ERX7881078 E-MTAB-11403:Sample 7_s ERP135195 PRJEB50601 RNAseq from macrophages and osteoclasts from wild-type and TRAP deficient bone cell reporter mice ERS10419847 SAMEA12812886 Sample 7_s ssRNA-seq TRANSCRIPTOMIC Oligo-dT Cells were washed with PBS 1x and the lysed with the lysis buffer provided by the manufacturer of the kit. Cells were harvested from the bone marrow of 2 femurs from 6-week old mice in the C57Bl6 background, expressing GFP under regulation of Ibsp and mCherry under regulation of Acp5. Due to the insertion of mCherry, the Acp5 gene product was alrered, rendering a TRAP deficient mouse strain. Cells were harvested in alpha MEM. After centrifugation at 1000 rpm for 5 min, the supernatant was removed and the red cells were lyzed using 4,5mL of water. 500uL of PBS 10x was added to equilibrate the pH and osmolarity, and the cells were centrifuged again at 1000 rpm for 5 min. The cells were resuspended in alpha-MEM containing 10% FBS and 30ng/mL of murine MCSF (R&D sytems) and seeded in suspension culture dishes (Corning) for 3 days. Cells described in the growth protocol were harvested from the plate using a cell scraper and seeded at the density of 5,000 cells/well in 96-well culture dishes. The cells were grown in alpha-MEM containing 10%FBS, antibiotics, and 30ng/mL MCSF RNA was extracted using RNAeasy Mini kit following manufacturer’s instructions (Cat no. 74104 - Qiagen) Illumina TruSeq Stranded mRNA Illumina NovaSeq 6000 Experimental Factor: genotype TRAP knockout Experimental Factor: cell type bone marrow macrophage ERX7881083 E-MTAB-11403:Sample 3_s ERP135195 PRJEB50601 RNAseq from macrophages and osteoclasts from wild-type and TRAP deficient bone cell reporter mice ERS10419852 SAMEA12812891 Sample 3_s ssRNA-seq TRANSCRIPTOMIC Oligo-dT Cells were washed with PBS 1x and the lysed with the lysis buffer provided by the manufacturer of the kit. Cells were harvested from the bone marrow of 2 femurs from 6-week old mice in the C57Bl6 background, wild type, in alpha-MEM. After centrifugation at 1000 rpm for 5 min, the supernatant was removed and the red cells were lyzed using 4,5mL of water. 500uL of PBS 10x was added to equilibrate the pH and osmolarity, and the cells were centrifuged again at 1000 rpm for 5 min. The cells were resuspended in alpha-MEM containing 10% FBS and 30ng/mL of murine MCSF (R&D sytems) and seeded in suspension culture dishes (Corning) for 3 days. Cells described in the growth protocol were harvested from the plate using a cell scraper and seeded at the density of 5,000 cells/well in 96-well culture dishes. The cells were grown in alpha-MEM containing 10%FBS, antibiotics, and 30ng/mL MCSF RNA was extracted using RNAeasy Mini kit following manufacturer’s instructions (Cat no. 74104 - Qiagen) Illumina TruSeq Stranded mRNA Illumina NovaSeq 6000 Experimental Factor: genotype wild type genotype Experimental Factor: cell type bone marrow macrophage ERX7881075 E-MTAB-11403:Sample 10_s ERP135195 PRJEB50601 RNAseq from macrophages and osteoclasts from wild-type and TRAP deficient bone cell reporter mice ERS10419844 SAMEA12812883 Sample 10_s ssRNA-seq TRANSCRIPTOMIC Oligo-dT Cells were washed with PBS 1x and the lysed with the lysis buffer provided by the manufacturer of the kit. Cells were harvested from the bone marrow of 2 femurs from 6-week old mice in the C57Bl6 background, expressing GFP under regulation of Ibsp and mCherry under regulation of Acp5. Due to the insertion of mCherry, the Acp5 gene product was alrered, rendering a TRAP deficient mouse strain. Cells were harvested in alpha MEM. After centrifugation at 1000 rpm for 5 min, the supernatant was removed and the red cells were lyzed using 4,5mL of water. 