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Supplementary tables for "Whole blood transcriptome profiles of trypanotolerant and trypanosusceptible cattle highlight a differential modulation of metabolism and immune response during infection by Trypanosoma congolense"
Supplementary tables for "Whole blood transcriptome profiles of trypanotolerant and trypanosusceptible cattle highlight a differential modulation of metabolism and immune response during infection by Trypanosoma congolense"
1 févr. 2023
Thévenon, Sophie, 2023, "Supplementary tables for "Whole blood transcriptome profiles of trypanotolerant and trypanosusceptible cattle highlight a differential modulation of metabolism and immune response during infection by Trypanosoma congolense"", https://doi.org/10.18167/DVN1/E3288X, CIRAD Dataverse, V1, UNF:6:PAv8RAjgQkbo5kXl4TpsEg== [fileUNF]
Supplementary figures and tables for "Whole blood transcriptome profiles of trypanotolerant and trypanosusceptible cattle highlight a differential modulation of metabolism and immune response during infection by Trypanosoma congolense"
AATTOL_Article_suppl_figures.1.pdf
AATTOL_Article_suppl_figures.1.pdf
1 févr. 2023 - Supplementary tables for "Whole blood transcriptome profiles of trypanotolerant and trypanosusceptible cattle highlight a differential modulation of metabolism and immune response during infection by Trypanosoma congolense"
Adobe PDF - 339,6 KB - MD5: e976912e257c177069aa2f7c799be1cb
Supplementary figures
AATTOL_Article_suppl_tables.1.tab
1 févr. 2023 - Supplementary tables for "Whole blood transcriptome profiles of trypanotolerant and trypanosusceptible cattle highlight a differential modulation of metabolism and immune response during infection by Trypanosoma congolense"
Tabular Data - 28,0 KB - 19 Variables, 126 Observations - UNF:6:PAv8RAjgQkbo5kXl4TpsEg==
Supplementary tables
Medium density genotyping dataset of 39 cattle from five West African breeds, associated to the article "A Comparison of Phenotypic Traits Related to Trypanotolerance in Five West African Cattle Breeds Highlights the Value of Shorthorn Taurine Breeds" (Berthier et al 2015)
2 déc. 2022
Thévenon, Sophie, 2022, "Medium density genotyping dataset of 39 cattle from five West African breeds, associated to the article "A Comparison of Phenotypic Traits Related to Trypanotolerance in Five West African Cattle Breeds Highlights the Value of Shorthorn Taurine Breeds" (Berthier et al 2015)", https://doi.org/10.18167/DVN1/APTZOC, CIRAD Dataverse, V1, UNF:6:YCYOQEERwlOPbFR85K9rtg== [fileUNF]
This dataset consists of genotypes of 39 animals belonging to five cattle breeds genotyped using the Illumina BovineSNP50 chip assay v2 [39] at the INRA Labogena platform (Jouy-en-Josas, France) using standard procedures. The animals were further infected by Trypanosoma congolens...
AATTOL_metadata_animal.tab
2 déc. 2022 - Medium density genotyping dataset of 39 cattle from five West African breeds, associated to the article "A Comparison of Phenotypic Traits Related to Trypanotolerance in Five West African Cattle Breeds Highlights the Value of Shorthorn Taurine Breeds" (Berthier et al 2015)
Tabular Data - 1,1 KB - 1 Variables, 39 Observations - UNF:6:YCYOQEERwlOPbFR85K9rtg==
Data
file containing the breed name, the breed code of the animals and two individual identifiers: Animal code as used in Berthier et al 2015 and in GEO GSE197108 dataset; and Animal ID as used in the genotyping file
cattle__54229variants__39individuals.ped
2 déc. 2022 - Medium density genotyping dataset of 39 cattle from five West African breeds, associated to the article "A Comparison of Phenotypic Traits Related to Trypanotolerance in Five West African Cattle Breeds Highlights the Value of Shorthorn Taurine Breeds" (Berthier et al 2015)
Unknown - 8,1 MB - MD5: 4f36457517bb8c027e514ea6c5eca96e
Data
genotyping data file named (39 rows, 108464 columns) that contains, for each individual, six information columns (Breed code, Animal ID and four columns with data coded 0 or U) and the genotypes (alleles 1 and 2, ACGT Illumina TOP format) for the 54229 SNPs.
cattle__54229variants.map
2 déc. 2022 - Medium density genotyping dataset of 39 cattle from five West African breeds, associated to the article "A Comparison of Phenotypic Traits Related to Trypanotolerance in Five West African Cattle Breeds Highlights the Value of Shorthorn Taurine Breeds" (Berthier et al 2015)
Unknown - 1,7 MB - MD5: ec27291dde99bfab017024bea7d202e8
Data
SNP map file named (54229 rows, 4 columns) that contains for each SNP, the autosome number, the SNP name, a column with data coded 0 and the SNP position on autosome. SNP are mapped on the bovine genome UMD3.1 assembly.
Whole blood transcriptome data of five West African cattle breeds before and during an infection by Trypanosoma congolense IL1180, inference on bovine trypanotolerance
2 déc. 2022
Thévenon, Sophie, 2022, "Whole blood transcriptome data of five West African cattle breeds before and during an infection by Trypanosoma congolense IL1180, inference on bovine trypanotolerance", https://doi.org/10.18167/DVN1/L9SHAX, CIRAD Dataverse, V1, UNF:6:wpyUSJA6nDclMtU/CKcEAA== [fileUNF]
Gene expression data, scripts for bioinformatic and statistical analyses, and output tables related to the paper entitled “Whole blood transcriptome profiles of trypanotolerant and trypanosusceptible cattle highlight a differential modulation of metabolism and immune response dur...
AATTOL_bioinformatic_steps.sh
2 déc. 2022 - Whole blood transcriptome data of five West African cattle breeds before and during an infection by Trypanosoma congolense IL1180, inference on bovine trypanotolerance
Shell Script - 5,6 KB - MD5: 20aecf6252bcb83508877b77c9bb4b1f
Code
script: This file describes the bioinformatic steps of the RNA-seq analysis (mapping, gene count)
AATTOL_IPA_EdgeR_108b_Nested_Comp15_CanPath.tab
2 déc. 2022 - Whole blood transcriptome data of five West African cattle breeds before and during an infection by Trypanosoma congolense IL1180, inference on bovine trypanotolerance
Tabular Data - 66,3 KB - 16 Variables, 363 Observations - UNF:6:jtQhSAP9C4+vXZ8EzW9cgQ==
Data
Output from IPA analysis for the input files edger_*_3DPI_0_13107_nested_IN_IPA.txt concerning the canonical pathways
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