INTRODUCTION
This directory is part of the official repository of public bioinformatics
data sets available from IFREMER research teams.

PROJECT PESTO
This study goes further previous investigations which highlited impacts of pesticides from the gene to the organism scales and sometimes in a multigenerational way.
However, ecotoxicological studies often investigate single contaminants and use high concentrations that are not ecologically relevant.
Moreover, multigenerationnal studies mostly investigate late exposure (during gametogenesis) whereas early developmental stages are windows of high susceptibility to environmental stressors.
therefore, the PESTO project has two main questions:
1) What are the effects of an early exposure to environmentally relevant pesticide mixture in the Pacific oyster;
2) Are those effects persistents across generations.

PUBLICATION
Published to ENA under the accession number PRJEB58545 (Methyl-Seq) and PRJEB58194 (RNA-Seq).
See: https://www.ebi.ac.uk/ena/browser/view/PRJEB58545 and https://www.ebi.ac.uk/ena/browser/view/PRJEB58194

DOI: https://doi.org/10.12770/32b0c391-81a5-4132-8dbe-cdd08cca98b3 (RNA-Seq) and https://doi.org/10.12770/36afef27-0fe0-4881-83e2-bfcfa9ccc52d (Methyl-Seq)

DATA ORGANIZATION
Project is organized as follows: data is distributed
within several sub-folders all of them being named using the
EDAM Ontology (https://www.ebi.ac.uk/ols/ontologies/edam).

1/ Raw data is available from the 'data' sub-folder.

2/ Results from processing raw data is available in 'operation' sub-folder.

3/ In turn, sub-folders within 'data' and 'operation' rely on EDAM terms
depending on data type (data sub-folder) or operation type (operation
sub-folder).

DIRECTORY CONTENT
Raw fastq files are located in data/dna-sequence-raw and data/rna-sequence-raw folders.
Metadata are located in data/report/athena where one can find 2022_Methyl-Seq_PESTO_PUBLIC.xlsx and 2022_RNA-Seq_PESTO_PUBLIC.xlsx
files.
Metadata are also accessible through data/report/athena/XML XML files.

DATA RETRIEVAL
wget -r -np -nH --cut-dirs=4 ftp://ftp.ifremer.fr/ifremer/dataref/bioinfo/be/PESTO

Command-line explained:

          -r: is for recursively download;
         -np: is for no parent ascending;
         -nH: is for disabling creation of directory having name same as URL i.e. ftp.ifremer.fr;
  --cut-dirs: is for ignoring number of parent directories.

see https://data-dataref.ifremer.fr/bioinfo/ifremer/README.txt for more details.