500uL of PBS 10x was added to equilibrate the pH and osmolarity, and the cells were centrifuged again at 1000 rpm for 5 min. The cells were resuspended in alpha-MEM containing 10% FBS and 30ng/mL of murine MCSF (R&D sytems) and seeded in suspension culture dishes (Corning) for 3 days. Cells described in the growth protocol were harvested from the plate using a cell scraper and seeded at the density of 5,000 cells/well in 96-well culture dishes. The cells were grown in alpha-MEM containing 10%FBS, antibiotics, 30ng/mL MCSF and 4ng/mL RANKL (R&D systems) RNA was extracted using RNAeasy Mini kit following manufacturer’s instructions (Cat no. 74104 - Qiagen) Illumina TruSeq Stranded mRNA Illumina NovaSeq 6000 Experimental Factor: genotype TRAP knockout Experimental Factor: cell type osteoclast ERX7881077 E-MTAB-11403:Sample 12_s ERP135195 PRJEB50601 RNAseq from macrophages and osteoclasts from wild-type and TRAP deficient bone cell reporter mice ERS10419846 SAMEA12812885 Sample 12_s ssRNA-seq TRANSCRIPTOMIC Oligo-dT Cells were washed with PBS 1x and the lysed with the lysis buffer provided by the manufacturer of the kit. Cells were harvested from the bone marrow of 2 femurs from 6-week old mice in the C57Bl6 background, expressing GFP under regulation of Ibsp and mCherry under regulation of Acp5. Due to the insertion of mCherry, the Acp5 gene product was alrered, rendering a TRAP deficient mouse strain. Cells were harvested in alpha MEM. After centrifugation at 1000 rpm for 5 min, the supernatant was removed and the red cells were lyzed using 4,5mL of water. 500uL of PBS 10x was added to equilibrate the pH and osmolarity, and the cells were centrifuged again at 1000 rpm for 5 min. The cells were resuspended in alpha-MEM containing 10% FBS and 30ng/mL of murine MCSF (R&D sytems) and seeded in suspension culture dishes (Corning) for 3 days. Cells described in the growth protocol were harvested from the plate using a cell scraper and seeded at the density of 5,000 cells/well in 96-well culture dishes. The cells were grown in alpha-MEM containing 10%FBS, antibiotics, 30ng/mL MCSF and 4ng/mL RANKL (R&D systems) RNA was extracted using RNAeasy Mini kit following manufacturer’s instructions (Cat no. 74104 - Qiagen) Illumina TruSeq Stranded mRNA Illumina NovaSeq 6000 Experimental Factor: genotype TRAP knockout Experimental Factor: cell type osteoclast ERX7881082 E-MTAB-11403:Sample 2_s ERP135195 PRJEB50601 RNAseq from macrophages and osteoclasts from wild-type and TRAP deficient bone cell reporter mice ERS10419851 SAMEA12812890 Sample 2_s ssRNA-seq TRANSCRIPTOMIC Oligo-dT Cells were washed with PBS 1x and the lysed with the lysis buffer provided by the manufacturer of the kit. Cells were harvested from the bone marrow of 2 femurs from 6-week old mice in the C57Bl6 background, wild type, in alpha-MEM. After centrifugation at 1000 rpm for 5 min, the supernatant was removed and the red cells were lyzed using 4,5mL of water. 