^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 = GSE137538
!Series_title = RNA sequencing of different neutrophil subpopulations from bone marrow
!Series_geo_accession = GSE137538
!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 purpose of this study is to learn the dynamic transcriptomic and molecular changes during neutrophil development. We investigated the gene expression profiles of purified morphology-defined neutrophil populations. Promyelocytes (PMs), myelocytes (MCs), metamyelocytes (MMs), band neutrophils and segmented neutrophils (BN/SNs) were isolated by FACS based on differential expression of C-Kit and Ly6g.Their identities were confirmed by morphological examination. Bulk RNA sequencing was then performed to reveal the gene expression profiles and molecular signatures of each cell population. Detailed analysis of gene expression revealed that MBs highly expressed the stem cell marker Cd34 and translation-related genes such as Eef1a1, while the highest expression of primary granule-related genes such as Mpo, Elane, Prtn3, and Cstg was detected in the PM population. MCs and MMs were highly proliferative neutrophils expressing high levels of cell cycle-related genes which were significantly downregulated in mature neutrophils. Finally, this study provides a framework for the detail study of the neutrophil development and for the future application in the modulation of the granulopoiesis under pathological conditions.
!Series_overall_design = Five neutrophil populations: promyelocytes (PMs), myelocytes (MCs), metamyelocytes (MMs), band neutrophils and segmented neutrophils (BN/SNs) were isolated by FACS based on differential expression of C-Kit and Ly6g.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Xiaoyu,,Zhang
!Series_contributor = Xuemei,,Xie
!Series_contributor = Qiang,,Shi
!Series_sample_id = GSM4081530
!Series_sample_id = GSM4081531
!Series_sample_id = GSM4081532
!Series_sample_id = GSM4081533
!Series_sample_id = GSM4081534
!Series_sample_id = GSM4081535
!Series_sample_id = GSM4081536
!Series_sample_id = GSM4081537
!Series_sample_id = GSM4081538
!Series_sample_id = GSM4081539
!Series_sample_id = GSM4081540
!Series_sample_id = GSM4081541
!Series_sample_id = GSM4081542
!Series_sample_id = GSM4081543
!Series_sample_id = GSM4081544
!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/GSE137538/suppl/GSE137538_2019Granulocyte_bulk_matrix.csv.gz
!Series_platform_id = GPL17021
!Series_platform_taxid = 10090
!Series_sample_taxid = 10090
!Series_relation = SubSeries of: GSE137540
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA565799
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP221813
^PLATFORM = GPL17021
!Platform_title = Illumina HiSeq 2500 (Mus musculus)
!Platform_geo_accession = GPL17021
!Platform_status = Public on Apr 16 2013
!Platform_submission_date = Apr 16 2013
!Platform_last_update_date = Mar 21 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
^SAMPLE = GSM4081530
!Sample_title = 20170926_BM_NEU1_XZ4704-1_S13
!Sample_geo_accession = GSM4081530
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 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: BN/SN neutrophils
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted from those populations using QIAGEN RNeasy Mini Kit. RNA quality was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer.
!Sample_extract_protocol_ch1 = RNA-sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (Illumina Platforms). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and were sequenced with paired-end on an Illumina HiSeq2500.
!Sample_description = processed data file: 2019Granulocyte_bulk_matrix.csv
!Sample_data_processing = QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
!Sample_data_processing = The resulting reads were then mapped to the mouse genome references sequence (GRCm38/mm10 Ensemble release 81) and counted using alignment software STAR2.5.2b.
!Sample_data_processing = Gene differential expression analysis were using EdgeR.
!Sample_data_processing = Genome_build: mm10 (GRCm38)
!Sample_data_processing = Supplementary_files_format_and_content: 2019Granulocyte_bulk_matrix.csv: Comma-separated text file.
!Sample_platform_id = GPL17021
!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 HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769006
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855602
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE137538
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081531
!Sample_title = 20170926_BM_NEU2_XZ4704-1_S14
!Sample_geo_accession = GSM4081531
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 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: BN/SN neutrophils
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted from those populations using QIAGEN RNeasy Mini Kit. RNA quality was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer.
!Sample_extract_protocol_ch1 = RNA-sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (Illumina Platforms). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and were sequenced with paired-end on an Illumina HiSeq2500.
!Sample_description = processed data file: 2019Granulocyte_bulk_matrix.csv
!Sample_data_processing = QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
!Sample_data_processing = The resulting reads were then mapped to the mouse genome references sequence (GRCm38/mm10 Ensemble release 81) and counted using alignment software STAR2.5.2b.
!Sample_data_processing = Gene differential expression analysis were using EdgeR.
