Journal
Elife
Publication Date
2021
Volume
10
First Page
e66703
Document Type
Open Access Publication
DOI
10.7554/eLife.66703
Rights and Permissions
eLife 2021;10:e66703 DOI: 10.7554/eLife.66703. © 2021, Santeford et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
Recommended Citation
Santeford, Andrea; Lee, Aaron Y.; Sene, Abdoulaye; Hassman, Lynn M.; Sergushichev, Alexey A.; Loginicheva, Ekaterina; Artyomov, Maxim N.; Ruzycki, Philip A.; and Apte, Rajendra S., "Loss of Mir146b with aging contributes to inflammation and mitochondrial dysfunction in thioglycollate-elicited peritoneal macrophages." Elife. 10, e66703 (2021).
https://digitalcommons.wustl.edu/open_access_pubs/10865
elife-66703-fig1-data1-v4.xlsx (866 kB)
Flow cytometry density plots from TGEMs isolated from (n = 5) 3-month (bottom row)- and (n = 5) 20-month-old (top row) mice and stained with CD11b eFluor 450 and F4/80 Allophycocyanin (APC) along with numerical values for each mouse indicating the percentage of cells stained double-positive for both markers (CD11b+/F4/80+).
elife-66703-fig1-data2-v4.xls (108 kB)
Figure 1—source data 2 miRNA expression values in reads per million from small RNA-seq of female TGEMs at 3, 6, 12, 18, 24, and 30 months of age (related to Figure 1A and Figure 1—figure supplement 2A and I).
elife-66703-fig1-data3-v4.xlsx (11 kB)
Relative miRNA expression values from qPCR of TGEMs from 3-month (n = 9 mice)-, 12-month (n = 8 mice)-, and 20-month (n = 9 mice)-old female mice. Numerical values are displayed in graphs for (B) Mir146b, (C) Mir22, (D) Mir15a, (E) Mir29a, (F) Mir423, (G) Mir146a, and (H) Mir18a.
elife-66703-fig1-data4-v4.xlsx (8 kB)
Relative Mir146b miRNA expression values used for the graph from qPCR of TGEMs from n = 9 young (3 months) or n = 8 old (30 months) female mice (related to Figure 1B).
elife-66703-fig1-data5-v4.xlsx (9 kB)
Relative Mir146b miRNA expression values used for the graph from qPCR of BMDMs from n = 9 young (3 months) or n = 9 old (30 months) female mice (related to Figure 1C ).
elife-66703-fig1-data6-v4.xlsx (8 kB)
Relative Mir146b miRNA expression values used for graphs from qPCR of young female TGEMs (n = 3 mice) vs BMDMs (n = 6 mice) (related to Figure 1D).
elife-66703-fig1-data7-v4.xlsx (8 kB)
Relative Mir146b miRNA expression values used for graphs from Quantigene 2.0 assay of TGEMs from n = 6 young (3 months) or n = 6 old (30 months) female mice (related to Figure 1E).
elife-66703-fig2-data1-v4.xlsx (8 kB)
Relative Mir146b miRNA expression values used for graphs from qPCR of sham-transfected (n = 6) or Mir146b inhibitor-transfected (n = 6) female TGEMs.
elife-66703-fig2-data2-v4.xlsx (21 kB)
Relative mRNA expression values of Nos2, Il1b, Il6, Ccl2, Mmp9, Il10, Arg1, and Cd163 used for graphs from qPCR of sham-transfected (n = 3 independent biological samples) vs Mir146b inhibitor-transfected (n = 3 independent biological samples) pooled female TGEMs.
elife-66703-fig2-data3-v4.xlsx (11 kB)
Relative Mir146b miRNA expression values used for graphs from qPCR of Control (n = 6 mice) vs cKO (n = 6 mice) TGEMs.
