical exposure sex or gender influence. Then we eliminated irrelevant literature by reading the titles and abstracts and supplemented our literature database by reading the references of the selected studies. We used the selected literature to inform whether genes highlighted from our NGS data as early expressed within juveniles could be candidates in drug trials. Finally we grouped early expressed genes from NGS data based on the literature search into three categories. If the study was shown to affect the expression of the selected genes then they were deemed not good to use in pharmaceutical trials. Conversely if it was not known from previous research that drugs affect the expression of a certain gene it was included as a potential candidate for revealing how sex response differs with drug exposure and further investigation of its use in this area is necessary in future research.		pubmed:37398910		Adult male Danio rerio 2	GSM7445819		source name:Whole body\|tissue:Whole body\|cell type:male\|developmental stage:Adult\|treatment:N/A\|geo loc name:missing\|collection date:missing	Adult male Danio rerio 2	All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al. 2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al. 2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al. 2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2 the NGS data was normalised and differential gene expression analysis of juvenile male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al. 2014; King et al. 2020. Normalisation was based on the ‘median of ratios’ the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Assembly: StringTie Galaxy Version 1.3.4 Pertea et al. 2015. Supplementary files format and content: Tables of gene expression	Whole body	No experiments were carried out with live adult nor subadult fish before euthanasia. Accordingly animal welfare guidelines were followed while zebrafish were kept by the breeder.	RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF Basel according to Illumina’s standard protocol for RNA sequencing Illumina Inc. San Diego USA Cat. # RS 100 0801. Galaxy server usegalaxy.org	NGS data was collected from 28 dpf and adult zebrafish which had already been euthanised with Tricaine by the breeder.	tissue:Whole body\|cell type:male\|developmental stage:Adult\|treatment:N/A	GSM7445819	GSM7445819: Adult male Danio rerio 2; Danio rerio; RNA Seq	GSM7445819 r1	GSM7445819	1	RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF Basel according to Illumina's standard protocol for RNA sequencing Illumina Inc. San Diego USA Cat. # RS 100 0801. Galaxy server usegalaxy.org		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP441132		loader:fastq load.py	adult_male2.fastq.gz	fastq	6427348500.0	84570375.0	GSM7445819 r1	0:76	A:1545286842;C:1577518751;G:1546293475;T:1758222296;N:27136	76				1545286842	1577518751	1546293475	1758222296	27136	SRX20592546	SRS17893038	SRA1649389	Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland	Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland	1	0.96097		0.05997		0.67892		0.50309		76		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown		Switzerland	2023-06-05	Adult	Adult	Trunk	Surface Structure