!Sample_data_processing = Genome_build: mm10 (GRCm38)
!Sample_data_processing = Supplementary_files_format_and_content: 2019Granulocyte_bulk_matrix.csv: Comma-separated text file.
!Sample_platform_id = GPL17021
!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 HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769005
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855603
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE137538
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081532
!Sample_title = 20170926_BM_NEU3_XZ4704-1_S15
!Sample_geo_accession = GSM4081532
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 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: BN/SN neutrophils
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted from those populations using QIAGEN RNeasy Mini Kit. RNA quality was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer.
!Sample_extract_protocol_ch1 = RNA-sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (Illumina Platforms). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and were sequenced with paired-end on an Illumina HiSeq2500.
!Sample_description = processed data file: 2019Granulocyte_bulk_matrix.csv
!Sample_data_processing = QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
!Sample_data_processing = The resulting reads were then mapped to the mouse genome references sequence (GRCm38/mm10 Ensemble release 81) and counted using alignment software STAR2.5.2b.
!Sample_data_processing = Gene differential expression analysis were using EdgeR.
!Sample_data_processing = Genome_build: mm10 (GRCm38)
!Sample_data_processing = Supplementary_files_format_and_content: 2019Granulocyte_bulk_matrix.csv: Comma-separated text file.
!Sample_platform_id = GPL17021
!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 HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769004
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855604
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE137538
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081533
!Sample_title = 20170926_MB1_XZ4704-1_S1
!Sample_geo_accession = GSM4081533
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 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: MB neutrophils
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted from those populations using QIAGEN RNeasy Mini Kit. RNA quality was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer.
!Sample_extract_protocol_ch1 = RNA-sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (Illumina Platforms). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and were sequenced with paired-end on an Illumina HiSeq2500.
!Sample_description = processed data file: 2019Granulocyte_bulk_matrix.csv
!Sample_data_processing = QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
!Sample_data_processing = The resulting reads were then mapped to the mouse genome references sequence (GRCm38/mm10 Ensemble release 81) and counted using alignment software STAR2.5.2b.
!Sample_data_processing = Gene differential expression analysis were using EdgeR.
!Sample_data_processing = Genome_build: mm10 (GRCm38)
!Sample_data_processing = Supplementary_files_format_and_content: 2019Granulocyte_bulk_matrix.csv: Comma-separated text file.
!Sample_platform_id = GPL17021
!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 HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769003
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855605
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE137538
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081534
!Sample_title = 20170926_MB2_XZ4704-1_S2
!Sample_geo_accession = GSM4081534
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 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: MB neutrophils
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted from those populations using QIAGEN RNeasy Mini Kit. RNA quality was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer.
!Sample_extract_protocol_ch1 = RNA-sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (Illumina Platforms). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and were sequenced with paired-end on an Illumina HiSeq2500.
!Sample_description = processed data file: 2019Granulocyte_bulk_matrix.csv
!Sample_data_processing = QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
!Sample_data_processing = The resulting reads were then mapped to the mouse genome references sequence (GRCm38/mm10 Ensemble release 81) and counted using alignment software STAR2.5.2b.
!Sample_data_processing = Gene differential expression analysis were using EdgeR.
!Sample_data_processing = Genome_build: mm10 (GRCm38)
!Sample_data_processing = Supplementary_files_format_and_content: 2019Granulocyte_bulk_matrix.csv: Comma-separated text file.
!Sample_platform_id = GPL17021
!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 HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769002
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855606
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE137538
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081535
!Sample_title = 20170926_MB3_XZ4704-1_S3
!Sample_geo_accession = GSM4081535
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 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: MB neutrophils
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted from those populations using QIAGEN RNeasy Mini Kit. RNA quality was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer.
!Sample_extract_protocol_ch1 = RNA-sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (Illumina Platforms). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and were sequenced with paired-end on an Illumina HiSeq2500.
!Sample_description = processed data file: 2019Granulocyte_bulk_matrix.csv
!Sample_data_processing = QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
!Sample_data_processing = The resulting reads were then mapped to the mouse genome references sequence (GRCm38/mm10 Ensemble release 81) and counted using alignment software STAR2.5.2b.
!Sample_data_processing = Gene differential expression analysis were using EdgeR.
!Sample_data_processing = Genome_build: mm10 (GRCm38)
!Sample_data_processing = Supplementary_files_format_and_content: 2019Granulocyte_bulk_matrix.csv: Comma-separated text file.
!Sample_platform_id = GPL17021
!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 HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769001
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855607
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE137538
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081536
!Sample_title = 20170926_MC_1_8_17_XZ4704-1_S7
!Sample_geo_accession = GSM4081536
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 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: MC neutrophils
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted from those populations using QIAGEN RNeasy Mini Kit. RNA quality was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer.
