mouse microarray datasets  (Allen Institute for Brain Science)

Journal: International Journal of Molecular Sciences

Article Title: Downregulation of Enteroendocrine Genes Predicts Survival in Colon Cancer: A Bioinformatics-Based Analysis

doi: 10.3390/ijms262211127

Figure Lengend Snippet: Differential expression analysis of microarray data from experimental and human colorectal cancer tissue. ( A , B ) Principal component analysis (PCA) plots of public microarray datasets from mouse GSE86299 ( A ) and human GSE8671 ( B ) tissue, comparing normal colon (blue) and colorectal cancer (CRC) (red). Mouse n = 8 per group; human n = 32 per group. These are representative datasets of a total of three analyzed . ( C , D ) Volcano plots displaying differential gene expression comparing murine ( C ) and human ( D ) CRC tissue with adjacent normal tissue. Genes down- and upregulated in cancer tissue are highlighted in blue and red, respectively. ( E ) Venn diagram illustrating the most common up- and downregulated genes across three experimental mouse models of colitis-associated colorectal cancer (CAC) derived from Gene Expression Omnibus (GEO) datasets. ( F ) Venn diagram illustrating the most common up- and downregulated genes across three human CRC datasets from GEO. The analysis was performed using the limma package version 3.16.2 with cut-offs of false discovery rate ( FDR ) < 0.05 (Benjamini–Hochberg method) and log 2 F C (fold change) < − 1 and > 1 .

Article Snippet: We explored the presence or absence of secretory IEC markers by analyzing three different mouse CRC microarray datasets from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database ( GSE86299 , GSE31105 , and GSE64658 ).

Techniques: Quantitative Proteomics, Microarray, Gene Expression, Derivative Assay

Journal: Cell reports

Article Title: Thbs1 regulates skeletal muscle mass in a TGFβ-Smad2/3-ATF4-dependent manner

doi: 10.1016/j.celrep.2024.114149

Figure Lengend Snippet: (A) Fold change in the expression of Thbs1 mRNA in soleus following 30 days of microgravity exposure (space flight) compared to control. Microarray dataset GEO: GSE80223 was analyzed from the Gene Expression Omnibus repository. Error bars denote ±SEM from n = 3 biologically independent animals per group; ** p < 0.01 by two-tailed unpaired Student’s t test. (B) RT-qPCR for Thbs1 , Thbs2 , Thbs3 , Thbs4 , and Thbs5 mRNA in the right tibialis anterior (TA) of 12-week-old wild-type (WT) mice subjected to 3 or 6 days (d) of unilateral hindlimb denervation, compared contralateral sham-operated leg. Error denote ±SEM from n = 3–5 biologically independent animals per group. * p < 0.05 by two-tailed unpaired Student’s t test. (C) Western blot for Thbs1 and Gapdh control in right TA of 12-week-old WT mice subjected to 3 or 10 days (d) of unilateral hindlimb denervation, compared to contralateral, sham-operated TA. n = 2 biologically independent animals per time point. (D) Representative immunohistochemistry for endogenous Thbs1 (green) and BiP (red) to visualize the endoplasmic reticulum (ER) on cryo-embedded TA of WT mice subjected to 10 days (d) of denervation compared to sham-operated controls at 12 weeks of age. Nuclei are shown in blue with DAPI. Scale bars represent 50 μm. (E) RT-qPCR for Thbs1 mRNA from TA of 8-week-old mice fed ad libitum or fasted for 48 h. Data are presented as fold expression over fed WT; error bars denote ±SEM from n = 4 biologically independent animals analyzed per group. * p < 0.05 by two-tailed unpaired Student’s t test. (F and G) Western blot for Thbs1 and Gapdh in TA of 8-week-old mice fed ad libitum or fasted for 48 h (F), and in young (12 weeks of age) and old (24 months of age) WT quadriceps (G). (H) Representative immunohistochemistry for endogenous Thbs1 (green), BiP (red), and the nucleus (DAPI, blue) on cryo-embedded 12-week-old (“young”) and 24-month-old (“old”) WT quadriceps. Scale bars represent 50 μm.

Article Snippet: A literature search yielded a publicly available Affymetrix Mouse Genome 430A 2.0 microarray dataset (NCBI GEO Repository, GSE80223) in which Gambara G. et al. compared the gene expression adaptation in soleus from adult C57Bl/n6 mice that were flown in space aboard the BION-M1 biosatelite for 30 days in orbit ( n = 3), and from sex- and age-matched control mice that were housed in standard vivarium cages ( n = 3).

Techniques: Expressing, Control, Microarray, Two Tailed Test, Quantitative RT-PCR, Western Blot, Immunohistochemistry

Journal: Cell reports

Article Title: Thbs1 regulates skeletal muscle mass in a TGFβ-Smad2/3-ATF4-dependent manner

doi: 10.1016/j.celrep.2024.114149

Figure Lengend Snippet:

Article Snippet: A literature search yielded a publicly available Affymetrix Mouse Genome 430A 2.0 microarray dataset (NCBI GEO Repository, GSE80223) in which Gambara G. et al. compared the gene expression adaptation in soleus from adult C57Bl/n6 mice that were flown in space aboard the BION-M1 biosatelite for 30 days in orbit ( n = 3), and from sex- and age-matched control mice that were housed in standard vivarium cages ( n = 3).

Techniques: Virus, Recombinant, Electron Microscopy, Plasmid Preparation, SYBR Green Assay, Membrane, Blocking Assay, Staining, Enzyme-linked Immunosorbent Assay, Activity Assay, Protein Extraction, Clone Assay, Expressing, Software, Microscopy, Real-time Polymerase Chain Reaction