BXD fasted gene expression liver microarray R5728

This work is licensed under a Creative Commons Attribution 4.0 International License.

© Copyright 2021 Laboratory of Integrative Systems Physiology, EPFL, Switzerland

This project is based on the following template: https://github.com/auwerxlab/renku-project-template/tree/master/R-renv (deb856b)

This is a Renku project, see https://renku.readthedocs.io for details.

Authors: Alexis Rapin (alexis.rapin@epfl.ch), Alexis Bachmann (alexis.bachmann@epfl.ch), Maroun Bou Sleiman (maroun.bousleiman@epfl.ch)

Description

This R project generates an expression matrix for microarray assays estimating genes expression in liver samples collected on the BXD mouse genetic diversity model.

Microarray assays intensities CEL files are downloaded from public sources (Gene Expression Omnibus) and are processed into an expression matrix using the Array Power Tool (APT) suite. All the processing is done within R notebooks located in the notebooks/ directory.

Data reuse

All that is needed for further gene expression analysis:

• Expression matrix: data/matrix/gc-sst-rma-sketch.summary.txt
  • Computation method description: data/matrix/gc-sst-rma-sketch.method_description.txt
• Metadata for samples included in expression matrix: data/run_samples.txt
  • Metadata fields description: data/run_samples_fields_description.txt

Ressources

• Knowledge base of the associated study: https://sv-renku-git.epfl.ch/lisp/bxd-fasted-knowledge-base

Get this project

You can clone this project from https://sv-renku-git.epfl.ch.

$ git clone https://sv-renku-git.epfl.ch/lisp/bxd-fasted-gene-expression-liver-microarray-r5728.git

If it is private, you would need a valid Gitlab token. Contact the authors if needed.

$ git clone https://< gitlab_token_name >:< gitlab_token >@sv-renku-git.epfl.ch/lisp/bxd-fasted-gene-expression-liver-microarray-r5728.git

You can get an archive of this project from https://github.com:

$ git clone https://github.com/auwerxlab/bxd-fasted-gene-expression-liver-microarray-r5728.git

And from Zenodo:

Requirements

• This is a Renku project, see https://renku.readthedocs.io for details
• R version 4.0.0
• renv R package
• See renv.lock for the complete list of R packages dependencies
• Array Power Tool binaries for the processing of microarray data (stored in opt/apt_2.11.3_linux_64_bit_x86_binaries): https://downloads.thermofisher.com/APT/APT_2.11.3/apt_2.11.3_linux_64_bit_x86_binaries.zip
• See Dockerfile for more system requirements
• A table of microarrays runs, in tab-delimited text format (included in the associated study knowledge base at https://sv-renku-git.epfl.ch/lisp/bxd-fasted-knowledge-base). See table below for format:

name	description	format	example	requirement
technology	Assay technology	Free text	microarray	Desired
platform_name	Platform name	Free text	Affymetrix Mouse Gene 1.0 ST Array	Required
platform_id	Platform accession number	GEO accession number (GPLxxxx)	GPL6246	Required
run_id	Unique run ID	Free text	R1234	Required
platform_support_files_misc	Platform manufacturer provided support files	URL	http://media.affymetrix.com/analysis/downloads/lf/wt/	Required
run_samples_source_private	Run samples metadata table	File URL	https://< server_name >:< path/to/run/metadata_file.txt >	Required
run_samples_fields_description_source_private	Run samples metadata fields description	File URL	https://< server_name >:< path/to/run/metadata_file.txt >	Required
run_protocols_source_private	Run protocols description table	File URL	https://< server_name >:< path/to/run/metadata_file.txt >	Desired
data_source_public_database_name	Public run data database name	Short name, see https://fairsharing.org	GEO	Desired
data_source_public_database_doi	Public run data database DOI	DOI, see https://fairsharing.org	10.25504/FAIRsharing.5hc8vt	Desired
data_source_public_accession	Public run data accession number	Accession number	GSE60149	Required
< additional_fields >	Any additional field			Optional

(Table created with https://www.tablesgenerator.com)

• Recommended minimal memory: 4GB

Data

Only essential data are archived. These include:

• Expression matrices: The expression matrix generated within this R project is available in data/matrix/gc-sst-rma-sketch.summary.txt.

Data that are not archived include:

• Microarray assay data: CEL files are not included. See data/microarray_runs.txt for the original data provenance.
• Microarray platform support files: Support files are not included. See data/microarray_runs.txt for sources.
• Transcript annotations: Transcript annotations are not included. See data/microarray_runs.txt for sources.

Usage

Run notebook/generate_expression_matrix.Rmd.

Render notebooks and archive essential files using make:

$ make
render               render all R notebooks located in notebooks/
commit               run git commit
archive              create an archive of this project in archive/ (CAUTION: will not include LFS objects)

Structure

.
├── archive                   Archives of this repos (not available in an archive)
├── data                      
│   ├── matrix                Expression values matrix
│   ├── raw                   Raw data (CEL files) (not available in an archive)
│   └── platform_files        
│       └── < platform_id >   Platform support files (not available in an archive)
├── lib                       Project R library
├── notebooks                 R notebooks
└── renv                      renv directory (set as a symbolic link in renku projects, not available in an archive)