Additional file 1 of Translatome analysis of tuberous sclerosis complex 1 patient-derived neural progenitor cells reveals rapamycin-dependent and independent alterations
Notice bibliographique
Résumé
Additional file 1. Figure S1. Quality control of RNA sequencing data of cytosolic and polysome-associated mRNA isolated from NPCs of different conditions. A Barplot showing overall number of reads that are aligned to adapter sequences, rRNA sequences, assigned to genes as well as unmapped/unassigned reads. B Boxplot showing TMM-log2 normalized counts of TSC1 transcript in TSC1−/− (red) and TSC1+/+ (blue) NPCs. C Scree-plot showing the percentage of variance explained by PC1-PC10. D Correlation of principal components (PC1-PC9) to experimental factors. E Projection of samples in principal components 1 and 2, with samples shaped according to library type (circle: polysome-associated mRNA; triangle: cytosolic mRNA) and colored according to genotype of samples (TSC1−/−, red; TSC1+/+, blue). Figure S2. Quality control of RNA sequencing data of postmortem samples of BA19 ASD and control. A Barplot showing overall number of reads that are aligned to adapter sequences, assigned to genes as well as unmapped/unassigned reads. B Scree-plot showing the percentage of variance explained by PC1-PC10. C Correlation of principal components (PC1-PC9) to experimental factors. D Projection of samples in principal components 1 and 2, with samples shaped according to library type (circle: polysome-associated mRNA; triangle:cytosolic mRNA) and colored according to condition (ASD: red; Control: blue). Figure S3. Immunoblotting in NPCs. A Immunoblotting for TSC1 in TSC1−/− compared with CRISPR-corrected TSC1+/+ NPCs. Ribosomal S6 protein serves as a loading control. B Immunoblot of NPCs treated with rapamycin (50 nM) and RMC-6272 (10 nM) for indicated proteins. β-tubulin served as a loading control. Images have been cropped for clarity and conciseness, and entire blots are shown in Additional file 9. Figure S4. Gene ontology analysis comparison for ASD and TSC1−/− NPCs. A and B Gene ontology analysis (similar to Fig. 1F) for genes categorized as “translation up” in TSC1−/− versus TSC1+/+ and ASD versus Ctrl BA19 comparisons (A); and genes categorized as “translation down” in TSC1−/− and TSC1+/+ and ASD versus Ctrl BA19 comparisons (B). The analysis was performed using ClueGO in “cluster mode.” Figure S5. Comparison of rapamycin-treated TSC1−/− to non-treated TSC1+/+ NPCs. A and B anota2seq analysis (A) and kernel densities for p value or FDR from anota2seq analysis (B) are shown comparing rapamycin-treated TSC1−/− to non-treated TSC1+/+ NPCs. (similar to Fig. 1B-C). Figure S6. Additional data related to changes in cells size and proliferation. A Bright field images (left panel) and cell size quantitation (right panel) of TSC1+/+ and TSC1−/− NPCs treated with 50 nM rapamycin or 10 nM RMC-6272 (n = 3 ± SD) are shown. Scale bar = 100 µm. B TSC1+/+ and TSC1−/− NPCs were treated with 10 nM RMC-6272 or DMSO as a control along with 1:500 dilution of the fluorescent nuclear marker NucSpot650 to visualize cell nuclei in the near infrared (NIR) spectrum. Using the Incucyte SX5 system, images were taken every 2 h for a total of 48 h. Graphs of NIR mean intensity (NIRCU) were generated using GraphPad Prism9 showing the average nuclei number/image field (36 non-overlapping image fields/well). Data represent three biological replicates per treatment group (± SEM). *p < 0.05, **p < 0.01, ***p < 0.001 calculated by Student’s t test. Figure S7. Additional data related to changes in neurite outgrowth. A and B Quantitation of neurite number (left), length (middle) and extremities (right) from trace images are shown for immunofluorescence staining of TSC1± (A) and TSC1+/+ (B) NPCs treated with DMSO, 50 nM rapamycin or 10 nM RMC-6272 using the neuronal marker MAP2 and HCA-Vision image quantitation software. Data represent eight non-overlapping field images/treatment generated using GraphPad Prism9 with relative fold change normalized to DMSO-treated NPCs (mean, ± SD). ** p < 0.01, ***p < 0.001, ****p < 0.0001, ns = not significant calculated by Student’s t test (A-B).
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,001 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,001 | 0,000 |
| Bibliométrie | 0,001 | 0,002 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,936 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule tête enseignante, pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».