Sex-specific effects of PM2.5 maternal exposure on offspring's serum lipoproteins and gut microbiota
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Air pollution air pollution,Air pollution
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mice dams exposed to filtered blanks PND 3
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ICR male mice exposed to PM 2.5
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ICR mice exposed to PM 2.5 air
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 7a & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: increased abundance in ICR male mice exposed to PM 2.5
NCBI | Quality Control | Links |
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Roseburia | ||
Alistipes | ||
Lachnospiraceae | ||
Rikenellaceae |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 7a & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: decreased abundance in ICR male mice exposed to PM 2.5
NCBI | Quality Control | Links |
---|---|---|
Aerococcaceae | ||
Facklamia | ||
Neisseria | ||
Neisseriaceae | ||
Neisseriales | ||
Staphylococcaceae | ||
Escherichia/Shigella sp. |
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mice dams exposed to filtered blanks PND 10
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ICR mice exposed to PM 2.5
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Curated date: 2021/01/10
Curator: Zyaijah Bailey
Source: Figure 7b & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: increased abundance in ICR male mice exposed to PM 2.5
NCBI | Quality Control | Links |
---|---|---|
Clostridiaceae | ||
Proteus | ||
Pseudonocardiales |
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mice dams exposed to filtered blanks PND 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 7c & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: increased abundance in ICR male mice exposed to PM 2.5
NCBI | Quality Control | Links |
---|---|---|
Bacillales | ||
Gemella | ||
Oscillibacter | ||
Roseburia | ||
Oscillibacter sp. | ||
Clostridium |
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mice dams exposed to filtered blanks PND 35
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 7d& text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: increased abundance in ICR male mice exposed to PM 2.5
NCBI | Quality Control | Links |
---|---|---|
Streptococcus | ||
Streptococcaceae |
Signature 2
Source: Figure 7d & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: decreased abundance in ICR male mice exposed to PM 2.5
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Desulfovibrio | ||
Bacteroidaceae | ||
Anaerotruncus |
Revision editor(s): Atrayees
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mice dams exposed to filtered blanks PND 10
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ICR female mice exposed to PM 2.5
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 2
Source: Figure 7f & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: decreased abundance in ICR female mice exposed to PM 2.5
NCBI | Quality Control | Links |
---|---|---|
Coriobacteriaceae | ||
Coriobacteriales | ||
Enterorhabdus | ||
Prevotellaceae | ||
Prevotella |
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mice dams exposed to filtered blanks PND 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 7g & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: increased abundance in ICR female mice exposed to PM 2.5
NCBI | Quality Control | Links |
---|---|---|
Deltaproteobacteria | ||
Desulfovibrionaceae | ||
Desulfovibrionales | ||
Verrucomicrobiaceae | ||
Verrucomicrobiia | ||
Verrucomicrobiales | ||
Verrucomicrobiota | ||
Anaerostipes sp. |
Signature 2
Curated date: 2021/01/10
Curator: Zyaijah Bailey
Source: Figure 7g & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: decreased abundance in ICR female mice exposed to PM 2.5
NCBI | Quality Control | Links |
---|---|---|
Lactobacillaceae | ||
Lactobacillus | ||
Streptophyta |
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mice dams exposed to filtered blanks PND 35
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 7h & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: increased abundance in ICR female mice exposed to PM 2.5
NCBI | Quality Control | Links |
---|---|---|
Oscillospiraceae |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 7h & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: decreased abundance in ICR female mice exposed to PM 2.5
NCBI | Quality Control | Links |
---|---|---|
Peptostreptococcaceae | ||
Clostridium |