elife-66703-fig2-data4-v4.xlsx (11 kB)
Relative Mir146a miRNA expression values used for graphs from qPCR of TGEMs from female Control (n = 6) vs cKO (n = 6) mice.
elife-66703-fig2-data5-v4.xlsx (24 kB)
Relative mRNA expression values of Nos2, Il1b, Il6, Ccl2, Mmp9, Il10, Arg1, and Cd163 used for graphs from qPCR of pooled TGEMs from female Control (n = 8 independent biological samples) vs cKO (n = 7 independent biological samples) mice.
elife-66703-fig3-data1-v4.zip (82949 kB)
Figure 3—source data 1 Representative x5000 transmission electron microscopy (TEM) images of Control (WT) TGEMs.
elife-66703-fig3-data2-v4.zip (79690 kB)
Figure 3—source data 2 Representative x5000 TEM images of cKO TGEMs.
elife-66703-fig3-data3-v4.xlsx (8 kB)
Figure 3—source data 3 Numerical values used in graphs from the number of mitochondrial structures per cell in Control (Cntl) (n = 12) vs cKO (n = 9) female TGEMs.
elife-66703-fig3-data4-v4.zip (61447 kB)
Figure 3—source data 4 Representative x25,000 TEM images of Control (WT) TGEMs.
elife-66703-fig3-data5-v4.zip (69201 kB)
Figure 3—source data 5 Representative x25,000 TEM images of cKO TGEMs.
elife-66703-fig3-data6-v4.xlsx (20 kB)
Figure 3—source data 6 Numerical values used for graphs from measurements of intracrystal space width (nm) in TGEMs from female Control (WT) vs cKO TGEMs.
elife-66703-fig3-data7-v4.xlsx (9 kB)
Figure 3—source data 7 Numerical values of absorbance at 590 nM used for graphs from the MTT assay of female Control (Cntl) (n = 7 mice) vs cKO (n = 7 mice) TGEMs.
elife-66703-fig3-data8-v4.xlsx (9 kB)
Figure 3—source data 8 Numerical values used for graphs of the oxygen consumption rate (pmol/min) from Seahorse Mitostress Assay of TGEMs from female Control (n = 3 mice) vs cKO (n = 4 mice) TGEMs.
elife-66703-fig3-data9-v4.xlsx (9 kB)
Figure 3—source data 9 Numerical values used for graphs of the extracellular acidification rate (mpH/min) from Seahorse Mitostress Assay of TGEMs from female Control (n = 3 mice) vs cKO (n = 4 mice) TGEMs.
elife-66703-fig3-data10-v4.xlsx (9 kB)
Figure 3—source data 10 Numerical values used for graph of the oxygen consumption rate (pmol/min) from Seahorse Mitostress Assay of TGEMs from female Control transfected (n = 6) vs Mir146b overexpression (n = 8).
elife-66703-fig3-data11-v4.xlsx (9 kB)
Figure 3—source data 11 Numerical values used for graphs of the extracellular acidification rate (mpH/min) from Seahorse Mitostress Assay of TGEMs from Control transfected (n = 6) vs Mir146b overexpression (n = 8).
elife-66703-fig4-data1-v4.xlsx (12 kB)
Figure 4—source data 1 DESeq2 result file used for creating heatmaps from bulk RNA-seq of TGEMs from female Control vs cKO mice.
elife-66703-fig4-data2-v4.txt (649 kB)
Figure 4—source data 2 Normalized average expression of each expressed gene within the three clusters defined by scRNA-seq analysis of young Control, young cKO, old Control, and old cKO TGEMs from female mice.
elife-66703-fig4-data3-v4.xlsx (12 kB)
Figure 4—source data 3 Genes from clustering results used for creating heatmaps from scRNA-seq of young Control, young cKO, old Control, and old cKO TGEMs from female mice.
