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pmid:26697343

Time-course investigation of the gene expression profile during Fasciola hepatica infection: A microarray-based study.

Jose Rojas-Caraballo · Julio López-Abán · Pedro Fernández-Soto · Belén Vicente · Francisco Collía · Antonio Muro

Genomics data · 2015 doi:10.1016/j.gdata.2015.08.020

Paper

complete

Experiment

complete

Data

partial

Analysis

complete

Execution

absent

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Time-course investigation of the gene expression profile during Fasciola hepatica infection: A microarray-based study.
doi
10.1016/j.gdata.2015.08.020
pmid
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Jose Rojas-Caraballo
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Julio López-Abán
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Pedro Fernández-Soto
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Belén Vicente
[4]
Francisco Collía
[5]
Antonio Muro
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Genomics data
year
2015
abstract
Fasciolosis is listed as one of the most important neglected tropical diseases according with the World Health Organization and is also considered as a reemerging disease in the human beings. Despite there are several studies describing the immune response induced by Fasciola hepatica in the mammalian host, investigations aimed at identifying the expression profile of genes involved in inducing hepatic injury are currently scarce. Data presented here belong to a time-course investigation of the gene expression profile in the liver of BALB/c mice infected with F. hepatica metacercariae at 7 and 21 days after experimental infection. The data published here have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE69588, previously published by Rojas-Caraballo et al. (2015) in PLoS One [1].
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Gene expression profile in the liver of BALB/c mice infected with Fasciola hepatica
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Three experimental groups were used. Group 1 remains untreated and served as control; group 2 was orally infected with Fasciola hepatica metacercariae on day 0 and humanely euthanized and necropsied at 7 days post-infection; group 3 was infected as above and humanely euthanized and necropsied at 21 days post-infection. In necropsy, liver of each mouse was removed and the RNA isolated. We investigated the gene expression profile in both early and late stages of infection compared to untreated group.
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We investigated the gene expression profile in both early and late stages of infection compared to untreated group."], ["Consent", "N/A"], ["Sample source location", "N/A"]], "row_count": 9, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0010"}}], "gaps": ["asset:data:geo:GSE69588 not downloaded", "asset:data:geo:GSE69588 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To assess differential gene expression, Limma moderated t-statistics [5], reporting a t-test statistic for each gene together with its corresponding p-value (generally called raw p-values) was used."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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