^DATABASE = GeoMiame
!Database_name = Gene Expression Omnibus (GEO)
!Database_institute = NCBI NLM NIH
!Database_web_link = http://www.ncbi.nlm.nih.gov/geo
!Database_email = geo@ncbi.nlm.nih.gov
^SERIES = GSE137539
!Series_title = Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection
!Series_geo_accession = GSE137539
!Series_status = Public on May 27 2020
!Series_submission_date = Sep 16 2019
!Series_last_update_date = Aug 26 2020
!Series_pubmed_id = 32719519
!Series_summary = The full neutrophil heterogeneity and differentiation landscape remains incompletely characterized. Here we profiled more than 25,000 mouse differentiating and mature neutrophils using single-cell RNA sequencing to provide a comprehensive transcriptional landscape of neutrophil maturation, function, and fate decision in their steady state and during bacterial infection. Eight neutrophil populations (including the GMP population) were defined by distinct molecular signatures, including a new circulating mature neutrophil population highly expressing interferon-stimulated genes. The three mature peripheral blood neutrophil subsets arise from distinct maturing bone marrow neutrophil subsets, a novel mechanism that highlights the complex and precise regulation of neutrophil production. Neutrophil heterogeneity and differentiation are driven by both known and uncharacterized transcription factors. Neutrophils gradually acquire microbicidal capability as cells traverse the transcriptional landscape, representing an evolved mechanism for fine-tuned regulation of an effective but balanced neutrophil response. Bacterial infection reprograms the genetic architecture of neutrophil population, alters dynamic transition between each subpopulation, and primes neutrophils for augmented functionality without affecting overall heterogeneity. Bacterial infection-induced emergency granulopoiesis is mediated by augmented proliferation of early-stage neutrophil progenitors and accelerated post-mitotic maturation. In summary, single-cell transcriptomics enabled the reconstruction of neutrophil differentiation and maturation trajectories and uncovered neutrophil subpopulations, gene pathways, and regulators of neutrophil function and fate decisions. These data establish a reference model and general framework for studying neutrophil-related disease mechanisms, biomarkers, and therapeutic targets at single-cell resolution.
!Series_overall_design = There are 10 mouse samples and 1 human sample. All relative organs consist of bone marrow (BM), peripheral blood (PB), spleen (SP), liver (LV) and peritoneal cavity (PC).
!Series_overall_design = 4 mouse control samples: BM sorted by cKit+ Gr1+; BM, PB, SP sorted by Gr1+.
!Series_overall_design = 6 mouse E. coli challenged samples: BM sorted by cKit+ Gr1+; BM, PB, SP, LV and PC sorted by Gr1+.
!Series_overall_design = 3 human control samples: PB sorted by CD33.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Xuemei,,Xie
!Series_contributor = Qiang,,Shi
!Series_contributor = Peng,,Wu
!Series_sample_id = GSM4081545
!Series_sample_id = GSM4081546
!Series_sample_id = GSM4081547
!Series_sample_id = GSM4081548
!Series_sample_id = GSM4081549
!Series_sample_id = GSM4081550
!Series_sample_id = GSM4081551
!Series_sample_id = GSM4081552
!Series_sample_id = GSM4081553
!Series_sample_id = GSM4081554
!Series_sample_id = GSM4081555
!Series_sample_id = GSM4473444
!Series_sample_id = GSM4473445
!Series_contact_name = Xuemei,,Xie
!Series_contact_email = xiexuemei.fiona@gmail.com
!Series_contact_laboratory = Luo's Lab
!Series_contact_department = Transfusion Medicine
!Series_contact_institute = Boston Children's Hospital
!Series_contact_address = 811 Enders Building, 320 Longwood Ave.