elife-66703-resp-fig1-v4.jpg (66 kB)
Author response image 1
elife-66703-resp-fig2-v4.jpg (22 kB)
Author response image 2
elife-66703-resp-fig3-v4.jpg (62 kB)
Author response image 3
elife-66703-supp1-v4.docx (13 kB)
Genes associated with each subcluster pattern from scRNA-seq analysis, graphically represented in Figure 4—figure supplement 2.
elife-66703-supp2-v4.docx (12 kB)
Supplementary file 2 Primers used for genotyping.
elife-66703-transrepform-v4.docx (245 kB)
Transparent reporting form
Flow cytometry density plots from TGEMs isolated from (n = 5) 3-month (bottom row)- and (n = 5) 20-month-old (top row) mice and stained with CD11b eFluor 450 and F4/80 Allophycocyanin (APC) along with numerical values for each mouse indicating the percentage of cells stained double-positive for both markers (CD11b+/F4/80+).
elife-66703-fig1-data2-v4.xls (108 kB)
Figure 1—source data 2 miRNA expression values in reads per million from small RNA-seq of female TGEMs at 3, 6, 12, 18, 24, and 30 months of age (related to Figure 1A and Figure 1—figure supplement 2A and I).
elife-66703-fig1-data3-v4.xlsx (11 kB)
Relative miRNA expression values from qPCR of TGEMs from 3-month (n = 9 mice)-, 12-month (n = 8 mice)-, and 20-month (n = 9 mice)-old female mice. Numerical values are displayed in graphs for (B) Mir146b, (C) Mir22, (D) Mir15a, (E) Mir29a, (F) Mir423, (G) Mir146a, and (H) Mir18a.
elife-66703-fig1-data4-v4.xlsx (8 kB)
Relative Mir146b miRNA expression values used for the graph from qPCR of TGEMs from n = 9 young (3 months) or n = 8 old (30 months) female mice (related to Figure 1B).
elife-66703-fig1-data5-v4.xlsx (9 kB)
Relative Mir146b miRNA expression values used for the graph from qPCR of BMDMs from n = 9 young (3 months) or n = 9 old (30 months) female mice (related to Figure 1C ).
elife-66703-fig1-data6-v4.xlsx (8 kB)
Relative Mir146b miRNA expression values used for graphs from qPCR of young female TGEMs (n = 3 mice) vs BMDMs (n = 6 mice) (related to Figure 1D).
elife-66703-fig1-data7-v4.xlsx (8 kB)
Relative Mir146b miRNA expression values used for graphs from Quantigene 2.0 assay of TGEMs from n = 6 young (3 months) or n = 6 old (30 months) female mice (related to Figure 1E).
elife-66703-fig2-data1-v4.xlsx (8 kB)
Relative Mir146b miRNA expression values used for graphs from qPCR of sham-transfected (n = 6) or Mir146b inhibitor-transfected (n = 6) female TGEMs.
elife-66703-fig2-data2-v4.xlsx (21 kB)
Relative mRNA expression values of Nos2, Il1b, Il6, Ccl2, Mmp9, Il10, Arg1, and Cd163 used for graphs from qPCR of sham-transfected (n = 3 independent biological samples) vs Mir146b inhibitor-transfected (n = 3 independent biological samples) pooled female TGEMs.
elife-66703-fig2-data3-v4.xlsx (11 kB)
Relative Mir146b miRNA expression values used for graphs from qPCR of Control (n = 6 mice) vs cKO (n = 6 mice) TGEMs.
elife-66703-fig2-data4-v4.xlsx (11 kB)
Relative Mir146a miRNA expression values used for graphs from qPCR of TGEMs from female Control (n = 6) vs cKO (n = 6) mice.
elife-66703-fig2-data5-v4.xlsx (24 kB)
Relative mRNA expression values of Nos2, Il1b, Il6, Ccl2, Mmp9, Il10, Arg1, and Cd163 used for graphs from qPCR of pooled TGEMs from female Control (n = 8 independent biological samples) vs cKO (n = 7 independent biological samples) mice.
