Paratya australiensis protein-coding transcriptome

A collection of DNA and deduced protein sequences corresponding to the protein-coding transcriptome of adult specimens of the freshwater atyid shrimp Paratya australiensis. The sequences are derived from specimens from a laboratory-based experiment involving the exposure of shrimp to drain water from a site affected by acidification due to oxidation and re-wetting of acid sulphate soils. Please see associated publication in BMC Genomics (Bain et al., De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water, BMC Genomics, accepted manuscript).\nLineage: Total RNA was isolated from control specimens and specimens exposed to acid drainage water and mRNA was sequenced by a service provider using an Illumina HiSeq2000 instrument. Library preparation was strand-specific and sequences were generated using paired-end mode with 100 cycles. Putative transcripts were assembled in a de novo fashion (without a reference genome) using Trinity software (v. 2.0.6). Protein sequences were deduced using Transdecoder software (v. 2.0.1). Likely descriptions and functions were assigned using Blast2GO command-line v. 1.0.2.

本数据集收录了淡水匙指虾科（Atyidae）澳洲拟匙指虾（Paratya australiensis）成体的蛋白编码转录组对应的DNA序列与推导蛋白质序列。这些序列来源于一项实验室暴露实验的虾样本，实验将虾暴露于因酸性硫酸盐土壤氧化与复湿导致酸化的场地排出的水体中。相关研究成果已被《BMC Genomics》期刊接收（Bain 等：《响应酸性硫酸盐排水的澳洲拟匙指虾（十足目：Decapoda，匙指虾科：Atyidae）蛋白编码转录组的从头组装与变化分析》，《BMC Genomics》，已接收稿件）。
实验流程：从对照组样本与酸性排水暴露组样本中分离总RNA，随后由测序服务提供商使用Illumina HiSeq2000测序仪对mRNA进行测序。文库制备采用链特异性建库策略，测序模式为双端100循环测序。使用Trinity软件（版本2.0.6）以从头组装方式（无参考基因组）拼接得到推定转录本；使用Transdecoder软件（版本2.0.1）推导得到蛋白质序列；并通过Blast2GO命令行工具（版本1.0.2）为序列注释推定的功能与描述信息。

搜集汇总

背景与挑战

背景概述

该数据集包含澳大利亚淡水虾Paratya australiensis的蛋白质编码转录组序列，来源于实验室实验研究虾暴露于酸性排水环境下的基因表达变化。数据通过Illumina HiSeq2000测序、Trinity软件从头组装和Transdecoder推导蛋白质序列生成，并附有功能注释，旨在支持环境毒理学和基因表达分析研究。