500uL of PBS 10x was added to equilibrate the pH and osmolarity, and the cells were centrifuged again at 1000 rpm for 5 min. The cells were resuspended in alpha-MEM containing 10% FBS and 30ng/mL of murine MCSF (R&D sytems) and seeded in suspension culture dishes (Corning) for 3 days. Cells described in the growth protocol were harvested from the plate using a cell scraper and seeded at the density of 5,000 cells/well in 96-well culture dishes. The cells were grown in alpha-MEM containing 10%FBS, antibiotics, and 30ng/mL MCSF RNA was extracted using RNAeasy Mini kit following manufacturer’s instructions (Cat no. 74104 - Qiagen) Illumina TruSeq Stranded mRNA Illumina NovaSeq 6000 Experimental Factor: genotype wild type genotype Experimental Factor: cell type bone marrow macrophage ERX7881084 E-MTAB-11403:Sample 4_s ERP135195 PRJEB50601 RNAseq from macrophages and osteoclasts from wild-type and TRAP deficient bone cell reporter mice ERS10419853 SAMEA12812892 Sample 4_s ssRNA-seq TRANSCRIPTOMIC Oligo-dT Cells were washed with PBS 1x and the lysed with the lysis buffer provided by the manufacturer of the kit. Cells were harvested from the bone marrow of 2 femurs from 6-week old mice in the C57Bl6 background, wild type, in alpha-MEM. After centrifugation at 1000 rpm for 5 min, the supernatant was removed and the red cells were lyzed using 4,5mL of water. 500uL of PBS 10x was added to equilibrate the pH and osmolarity, and the cells were centrifuged again at 1000 rpm for 5 min. The cells were resuspended in alpha-MEM containing 10% FBS and 30ng/mL of murine MCSF (R&D sytems) and seeded in suspension culture dishes (Corning) for 3 days. Cells described in the growth protocol were harvested from the plate using a cell scraper and seeded at the density of 5,000 cells/well in 96-well culture dishes. The cells were grown in alpha-MEM containing 10%FBS, antibiotics, 30ng/mL MCSF and 4ng/mL RANKL (R&D systems) RNA was extracted using RNAeasy Mini kit following manufacturer’s instructions (Cat no. 74104 - Qiagen) Illumina TruSeq Stranded mRNA Illumina NovaSeq 6000 Experimental Factor: genotype wild type genotype Experimental Factor: cell type osteoclast ERX7881081 E-MTAB-11403:Sample 1_s ERP135195 PRJEB50601 RNAseq from macrophages and osteoclasts from wild-type and TRAP deficient bone cell reporter mice ERS10419850 SAMEA12812889 Sample 1_s ssRNA-seq TRANSCRIPTOMIC Oligo-dT Cells were washed with PBS 1x and the lysed with the lysis buffer provided by the manufacturer of the kit. Cells were harvested from the bone marrow of 2 femurs from 6-week old mice in the C57Bl6 background, wild type, in alpha-MEM. After centrifugation at 1000 rpm for 5 min, the supernatant was removed and the red cells were lyzed using 4,5mL of water. 500uL of PBS 10x was added to equilibrate the pH and osmolarity, and the cells were centrifuged again at 1000 rpm for 5 min. The cells were resuspended in alpha-MEM containing 10% FBS and 30ng/mL of murine MCSF (R&D sytems) and seeded in suspension culture dishes (Corning) for 3 days. Cells described in the growth protocol were harvested from the plate using a cell scraper and seeded at the density of 5,000 cells/well in 96-well culture dishes. The cells were grown in alpha-MEM containing 10%FBS, antibiotics, and 30ng/mL MCSF RNA was extracted using RNAeasy Mini kit following manufacturer’s instructions (Cat no. 74104 - Qiagen) Illumina TruSeq Stranded mRNA Illumina NovaSeq 6000 Experimental Factor: genotype wild type genotype Experimental Factor: cell type bone marrow macrophage ERX7881079 E-MTAB-11403:Sample 8_s ERP135195 PRJEB50601 RNAseq from macrophages and osteoclasts from wild-type and TRAP deficient bone cell reporter mice ERS10419848 SAMEA12812887 Sample 8_s ssRNA-seq TRANSCRIPTOMIC Oligo-dT Cells were washed with PBS 1x and the lysed with the lysis buffer provided by the manufacturer of the kit. Cells were harvested from the bone marrow of 2 femurs from 6-week old mice in the C57Bl6 background, expressing GFP under regulation of Ibsp and mCherry under regulation of Acp5. Due to the insertion of mCherry, the Acp5 gene product was alrered, rendering a TRAP deficient mouse strain. Cells were harvested in alpha MEM. After centrifugation at 1000 rpm for 5 min, the supernatant was removed and the red cells were lyzed using 4,5mL of water. 