LMJFC_RNA-seq-heat shock

Published: 6 June 2022| Version 1 | DOI: 10.17632/g4hjfnvk46.1
Contributors:
Jose M. Requena,
Jose C. Solana

Description

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).

Files

Steps to reproduce

These data can be visualized using the IGV tool. For this purpose, you can download the genome available in Mendeley dataset LMJFC_Genome sequence (DOI:10.17632/mcxg7rt2rv.1) and LMJFC_Transcriptome (DOI:10.17632/fz855n45jr.1)

Institutions

Universidad Autonoma de Madrid

Categories

RNA Sequencing, Transcriptome, Heat Shock Response, Leishmania

License