LMJFC_RNA-seq-heat shock

This dataset contains the alignment archives of RNA-seq reads derived from a project aimed to analyze variations in the Leishmania major (Friedlin strain) transcriptome elicited by a moderate heat shock treatment of the promastigote stage. Experimental details of this study were published in the article: Rastrojo, A., Corvo, L., Lombraña, R., Solana, J.C., Aguado, B., and Requena, J.M. (2019). Analysis by RNA-seq of transcriptomic changes elicited by heat shock in Leishmania major. Sci Rep 9, 6919. [PMID: 31061406].
In the mentioned article, RNA-seq reads were mapped on a previous L. major genome assembly, but in 2021 a new genome assembly was attained (Camacho, E., González-de la Fuente, S., Solana, J.C., Rastrojo, A., Carrasco-Ramiro, F., Requena, J.M., and Aguado, B. (2021). Gene annotation and transcriptome delineation on a de novo genome assembly for the reference Leishmania major Friedlin strain. Genes (Basel). 12, 1359. [PMID: 34573340]. Then, this dataset contains the alignment of those RNA-seq data on this new genome assembly.
In brief, the files were generated following these steps. First, RNA-seq reads were downloaded from the PRJEB27042 bioproject at ENA (https://www.ebi.ac.uk/ena/browser/view/PRJEB27042?show=reads). Second, RNA-seq reads were quality filtered using the Trimmomatic (v0.36) tool (parameters: quality > 25; length read >60). Finally, selected reads were mapped to the new L. major genome using bowtie2.
There are six bam files (and their auxiliary bam.bai ones) corresponding to the following biological samples: RNA-polyA from promastigotes growing at 26ºC (three replicates, LMJFC_Pro-26-R1 to –R3) and RNA-polyA from promastigotes heat-shocked for two hours at 37ºC (three replicates, LMJFC_Pro-37-R1 to –R3).

本数据集包含某研究项目生成的RNA测序（RNA-seq）读段比对存档，该项目旨在分析前鞭毛体阶段的利什曼原虫（Leishmania major）Friedlin株经适度热激处理诱导的转录组变化。本研究的实验细节已发表于以下论文：Rastrojo, A., Corvo, L., Lombraña, R., Solana, J.C., Aguado, B., and Requena, J.M. (2019). Analysis by RNA-seq of transcriptomic changes elicited by heat shock in Leishmania major. Sci Rep 9, 6919. [PMID: 31061406]。
在上述论文中，研究人员将RNA-seq读段比对至早期发布的L. major基因组组装版本，但2021年该团队获得了新的基因组组装结果（Camacho, E., González-de la Fuente, S., Solana, J.C., Rastrojo, A., Carrasco-Ramiro, F., Requena, J.M., and Aguado, B. (2021). Gene annotation and transcriptome delineation on a de novo genome assembly for the reference Leishmania major Friedlin strain. Genes (Basel). 12, 1359. [PMID: 34573340]）。本数据集即包含上述RNA-seq数据与该新版基因组组装序列的比对结果。
简言之，本数据集文件的生成流程如下：首先，从欧洲核苷酸档案馆（ENA）的PRJEB27042生物项目中下载RNA-seq读段（链接：https://www.ebi.ac.uk/ena/browser/view/PRJEB27042?show=reads）；其次，使用Trimmomatic（v0.36）工具对RNA-seq读段进行质量过滤，过滤参数为：质量值>25，读段长度>60；最后，利用bowtie2工具将筛选后的读段比对至新版L. major基因组。
本数据集包含6个BAM格式文件（及其配套的bam.bai索引文件），对应以下生物学样本：26℃下培养的前鞭毛体的polyA富集RNA（3个生物学重复，编号LMJFC_Pro-26-R1至-R3），以及经37℃热激2小时的前鞭毛体的polyA富集RNA（3个生物学重复，编号LMJFC_Pro-37-R1至-R3）。