ERX4432357 E-MTAB-9478:Sample 1_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4981999 SAMEA7221857 Sample 1_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). NextSeq 500 Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3-NK1.1- B220+ IgD-HA+ ERX4432358 E-MTAB-9478:Sample 10_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982000 SAMEA7221858 Sample 10_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432359 E-MTAB-9478:Sample 11_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982001 SAMEA7221859 Sample 11_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432360 E-MTAB-9478:Sample 12_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982002 SAMEA7221860 Sample 12_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432361 E-MTAB-9478:Sample 13_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982003 SAMEA7221861 Sample 13_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432362 E-MTAB-9478:Sample 14_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982004 SAMEA7221862 Sample 14_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432363 E-MTAB-9478:Sample 15_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982005 SAMEA7221863 Sample 15_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432364 E-MTAB-9478:Sample 16_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982006 SAMEA7221864 Sample 16_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432365 E-MTAB-9478:Sample 17_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982007 SAMEA7221865 Sample 17_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432366 E-MTAB-9478:Sample 18_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982008 SAMEA7221866 Sample 18_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432367 E-MTAB-9478:Sample 19_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982009 SAMEA7221867 Sample 19_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432368 E-MTAB-9478:Sample 2_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982010 SAMEA7221868 Sample 2_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). NextSeq 500 Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3-NK1.1- B220+ IgD-HA+ ERX4432369 E-MTAB-9478:Sample 20_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982011 SAMEA7221869 Sample 20_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432370 E-MTAB-9478:Sample 21_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982012 SAMEA7221870 Sample 21_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432371 E-MTAB-9478:Sample 22_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982013 SAMEA7221871 Sample 22_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect PBS Experimental Factor: immunophenotype 50% Live CD3- B220+IgD-GL7+ 50% Live CD3- B220+ ERX4432372 E-MTAB-9478:Sample 23_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982014 SAMEA7221872 Sample 23_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect PBS Experimental Factor: immunophenotype 50% Live CD3- B220+IgD-GL7+ 50% Live CD3- B220+ ERX4432373 E-MTAB-9478:Sample 24_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982015 SAMEA7221873 Sample 24_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect PBS Experimental Factor: immunophenotype 50% Live CD3- B220+IgD-GL7+ 50% Live CD3- B220+ ERX4432374 E-MTAB-9478:Sample 3_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982016 SAMEA7221874 Sample 3_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). NextSeq 500 Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3-NK1.1- B220+ IgD-HA+ ERX4432375 E-MTAB-9478:Sample 4_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982017 SAMEA7221875 Sample 4_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). NextSeq 500 Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3-NK1.1- B220+ IgD-HA+ ERX4432376 E-MTAB-9478:Sample 5_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982018 SAMEA7221876 Sample 5_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). NextSeq 500 Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3-NK1.1- B220+ IgD-HA+ ERX4432377 E-MTAB-9478:Sample 6_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982019 SAMEA7221877 Sample 6_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432378 E-MTAB-9478:Sample 7_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982020 SAMEA7221878 Sample 7_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432379 E-MTAB-9478:Sample 8_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982021 SAMEA7221879 Sample 8_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+ ERX4432380 E-MTAB-9478:Sample 9_p ERP123570 PRJEB39986 Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: VDJ data ERS4982022 SAMEA7221880 Sample 9_p RNA-Seq GENOMIC SINGLE CELL PCR C57BL/6 mice were infected with PR8 H1N1 virus and were euthanized on different days post- infection. Organs such as lungs, spleen and mediastinal lymph nodes (mln) were isolated. The same organs from naïve mice were used as controls. Spleen and mln were mashed and passed through a 70µm filter to obtain single cell suspension. Lungs were processed into single cell suspension using the mouse lung dissociation kit (Miltenyi Biotec) according to manufacturer's instruction. Splenocytes and lung cells were enriched for total B cells using the EasySep Mouse Pan-B Cell Isolation kit (Stemcell Technologies) while whole mln cells were used for downstream processing. The cells were incubated for one hour at 4°C with a cocktail of fluorochrome-labelled antibodies consisting of anti-CD3-BV510 (cat. no: 563024, BD Biosciences), anti-B220-APC-Cy7 (cat. no: 552094, BD Biosciences) and anti-IgD-Pacific Blue (cat. no: 405712, BD Biosciences), and 1µg/ml biotinylated recombinant hemagglutinin (rHA) (Whittle et al., 2014) conjugated to streptavidin APC (cat. no: S868, Invitrogen). To exclude dead cells, the cells were washed and stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain (cat. no: L34957, Invitrogen) according to manufacturer's instruction. Mice were anesthetized with isoflurane and infected through nasal inoculation with 50 TCID50 Influenza A/Puerto Rico/8/34 (PR8) (Molecular clone; H1N1) diluted in HBBS containing 0.1% BSA. A maximum of 10,000 live HA-specific mature B cells (CD3-B220+IgD-rHA+) were sorted and collected in a BD FACSAria fusion or BD FACSAria III (BD Biosciences) cell sorter. Between 1500-10,000 sorted HA-specific mature B cells from individual organs were processed into single cells in a chromium controller (10X genomics) Libraries were generated following standard10x protocol . After amplification of the cDNA, 5´gene expression library and enriched B cell library, with paired heavy and light chain were generated from cDNA of the same cell using Chromium single cell VDJ reagent kit (V1.1 chemistry, 10X genomics). Illumina MiSeq Experimental Factor: infect Influenza A virus PR8 Experimental Factor: immunophenotype Live CD3- B220+ IgD- HA+