Journal: eLife

Article Title: Unsupervised machine learning reveals risk stratifying glioblastoma tumor cells

doi: 10.7554/eLife.56879

Figure Lengend Snippet:

Article Snippet: Antibody , Anti-p-AKT (S473) (rabbit-monoclonal) , Fluidigm , RRID: AB_2811246 Cat#3152005A Clone: D9E , MC (1:100).

Techniques: Isolation, Software

Journal: Cell metabolism

Article Title: Fructose-1,6-bisphosphatase is a nonenzymatic safety valve that curtails AKT activation to prevent insulin hyperresponsiveness

doi: 10.1016/j.cmet.2023.03.021

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Rabbit monoclonal anti-P-AKT (T308) , Cell Signaling , Cat# 4056; RRID:AB_331163.

Techniques: Immunoprecipitation, Transfection, Extraction, Enzyme-linked Immunosorbent Assay, ATP Assay, Colorimetric Assay, Activity Assay, Glucose Assay, In Situ, cDNA Synthesis, Recombinant, Sequencing, Construct, Software

Journal: Nature Communications

Article Title: Bipolar and schizophrenia risk gene AKAP11 encodes an autophagy receptor coupling the regulation of PKA kinase network homeostasis to synaptic transmission

doi: 10.1038/s41467-025-66356-w

Figure Lengend Snippet: a The predicted kinase activity scores for representative kinases. The scores were generated by PhosR based on the phosphorylation levels of predicted substrates. Statistical significance was determined using two-sided t -test. b, d Volcano plot of the top 200 predicted GSK3β ( b ) / AKT1 ( d ) phosphorylation sites (normalized by the total protein level) detected by mass-spectrometry in Akap11 -cKO mouse brains. A positive score indicates enrichment, a negative score indicates depletion. The y axis represents statistical confidence for each x axis point. Enriched proteins, defined by FDR < 0.05 and |Log2FC | > 2 SD, are colored in red. FDR was calculated with the moderated two-sided t -test in the LIMMA package for multiple comparisons. c Immunoblotting using antibodies against AKAP11, GSK3α/β and p-GSK3α/β (S21/S9) and quantification of the results. Data are presented as mean ± SEM ( n = 11 per genotype). Statistical analysis was performed using an unpaired two-tailed t -test (p-GSK3α/GSK3α, p = 0.0036; p-GSK3β/ GSK3β, p = 0.0053). Each experiment was independently repeated three times with similar results. e Immunoblotting using antibodies against p-GSK3α/β (S21/S9), GSK3α/β, p-Akt1 S473 , and Akt1 in cytosolic and synaptosome fractions and quantification of the results. Data are presented as mean ± SEM (p-GSK3β: n = 4 per genotype; p-Akt1: n = 5 for Akap11 F /F and n = 4 for Akap11 F/F ; Syn-cre). Statistical analysis was performed using an unpaired two-tested t -test (cytosolic p-GSK3β: p = 0.0007; synaptosome p-GSK3β: p = 0.1206; synaptosome p-Akt1: p = 0.0154). Each experiment was independently repeated three times with similar results.

Article Snippet: Primary antibodies, Rabbit anti-AKAP11 (LS-Bio, LS-C374339), Rabbit anti-RIα (Cell signaling, 5675S), Sheep anti-RIβ (R&D, AF4177), Mouse anti-RIIα (BD, 612242), Rabbit anti-PKACα (Cell signaling, 4782S), Rabbit anti-p-PKACα T197 (Cell signaling, 5661S), Mouse anti-β-actin (Cell signaling, 3700S), Rabbit anti-ADRA2A (Proteintech, 14266-1-AP), Rabbit anti-SPHKAP (Thermo, PA5-27581), Rabbit anti-Synaptophysin (Thermo, MA5-14532), Rabbit anti-GSK3α/β (Cell signaling, 5676S), Rabbit anti-p-GSK3α/β (S21/S9) (Cell signaling, 9331S), Rabbit anti-p-GluA1 S845 (Cell signaling, 8084), Rabbit anti-GluA1 (Cell signaling, 13185), Rabbit anti-Akt1 (Cell signaling, 4691S), Rabbit anti-p-Akt1 S473 (Cell signaling, 4060S), Chicken anti-GFP (Invitrogen, A10262), Rabbit anti-VAPA (Proteintech, 15275-1-AP), Rabbit anti-VAPB (Proteintech, 14477-1-AP), Guinea pig anti-p62 (PROGEN, GP62-C), Rabbit anti-LC3A/B (Cell signaling, 12742S), were diluted in blocking buffer with 0.2% Tween-20 and incubated overnight at 4 °C.

Techniques: Activity Assay, Generated, Phospho-proteomics, Mass Spectrometry, Western Blot, Two Tailed Test