!Series_contact_city = Boston
!Series_contact_state = MA
!Series_contact_zip/postal_code = 02115
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137539/suppl/GSE137539_Cell_index_Barcode.txt.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137539/suppl/GSE137539_Human_donor_meta.txt.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137539/suppl/GSE137539_Mouse_WT_Eco_meta.txt.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137539/suppl/GSE137539_Mouse_WT_blank_meta.txt.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137539/suppl/GSE137539_RAW.tar
!Series_platform_id = GPL24247
!Series_platform_id = GPL24676
!Series_platform_taxid = 9606
!Series_platform_taxid = 10090
!Series_sample_taxid = 9606
!Series_sample_taxid = 10090
!Series_relation = SubSeries of: GSE137540
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA565803
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP221817
^PLATFORM = GPL24247
!Platform_title = Illumina NovaSeq 6000 (Mus musculus)
!Platform_geo_accession = GPL24247
!Platform_status = Public on Nov 08 2017
!Platform_submission_date = Nov 08 2017
!Platform_last_update_date = Mar 08 2019
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Mus musculus
!Platform_taxid = 10090
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^PLATFORM = GPL24676
!Platform_title = Illumina NovaSeq 6000 (Homo sapiens)
!Platform_geo_accession = GPL24676
!Platform_status = Public on Mar 02 2018
!Platform_submission_date = Mar 02 2018
!Platform_last_update_date = Nov 05 2018
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Homo sapiens
!Platform_taxid = 9606
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM4081545
!Sample_title = wt_ctl_bm1
!Sample_geo_accession = GSM4081545
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 27 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow neutrophil
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain/background: C57BL/6
!Sample_characteristics_ch1 = cell type: Bone marrow neutrophil
!Sample_characteristics_ch1 = condition: Steady state
!Sample_characteristics_ch1 = sorting: Sorted by cKit+ Gr1+
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = 10x Genomics Single Cell 3’ Library Kit V2.
!Sample_description = Single cell RNA-seq
!Sample_data_processing = Sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell Ranger v2.2.0.
!Sample_data_processing = Sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline.
!Sample_data_processing = Genome_build: mm10 (mouse) or hg38 (human)
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Text files include UMIs for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
!Sample_contact_institute = Boston Children's Hospital
!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769555
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855648
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4081nnn/GSM4081545/suppl/GSM4081545_wt_ctl_bm1.txt.gz
!Sample_series_id = GSE137539
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081546
!Sample_title = wt_ctl_bm2
!Sample_geo_accession = GSM4081546
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 27 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow neutrophil
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain/background: C57BL/6
!Sample_characteristics_ch1 = cell type: Bone marrow neutrophil
!Sample_characteristics_ch1 = condition: Steady state
!Sample_characteristics_ch1 = sorting: Sorted by Gr1+
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = 10x Genomics Single Cell 3’ Library Kit V2.
!Sample_description = Single cell RNA-seq
!Sample_data_processing = Sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell Ranger v2.2.0.
!Sample_data_processing = Sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline.
!Sample_data_processing = Genome_build: mm10 (mouse) or hg38 (human)
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Text files include UMIs for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
!Sample_contact_institute = Boston Children's Hospital
!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769554
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855649
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4081nnn/GSM4081546/suppl/GSM4081546_wt_ctl_bm2.txt.gz
!Sample_series_id = GSE137539
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081547
!Sample_title = wt_ctl_pb2
!Sample_geo_accession = GSM4081547
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 27 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = peripheral blood neutrophil
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain/background: C57BL/6
!Sample_characteristics_ch1 = cell type: Peripheral blood neutrophil
!Sample_characteristics_ch1 = condition: Steady state
!Sample_characteristics_ch1 = sorting: Sorted by Gr1+
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = 10x Genomics Single Cell 3’ Library Kit V2.
!Sample_description = Single cell RNA-seq
!Sample_data_processing = Sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell Ranger v2.2.0.
!Sample_data_processing = Sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline.
!Sample_data_processing = Genome_build: mm10 (mouse) or hg38 (human)
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Text files include UMIs for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
!Sample_contact_institute = Boston Children's Hospital
!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769553
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855650
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4081nnn/GSM4081547/suppl/GSM4081547_wt_ctl_pb2.txt.gz
!Sample_series_id = GSE137539
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081548
!Sample_title = wt_ctl_sp2
!Sample_geo_accession = GSM4081548
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 27 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = spleen neutrophil
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain/background: C57BL/6
!Sample_characteristics_ch1 = cell type: Spleen neutrophil
!Sample_characteristics_ch1 = condition: Steady state
!Sample_characteristics_ch1 = sorting: Sorted by Gr1+
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = 10x Genomics Single Cell 3’ Library Kit V2.
!Sample_description = Single cell RNA-seq
!Sample_data_processing = Sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell Ranger v2.2.0.
!Sample_data_processing = Sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline.
