GENERAL INFORMATION
Title of Dataset: Transcriptomic MeRIP-Seq data of Lupinus angustifolius roots
The datasets contain the results of MeRIP-Seq analysis of 24 libraries, including three biological replicates for input samples [I] and after m6A immunoprecipitation [dM], obtained from the roots of narrow-leafed lupin (Lupinus angustifolius) grown under physiological conditions, 6-hour hypoxia, 15-hour hypoxia, and 6-hour reoxygenation
Author:
Dawid Jakub Kubiak, (dawidk@doktorant.umk.pl)
Institution:
Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Torun, Poland
Date of data collection: 2024
Geographic location of data collection: Poland
Keywords: stress granules, hypoxia, lupinus, transcriptome, m6A, MeRIP
Language information: English
Information about funding sources that supported the collection of the data: Polish National Science Center, grant PRELUDIUM; 2022/45/N/NZ9/04015
SHARING/ACCESS INFORMATION
Licenses/restrictions placed on the data: CC0
DATA & FILE OVERVIEW
File List:
1_Fastqc (Archive containing quality report results for raw sequencing reads of analyzed samples)
2_multiqc_trimmed (Summary report of read quality analysis after adapter filtering and trimming using the BBDuk tool)
3_multiqc_bowtie2 (Summary report of read mapping to rRNA using the Bowtie2 tool)
4_multiqc_clean (Quality analysis report of sequencing reads after rRNA removal)
5_multiqc_raw (Summary quality report of raw sequencing reads)
6_multiqc_STAR (Summary report of read mapping to the Lupinus genome using the STAR tool)
METHODOLOGICAL INFORMATION
Description of methods used for collection/generation of data: Quality control of raw sequencing reads was performed using FastQC software and then read filtering and adaptor pruning were performed using the BBDUK tool from the BBMAP package. Reads corresponding to rRNAs were knocked down using Bowtie2, using L. angustifolius ribosomal RNA sequences available in the Ensembl Plants 56 database.Purified reads were mapped to the reference genome using the STAR program.
Abbreviation list: I - Input, dM - m6A immunoprecipiation, K - control condition, 6 - 6h hypoxia H - 15h hypoxia, R - 15h hypoxia followed by 6h reoxygenation
