14 research outputs found
summary_statistics
This file contains the details about the number of raw reads and the mapping statistics such as uniquely mapped reads, mapped to multiple loci and unmapped reads for all the samples
KEGG and Gene Ontology Pathway analysis of the downregulated genes in the brain
This file contains the list of genes associated with each enriched KEGG and GO terms in the whole brain samples of 0.3nM and 1.2nM PCB126 exposed adult fish. These GO and KEGG terms are enriched in the downregulated gene set
GSE98741
Strand-specific RNAsequencing data from zebrafish embryos, larvae and adult brain tissue developmentally exposed to two different concentrations of PCB126. Raw data files (fastq) were pre-processed, reads were mapped to the zebrafish genome (GRCz10; ensembl version 87) using STAR aligner. Read counts were obtained using HTSeq-count and differential gene expression analysis was done using edgeR
Differentially expressed genes
Each spread sheet contains the list of differentially expressed genes (FDR <5%) at each time point and concentration
Common genes
This is the list of genes that are common to both 0.3 nM and 1.2 nM PCB126 exposed adult whole brain samples
Common genes
This is the list of genes that are common to both 0.3 nM and 1.2 nM PCB126 exposed adult whole brain samples
KEGG and Geno Ontology Pathway analysis of upregulated genes in the brain
This file contains the list of genes that are represented under each enriched GO and KEGG pathway terms. These genes are differentially expressed in the adult brain samples exposed to either 0.3nM or 1.2nM PCB126
Binary Gene Expression Patterning of the Molt Cycle: The Case of Chitin Metabolism
<div><p>In crustaceans, like all arthropods, growth is accompanied by a molting cycle. This cycle comprises major physiological events in which mineralized chitinous structures are built and degraded. These events are in turn governed by genes whose patterns of expression are presumably linked to the molting cycle. To study these genes we performed next generation sequencing and constructed a molt-related transcriptomic library from two exoskeletal-forming tissues of the crayfish <i>Cherax quadricarinatus</i>, namely the gastrolith and the mandible cuticle-forming epithelium. To simplify the study of such a complex process as molting, a novel approach, binary patterning of gene expression, was employed. This approach revealed that key genes involved in the synthesis and breakdown of chitin exhibit a molt-related pattern in the gastrolith-forming epithelium. On the other hand, the same genes in the mandible cuticle-forming epithelium showed a molt-independent pattern of expression. Genes related to the metabolism of glucosamine-6-phosphate, a chitin precursor synthesized from simple sugars, showed a molt-related pattern of expression in both tissues. The binary patterning approach unfolds typical patterns of gene expression during the molt cycle of a crustacean. The use of such a simplifying integrative tool for assessing gene patterning seems appropriate for the study of complex biological processes.</p></div
Enrichment analysis test results for different tissues.
<p>Enrichment analysis test results of contigs in patterns 1111, 0110 and 0111 (a, b, and c, respectively) from the gastrolith- (left) and mandible cuticle-forming (right) epithelia. Black bars represent the observed number of hits in the sample, while grey bars represent the expected number of hits if the sample was chosen randomly. Significant differences between observed and expected number of hits are indicated by * (FDR <0.05) or ** (<i>p</i>-value <0.05).</p
Normalized read count of key chitin metabolism-related genes transcripts.
<p>Read count of key chitin metabolism-related genes transcripts from the gastrolith-forming epithelium (left) and the mandible cuticle-forming epithelium (right). Numbers on the X axis represent the four molt stages, 1 inter-molt (pool of animals, n = 1), 2 early pre-molt (pool of animals, n = 1), 3 late pre-molt (two single animals and one pool, n = 3) and 4 post-molt (all single animals, n = 2). Presented transcripts are (a) chitin synthase, (b) chitinase, (c) chitin deacetylase, (d) GlcN-6P synthase and (e) GlcN-6P deaminase. Letters represent statistical groups which are significantly different (<i>p</i>-value <0.05), error bars represent standard error.</p