!Sample_data_processing = Genome_build: mm10 (mouse) or hg38 (human)
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Text files include UMIs for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
!Sample_contact_institute = Boston Children's Hospital
!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769552
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855651
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4081nnn/GSM4081548/suppl/GSM4081548_wt_ctl_sp2.txt.gz
!Sample_series_id = GSE137539
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081549
!Sample_title = wt_eco_bm1
!Sample_geo_accession = GSM4081549
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 27 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow neutrophil
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain/background: C57BL/6
!Sample_characteristics_ch1 = cell type: Bone marrow neutrophil
!Sample_characteristics_ch1 = condition: E. coli challenge (24h)
!Sample_characteristics_ch1 = sorting: Sorted by cKit+ Gr1+
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = 10x Genomics Single Cell 3’ Library Kit V2.
!Sample_description = Single cell RNA-seq
!Sample_data_processing = Sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell Ranger v2.2.0.
!Sample_data_processing = Sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline.
!Sample_data_processing = Genome_build: mm10 (mouse) or hg38 (human)
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Text files include UMIs for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
!Sample_contact_institute = Boston Children's Hospital
!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769551
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855652
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4081nnn/GSM4081549/suppl/GSM4081549_wt_eco_bm1.txt.gz
!Sample_series_id = GSE137539
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081550
!Sample_title = wt_eco_bm2
!Sample_geo_accession = GSM4081550
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 27 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow neutrophil
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain/background: C57BL/6
!Sample_characteristics_ch1 = cell type: Bone marrow neutrophil
!Sample_characteristics_ch1 = condition: E. coli challenge (24h)
!Sample_characteristics_ch1 = sorting: Sorted by Gr1+
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = 10x Genomics Single Cell 3’ Library Kit V2.
!Sample_description = Single cell RNA-seq
!Sample_data_processing = Sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell Ranger v2.2.0.
!Sample_data_processing = Sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline.
!Sample_data_processing = Genome_build: mm10 (mouse) or hg38 (human)
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Text files include UMIs for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
!Sample_contact_institute = Boston Children's Hospital
!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769550
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855653
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4081nnn/GSM4081550/suppl/GSM4081550_wt_eco_bm2.txt.gz
!Sample_series_id = GSE137539
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081551
!Sample_title = wt_eco_pb2
!Sample_geo_accession = GSM4081551
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 27 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = peripheral blood neutrophil
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain/background: C57BL/6
!Sample_characteristics_ch1 = cell type: Peripheral blood neutrophil
!Sample_characteristics_ch1 = condition: E. coli challenge (24h)
!Sample_characteristics_ch1 = sorting: Sorted by Gr1+
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = 10x Genomics Single Cell 3’ Library Kit V2.
!Sample_description = Single cell RNA-seq
!Sample_data_processing = Sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell Ranger v2.2.0.
!Sample_data_processing = Sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline.
!Sample_data_processing = Genome_build: mm10 (mouse) or hg38 (human)
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Text files include UMIs for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
!Sample_contact_institute = Boston Children's Hospital
!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769549
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855654
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4081nnn/GSM4081551/suppl/GSM4081551_wt_eco_pb2.txt.gz
!Sample_series_id = GSE137539
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081552
!Sample_title = wt_eco_sp2
!Sample_geo_accession = GSM4081552
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 27 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = spleen neutrophil
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain/background: C57BL/6
!Sample_characteristics_ch1 = cell type: Spleen neutrophil
!Sample_characteristics_ch1 = condition: E. coli challenge (24h)
!Sample_characteristics_ch1 = sorting: Sorted by Gr1+
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = 10x Genomics Single Cell 3’ Library Kit V2.
!Sample_description = Single cell RNA-seq
!Sample_data_processing = Sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell Ranger v2.2.0.
!Sample_data_processing = Sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline.
!Sample_data_processing = Genome_build: mm10 (mouse) or hg38 (human)
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Text files include UMIs for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
!Sample_contact_institute = Boston Children's Hospital
!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769548
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855655
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4081nnn/GSM4081552/suppl/GSM4081552_wt_eco_sp2.txt.gz
!Sample_series_id = GSE137539
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081553
!Sample_title = wt_eco_lv2
!Sample_geo_accession = GSM4081553
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 27 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = liver neutrophil
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain/background: C57BL/6
!Sample_characteristics_ch1 = cell type: Liver neutrophil
!Sample_characteristics_ch1 = condition: E. coli challenge (24h)
!Sample_characteristics_ch1 = sorting: Sorted by Gr1+
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = 10x Genomics Single Cell 3’ Library Kit V2.
