Additional file 1 of Combined proteomics and CRISPR‒Cas9 screens in PDX identify ADAM10 as essential for leukemia in vivo
Creators: name: Bahrami, Ehsan
name: Schmid, Jan Philipp
name: Jurinovic, Vindi
name: Becker, Martin
name: Wirth, Anna-Katharina
name: Ludwig, Romina
name: Kreissig, Sophie
name: Duque Angel, Tania Vanessa
name: Amend, Diana
name: Hunt, Katharina
name: Öllinger, Rupert
name: Rad, Roland
name: Frenz, Joris Maximilian
name: Solovey, Maria
name: Ziemann, Frank
name: Mann, Matthias
name: Vick, Binje
name: Wichmann, Christian
name: Herold, Tobias
name: Jayavelu, Ashok Kumar
name: Jeremias, Irmela
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
classificationCode: 39999
subject: Chemical Sciences not elsewhere classified
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
classificationCode: 19999
subject: Mathematical Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: Additional file 1: Supplemental Table 1. PDX Patient data. Supplemental Table 2. LRC vs. Non-LRC proteome. Supplemental Table 3. Surface molecules library genes. Supplemental Table 4. sgRNA oligo sequences. Supplemental Table 5. NGS PCR primers. Supplemental Table 6. Gini indices – ALL-199 BM &amp; SPL samples. Supplemental Table 7. Gini indices – Sublibrary plasmid &amp; ALL-265 BM &amp; SPL samples. Supplemental Table 8. SEM ADAM10 KO proteome. Supplemental Table 9. NALM-6 &amp; SEM secretome. Supplemental Table 10. PDX transcriptome. Supplemental Table 11. PDX proteome - significant genes. Supplemental Table 12. Competitive LDTA. Supplemental Figure S1. Ultra-sensitive diaPASEF proteome workflow and proteomic characterization of slow-cycling PDX ALL cells. Supplemental Figure 2. Quality controls for generating Split-Cas9-transgenic PDX models. Supplemental Figure S3. Quality controls for generating CRISPR-Cas9 library-transgenic PDX models. Supplemental Figure S4. Nested PCR. Supplemental Figure S5. Quality controls for the in vivo CRISPR dropout screens. Supplemental Figure S6. Dropouts of the in vivo CRISPR screens in PDX ALL samples. Supplemental Figure S7. In vivo competitive validation assay. Supplemental Figure S8. Quality controls for in vivo validation assays for CXCR4 and ITGB1. Supplemental Figure S9. ADAM10 expression in tumor cells and their impact on patient survival. Supplemental Figure S10. ADAM10 in vivo validation assay. Supplemental Figure S11. ADAM10 reconstitution in HEK293T cells. Supplemental Figure S12. Pathway enrichment results of ADAM10 KO proteome analyses in SEM cells. Supplemental Figure S13. Secretome analysis of ADAM10 KO cells. Supplemental Figure S14. ADAM10 KO transcriptome and proteome analyses in ALL PDX cells. Supplemental Figure S15. Quality controls for experiments on cell cycle and apoptosis. Supplemental Figure S16. Quality controls and raw data for Figure 6BC. Supplemental Figure S17. ADAM10 inhibits colony formation in PDX AML cells in vitro. Supplemental Figure S18. ADAM10 KO increases the anti-leukemia efficacy of AraC and cyclo in vivo. Supplemental Figure S19. ADAM10 KO increases the anti-leukemia efficacy of AraC, Daunorubicin and Doxorubicin in vitro.