500uL of PBS 10x was added to equilibrate the pH and osmolarity, and the cells were centrifuged again at 1000 rpm for 5 min. The cells were resuspended in alpha-MEM containing 10% FBS and 30ng/mL of murine MCSF (R&D sytems) and seeded in suspension culture dishes (Corning) for 3 days. Cells described in the growth protocol were harvested from the plate using a cell scraper and seeded at the density of 5,000 cells/well in 96-well culture dishes. The cells were grown in alpha-MEM containing 10%FBS, antibiotics, and 30ng/mL MCSF RNA was extracted using RNAeasy Mini kit following manufacturer’s instructions (Cat no. 74104 - Qiagen) Illumina TruSeq Stranded mRNA Illumina NovaSeq 6000 Experimental Factor: genotype TRAP knockout Experimental Factor: cell type bone marrow macrophage ERX7881086 E-MTAB-11403:Sample 6_s ERP135195 PRJEB50601 RNAseq from macrophages and osteoclasts from wild-type and TRAP deficient bone cell reporter mice ERS10419855 SAMEA12812894 Sample 6_s ssRNA-seq TRANSCRIPTOMIC Oligo-dT Cells were washed with PBS 1x and the lysed with the lysis buffer provided by the manufacturer of the kit. Cells were harvested from the bone marrow of 2 femurs from 6-week old mice in the C57Bl6 background, wild type, in alpha-MEM. After centrifugation at 1000 rpm for 5 min, the supernatant was removed and the red cells were lyzed using 4,5mL of water. 500uL of PBS 10x was added to equilibrate the pH and osmolarity, and the cells were centrifuged again at 1000 rpm for 5 min. The cells were resuspended in alpha-MEM containing 10% FBS and 30ng/mL of murine MCSF (R&D sytems) and seeded in suspension culture dishes (Corning) for 3 days. Cells described in the growth protocol were harvested from the plate using a cell scraper and seeded at the density of 5,000 cells/well in 96-well culture dishes. The cells were grown in alpha-MEM containing 10%FBS, antibiotics, 30ng/mL MCSF and 4ng/mL RANKL (R&D systems) RNA was extracted using RNAeasy Mini kit following manufacturer’s instructions (Cat no. 74104 - Qiagen) Illumina TruSeq Stranded mRNA Illumina NovaSeq 6000 Experimental Factor: genotype wild type genotype Experimental Factor: cell type osteoclast ERX7881080 E-MTAB-11403:Sample 9_s ERP135195 PRJEB50601 RNAseq from macrophages and osteoclasts from wild-type and TRAP deficient bone cell reporter mice ERS10419849 SAMEA12812888 Sample 9_s ssRNA-seq TRANSCRIPTOMIC Oligo-dT Cells were washed with PBS 1x and the lysed with the lysis buffer provided by the manufacturer of the kit. Cells were harvested from the bone marrow of 2 femurs from 6-week old mice in the C57Bl6 background, expressing GFP under regulation of Ibsp and mCherry under regulation of Acp5. Due to the insertion of mCherry, the Acp5 gene product was alrered, rendering a TRAP deficient mouse strain. Cells were harvested in alpha MEM. After centrifugation at 1000 rpm for 5 min, the supernatant was removed and the red cells were lyzed using 4,5mL of water. 