!Sample_description = Single cell RNA-seq
!Sample_data_processing = Sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell Ranger v2.2.0.
!Sample_data_processing = Sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline.
!Sample_data_processing = Genome_build: mm10 (mouse) or hg38 (human)
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Text files include UMIs for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
!Sample_contact_institute = Boston Children's Hospital
!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769547
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855656
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4081nnn/GSM4081553/suppl/GSM4081553_wt_eco_lv2.txt.gz
!Sample_series_id = GSE137539
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081554
!Sample_title = wt_eco_pc2
!Sample_geo_accession = GSM4081554
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 27 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = peritoneal cavity neutrophil
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain/background: C57BL/6
!Sample_characteristics_ch1 = cell type: Peritoneal cavity neutrophil
!Sample_characteristics_ch1 = condition: E. coli challenge (24h)
!Sample_characteristics_ch1 = sorting: Sorted by Gr1+
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = 10x Genomics Single Cell 3’ Library Kit V2.
!Sample_description = Single cell RNA-seq
!Sample_data_processing = Sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell Ranger v2.2.0.
!Sample_data_processing = Sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline.
!Sample_data_processing = Genome_build: mm10 (mouse) or hg38 (human)
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Text files include UMIs for each Sample.
!Sample_platform_id = GPL24247
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
!Sample_contact_institute = Boston Children's Hospital
!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769546
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855657
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4081nnn/GSM4081554/suppl/GSM4081554_wt_eco_pc2.txt.gz
!Sample_series_id = GSE137539
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081555
!Sample_title = NKD181202670
!Sample_geo_accession = GSM4081555
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 27 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = peripheral blood neutrophil
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Peripheral blood neutrophil
!Sample_characteristics_ch1 = condition: Steady state
!Sample_characteristics_ch1 = sorting: Sorted by CD33+
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = BD Rhapsody Cartridge Reagent Kit.
!Sample_description = Single cell RNA-seq
!Sample_data_processing = Sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell Ranger v2.2.0.
!Sample_data_processing = Sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline.
!Sample_data_processing = Genome_build: mm10 (mouse) or hg38 (human)
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Text files include UMIs for each Sample.
!Sample_platform_id = GPL24676
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
!Sample_contact_institute = Boston Children's Hospital
!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769545
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855658
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4081nnn/GSM4081555/suppl/GSM4081555_NKD181202670.txt.gz
!Sample_series_id = GSE137539
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4473444
!Sample_title = RBD00006-T
!Sample_geo_accession = GSM4473444
!Sample_status = Public on May 26 2020
!Sample_submission_date = Apr 13 2020
!Sample_last_update_date = May 27 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = peripheral blood neutrophil
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: peripheral blood neutrophil
!Sample_characteristics_ch1 = condition: steady state
!Sample_characteristics_ch1 = sorting: Sorted by CD33+
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = BD Rhapsody Cartridge Reagent Kit
!Sample_data_processing = sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline
!Sample_data_processing = Genome_build: hg38 (human)
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include UMIs for each Sample
!Sample_platform_id = GPL24676
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
!Sample_contact_institute = Boston Children's Hospital
!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14591038
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8108915
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4473nnn/GSM4473444/suppl/GSM4473444_RBD00006.txt.gz
!Sample_series_id = GSE137539
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4473445
!Sample_title = HDY_PB
!Sample_geo_accession = GSM4473445
!Sample_status = Public on May 26 2020
!Sample_submission_date = Apr 13 2020
!Sample_last_update_date = May 27 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = peripheral blood neutrophil
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: peripheral blood neutrophil
!Sample_characteristics_ch1 = condition: steady state
!Sample_characteristics_ch1 = sorting: Sorted by CD33+
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = BD Rhapsody Cartridge Reagent Kit
!Sample_data_processing = sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline
!Sample_data_processing = Genome_build: hg38 (human)
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include UMIs for each Sample
!Sample_platform_id = GPL24676
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
!Sample_contact_institute = Boston Children's Hospital
!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14591037
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8108916
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4473nnn/GSM4473445/suppl/GSM4473445_HDY.txt.gz
!Sample_series_id = GSE137539
!Sample_series_id = GSE137540
!Sample_data_row_count = 0