elife-66703-fig3-data1-v4.zip (82949 kB)
Figure 3—source data 1 Representative x5000 transmission electron microscopy (TEM) images of Control (WT) TGEMs.
elife-66703-fig3-data2-v4.zip (79690 kB)
Figure 3—source data 2 Representative x5000 TEM images of cKO TGEMs.
elife-66703-fig3-data3-v4.xlsx (8 kB)
Figure 3—source data 3 Numerical values used in graphs from the number of mitochondrial structures per cell in Control (Cntl) (n = 12) vs cKO (n = 9) female TGEMs.
elife-66703-fig3-data4-v4.zip (61447 kB)
Figure 3—source data 4 Representative x25,000 TEM images of Control (WT) TGEMs.
elife-66703-fig3-data5-v4.zip (69201 kB)
Figure 3—source data 5 Representative x25,000 TEM images of cKO TGEMs.
elife-66703-fig3-data6-v4.xlsx (20 kB)
Figure 3—source data 6 Numerical values used for graphs from measurements of intracrystal space width (nm) in TGEMs from female Control (WT) vs cKO TGEMs.
elife-66703-fig3-data7-v4.xlsx (9 kB)
Figure 3—source data 7 Numerical values of absorbance at 590 nM used for graphs from the MTT assay of female Control (Cntl) (n = 7 mice) vs cKO (n = 7 mice) TGEMs.
elife-66703-fig3-data8-v4.xlsx (9 kB)
Figure 3—source data 8 Numerical values used for graphs of the oxygen consumption rate (pmol/min) from Seahorse Mitostress Assay of TGEMs from female Control (n = 3 mice) vs cKO (n = 4 mice) TGEMs.
elife-66703-fig3-data9-v4.xlsx (9 kB)
Figure 3—source data 9 Numerical values used for graphs of the extracellular acidification rate (mpH/min) from Seahorse Mitostress Assay of TGEMs from female Control (n = 3 mice) vs cKO (n = 4 mice) TGEMs.
elife-66703-fig3-data10-v4.xlsx (9 kB)
Figure 3—source data 10 Numerical values used for graph of the oxygen consumption rate (pmol/min) from Seahorse Mitostress Assay of TGEMs from female Control transfected (n = 6) vs Mir146b overexpression (n = 8).
elife-66703-fig3-data11-v4.xlsx (9 kB)
Figure 3—source data 11 Numerical values used for graphs of the extracellular acidification rate (mpH/min) from Seahorse Mitostress Assay of TGEMs from Control transfected (n = 6) vs Mir146b overexpression (n = 8).
elife-66703-fig4-data1-v4.xlsx (12 kB)
Figure 4—source data 1 DESeq2 result file used for creating heatmaps from bulk RNA-seq of TGEMs from female Control vs cKO mice.
elife-66703-fig4-data2-v4.txt (649 kB)
Figure 4—source data 2 Normalized average expression of each expressed gene within the three clusters defined by scRNA-seq analysis of young Control, young cKO, old Control, and old cKO TGEMs from female mice.
elife-66703-fig4-data3-v4.xlsx (12 kB)
Figure 4—source data 3 Genes from clustering results used for creating heatmaps from scRNA-seq of young Control, young cKO, old Control, and old cKO TGEMs from female mice.
elife-66703-resp-fig1-v4.jpg (66 kB)
Author response image 1
elife-66703-resp-fig2-v4.jpg (22 kB)
Author response image 2
elife-66703-resp-fig3-v4.jpg (62 kB)
Author response image 3
elife-66703-supp1-v4.docx (13 kB)
Genes associated with each subcluster pattern from scRNA-seq analysis, graphically represented in Figure 4—figure supplement 2.
elife-66703-supp2-v4.docx (12 kB)
Supplementary file 2 Primers used for genotyping.
elife-66703-transrepform-v4.docx (245 kB)
Transparent reporting form
