SRX23772352 GSM8115440_r1 SRP492166 PRJNA1081403 SRS20598067 GSM8115440 GSM8115440 OTHER GENOMIC other Cells were resuspended in 3 mL NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8), and 100 μg/mL Proteinase K to every 15 x106 cells (>500x coverage) and incubated at 55°C overnight. 50 μg/mL RNAse A was added to the lysed sample and then incubated at 37°C for 30 min. Samples were chilled on ice before the addition of 1 mL of pre-chilled 7.5 M ammonium acetate to precipitate proteins, DNA was extracted by isopropanol, washed, dried and resuspended in water. For "progenitors_0" and "progenitors" samples, 54 μg DNA corresponding to 500x coverage of the library were amplified in 5 parallel PCR1 reactions using 10.8 μg per reaction. For the "DC" sample, 24 PCR1 reactions were similarly setup for the amplification of ~250 μg of DNA corresponding to >1000x coverage of the library. For sorted cDC and pDC samples library coverage was lower (~ 240x) due to cell numbers. Two PCR1 reactions were setup for each sorted subset for the amplification of ~24-26 μg gDNA. PCR1 and subsequent PCR2 reactions for the addition of Illumina barcodes were performed as previously described (PMID: 35294876). All samples were pooled in equimolar ratio and purified with QIAquick PCR Purification Kit (Qiagen). The purified sample was run on a 2% gel and the correct size band (250–270 bp) was extracted and purified with QIAquick Gel Extraction Kit (Qiagen). NextSeq 500 SRX23772353 GSM8115441_r1 SRP492166 PRJNA1081403 SRS20597737 GSM8115441 GSM8115441 OTHER GENOMIC other Cells were resuspended in 3 mL NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8), and 100 μg/mL Proteinase K to every 15 x106 cells (>500x coverage) and incubated at 55°C overnight. 50 μg/mL RNAse A was added to the lysed sample and then incubated at 37°C for 30 min. Samples were chilled on ice before the addition of 1 mL of pre-chilled 7.5 M ammonium acetate to precipitate proteins, DNA was extracted by isopropanol, washed, dried and resuspended in water. For "progenitors_0" and "progenitors" samples, 54 μg DNA corresponding to 500x coverage of the library were amplified in 5 parallel PCR1 reactions using 10.8 μg per reaction. For the "DC" sample, 24 PCR1 reactions were similarly setup for the amplification of ~250 μg of DNA corresponding to >1000x coverage of the library. For sorted cDC and pDC samples library coverage was lower (~ 240x) due to cell numbers. Two PCR1 reactions were setup for each sorted subset for the amplification of ~24-26 μg gDNA. PCR1 and subsequent PCR2 reactions for the addition of Illumina barcodes were performed as previously described (PMID: 35294876). All samples were pooled in equimolar ratio and purified with QIAquick PCR Purification Kit (Qiagen). The purified sample was run on a 2% gel and the correct size band (250–270 bp) was extracted and purified with QIAquick Gel Extraction Kit (Qiagen). NextSeq 500 SRX23772354 GSM8115442_r1 SRP492166 PRJNA1081403 SRS20597736 GSM8115442 GSM8115442 OTHER GENOMIC other Cells were resuspended in 3 mL NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8), and 100 μg/mL Proteinase K to every 15 x106 cells (>500x coverage) and incubated at 55°C overnight. 50 μg/mL RNAse A was added to the lysed sample and then incubated at 37°C for 30 min. Samples were chilled on ice before the addition of 1 mL of pre-chilled 7.5 M ammonium acetate to precipitate proteins, DNA was extracted by isopropanol, washed, dried and resuspended in water. For "progenitors_0" and "progenitors" samples, 54 μg DNA corresponding to 500x coverage of the library were amplified in 5 parallel PCR1 reactions using 10.8 μg per reaction. For the "DC" sample, 24 PCR1 reactions were similarly setup for the amplification of ~250 μg of DNA corresponding to >1000x coverage of the library. For sorted cDC and pDC samples library coverage was lower (~ 240x) due to cell numbers. Two PCR1 reactions were setup for each sorted subset for the amplification of ~24-26 μg gDNA. PCR1 and subsequent PCR2 reactions for the addition of Illumina barcodes were performed as previously described (PMID: 35294876). All samples were pooled in equimolar ratio and purified with QIAquick PCR Purification Kit (Qiagen). The purified sample was run on a 2% gel and the correct size band (250–270 bp) was extracted and purified with QIAquick Gel Extraction Kit (Qiagen). NextSeq 500 SRX23772355 GSM8115443_r1 SRP492166 PRJNA1081403 SRS20597738 GSM8115443 GSM8115443 OTHER GENOMIC other Cells were resuspended in 3 mL NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8), and 100 μg/mL Proteinase K to every 15 x106 cells (>500x coverage) and incubated at 55°C overnight. 50 μg/mL RNAse A was added to the lysed sample and then incubated at 37°C for 30 min. Samples were chilled on ice before the addition of 1 mL of pre-chilled 7.5 M ammonium acetate to precipitate proteins, DNA was extracted by isopropanol, washed, dried and resuspended in water. For "progenitors_0" and "progenitors" samples, 54 μg DNA corresponding to 500x coverage of the library were amplified in 5 parallel PCR1 reactions using 10.8 μg per reaction. For the "DC" sample, 24 PCR1 reactions were similarly setup for the amplification of ~250 μg of DNA corresponding to >1000x coverage of the library. For sorted cDC and pDC samples library coverage was lower (~ 240x) due to cell numbers. Two PCR1 reactions were setup for each sorted subset for the amplification of ~24-26 μg gDNA. PCR1 and subsequent PCR2 reactions for the addition of Illumina barcodes were performed as previously described (PMID: 35294876). All samples were pooled in equimolar ratio and purified with QIAquick PCR Purification Kit (Qiagen). The purified sample was run on a 2% gel and the correct size band (250–270 bp) was extracted and purified with QIAquick Gel Extraction Kit (Qiagen). NextSeq 500 SRX23772356 GSM8115444_r1 SRP492166 PRJNA1081403 SRS20597739 GSM8115444 GSM8115444 OTHER GENOMIC other Cells were resuspended in 3 mL NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8), and 100 μg/mL Proteinase K to every 15 x106 cells (>500x coverage) and incubated at 55°C overnight. 50 μg/mL RNAse A was added to the lysed sample and then incubated at 37°C for 30 min. Samples were chilled on ice before the addition of 1 mL of pre-chilled 7.5 M ammonium acetate to precipitate proteins, DNA was extracted by isopropanol, washed, dried and resuspended in water. For "progenitors_0" and "progenitors" samples, 54 μg DNA corresponding to 500x coverage of the library were amplified in 5 parallel PCR1 reactions using 10.8 μg per reaction. For the "DC" sample, 24 PCR1 reactions were similarly setup for the amplification of ~250 μg of DNA corresponding to >1000x coverage of the library. For sorted cDC and pDC samples library coverage was lower (~ 240x) due to cell numbers. Two PCR1 reactions were setup for each sorted subset for the amplification of ~24-26 μg gDNA. PCR1 and subsequent PCR2 reactions for the addition of Illumina barcodes were performed as previously described (PMID: 35294876). All samples were pooled in equimolar ratio and purified with QIAquick PCR Purification Kit (Qiagen). The purified sample was run on a 2% gel and the correct size band (250–270 bp) was extracted and purified with QIAquick Gel Extraction Kit (Qiagen). NextSeq 500