500uL of PBS 10x was added to equilibrate the pH and osmolarity, and the cells were centrifuged again at 1000 rpm for 5 min. The cells were resuspended in alpha-MEM containing 10% FBS and 30ng/mL of murine MCSF (R&D sytems) and seeded in suspension culture dishes (Corning) for 3 days. Cells described in the growth protocol were harvested from the plate using a cell scraper and seeded at the density of 5,000 cells/well in 96-well culture dishes. The cells were grown in alpha-MEM containing 10%FBS, antibiotics, and 30ng/mL MCSF RNA was extracted using RNAeasy Mini kit following manufacturer’s instructions (Cat no. 74104 - Qiagen) Illumina TruSeq Stranded mRNA Illumina NovaSeq 6000 Experimental Factor: genotype TRAP knockout Experimental Factor: cell type bone marrow macrophage ERX7881085 E-MTAB-11403:Sample 5_s ERP135195 PRJEB50601 RNAseq from macrophages and osteoclasts from wild-type and TRAP deficient bone cell reporter mice ERS10419854 SAMEA12812893 Sample 5_s ssRNA-seq TRANSCRIPTOMIC Oligo-dT Cells were washed with PBS 1x and the lysed with the lysis buffer provided by the manufacturer of the kit. Cells were harvested from the bone marrow of 2 femurs from 6-week old mice in the C57Bl6 background, wild type, in alpha-MEM. After centrifugation at 1000 rpm for 5 min, the supernatant was removed and the red cells were lyzed using 4,5mL of water. 500uL of PBS 10x was added to equilibrate the pH and osmolarity, and the cells were centrifuged again at 1000 rpm for 5 min. The cells were resuspended in alpha-MEM containing 10% FBS and 30ng/mL of murine MCSF (R&D sytems) and seeded in suspension culture dishes (Corning) for 3 days. Cells described in the growth protocol were harvested from the plate using a cell scraper and seeded at the density of 5,000 cells/well in 96-well culture dishes. The cells were grown in alpha-MEM containing 10%FBS, antibiotics, 30ng/mL MCSF and 4ng/mL RANKL (R&D systems) RNA was extracted using RNAeasy Mini kit following manufacturer’s instructions (Cat no. 74104 - Qiagen) Illumina TruSeq Stranded mRNA Illumina NovaSeq 6000 Experimental Factor: genotype wild type genotype Experimental Factor: cell type osteoclast ERX7881076 E-MTAB-11403:Sample 11_s ERP135195 PRJEB50601 RNAseq from macrophages and osteoclasts from wild-type and TRAP deficient bone cell reporter mice ERS10419845 SAMEA12812884 Sample 11_s ssRNA-seq TRANSCRIPTOMIC Oligo-dT Cells were washed with PBS 1x and the lysed with the lysis buffer provided by the manufacturer of the kit. Cells were harvested from the bone marrow of 2 femurs from 6-week old mice in the C57Bl6 background, expressing GFP under regulation of Ibsp and mCherry under regulation of Acp5. Due to the insertion of mCherry, the Acp5 gene product was alrered, rendering a TRAP deficient mouse strain. Cells were harvested in alpha MEM. After centrifugation at 1000 rpm for 5 min, the supernatant was removed and the red cells were lyzed using 4,5mL of water. 500uL of PBS 10x was added to equilibrate the pH and osmolarity, and the cells were centrifuged again at 1000 rpm for 5 min. The cells were resuspended in alpha-MEM containing 10% FBS and 30ng/mL of murine MCSF (R&D sytems) and seeded in suspension culture dishes (Corning) for 3 days. Cells described in the growth protocol were harvested from the plate using a cell scraper and seeded at the density of 5,000 cells/well in 96-well culture dishes. The cells were grown in alpha-MEM containing 10%FBS, antibiotics, 30ng/mL MCSF and 4ng/mL RANKL (R&D systems) RNA was extracted using RNAeasy Mini kit following manufacturer’s instructions (Cat no. 74104 - Qiagen) Illumina TruSeq Stranded mRNA Illumina NovaSeq 6000 Experimental Factor: genotype TRAP knockout Experimental Factor: cell type osteoclast