!Sample_extract_protocol_ch1 = RNA-sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (Illumina Platforms). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and were sequenced with paired-end on an Illumina HiSeq2500.
!Sample_description = processed data file: 2019Granulocyte_bulk_matrix.csv
!Sample_data_processing = QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
!Sample_data_processing = The resulting reads were then mapped to the mouse genome references sequence (GRCm38/mm10 Ensemble release 81) and counted using alignment software STAR2.5.2b.
!Sample_data_processing = Gene differential expression analysis were using EdgeR.
!Sample_data_processing = Genome_build: mm10 (GRCm38)
!Sample_data_processing = Supplementary_files_format_and_content: 2019Granulocyte_bulk_matrix.csv: Comma-separated text file.
!Sample_platform_id = GPL17021
!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 HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12769000
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855608
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE137538
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081537
!Sample_title = 20170926_MC2_XZ4704-1_S8
!Sample_geo_accession = GSM4081537
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 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: MC neutrophils
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted from those populations using QIAGEN RNeasy Mini Kit. RNA quality was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer.
!Sample_extract_protocol_ch1 = RNA-sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (Illumina Platforms). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and were sequenced with paired-end on an Illumina HiSeq2500.
!Sample_description = processed data file: 2019Granulocyte_bulk_matrix.csv
!Sample_data_processing = QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
!Sample_data_processing = The resulting reads were then mapped to the mouse genome references sequence (GRCm38/mm10 Ensemble release 81) and counted using alignment software STAR2.5.2b.
!Sample_data_processing = Gene differential expression analysis were using EdgeR.
!Sample_data_processing = Genome_build: mm10 (GRCm38)
!Sample_data_processing = Supplementary_files_format_and_content: 2019Granulocyte_bulk_matrix.csv: Comma-separated text file.
!Sample_platform_id = GPL17021
!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 HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12768999
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855609
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE137538
!Sample_series_id = GSE137540
!Sample_data_row_count = 0
^SAMPLE = GSM4081538
!Sample_title = 20170926_MC3_XZ4704-1_S9
!Sample_geo_accession = GSM4081538
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 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: MC neutrophils
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted from those populations using QIAGEN RNeasy Mini Kit. RNA quality was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer.
!Sample_extract_protocol_ch1 = RNA-sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (Illumina Platforms). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and were sequenced with paired-end on an Illumina HiSeq2500.
!Sample_description = processed data file: 2019Granulocyte_bulk_matrix.csv
!Sample_data_processing = QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
!Sample_data_processing = The resulting reads were then mapped to the mouse genome references sequence (GRCm38/mm10 Ensemble release 81) and counted using alignment software STAR2.5.2b.
!Sample_data_processing = Gene differential expression analysis were using EdgeR.
!Sample_data_processing = Genome_build: mm10 (GRCm38)
!Sample_data_processing = Supplementary_files_format_and_content: 2019Granulocyte_bulk_matrix.csv: Comma-separated text file.
!Sample_platform_id = GPL17021
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
!Sample_contact_department = Transfusion Medicine
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!Sample_contact_address = 811 Enders Building, 320 Longwood Ave.
!Sample_contact_city = Boston
!Sample_contact_state = MA
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!Sample_contact_country = USA
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!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12768998
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855610
!Sample_supplementary_file_1 = NONE
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!Sample_geo_accession = GSM4081539
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 2020
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!Sample_data_processing = QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
!Sample_data_processing = The resulting reads were then mapped to the mouse genome references sequence (GRCm38/mm10 Ensemble release 81) and counted using alignment software STAR2.5.2b.
!Sample_data_processing = Gene differential expression analysis were using EdgeR.
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855611
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!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 2020
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!Sample_data_processing = QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
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!Sample_data_processing = Gene differential expression analysis were using EdgeR.
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6855612
!Sample_supplementary_file_1 = NONE
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^SAMPLE = GSM4081541
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!Sample_geo_accession = GSM4081541
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 2020
!Sample_type = SRA
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!Sample_data_processing = Gene differential expression analysis were using EdgeR.
!Sample_data_processing = Genome_build: mm10 (GRCm38)
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!Sample_platform_id = GPL17021
!Sample_contact_name = Xuemei,,Xie
!Sample_contact_email = xiexuemei.fiona@gmail.com
!Sample_contact_laboratory = Luo's Lab
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!Sample_contact_zip/postal_code = 02115
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^SAMPLE = GSM4081542
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!Sample_geo_accession = GSM4081542
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 2020
!Sample_type = SRA
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!Sample_extract_protocol_ch1 = RNA-sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (Illumina Platforms). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and were sequenced with paired-end on an Illumina HiSeq2500.
!Sample_description = processed data file: 2019Granulocyte_bulk_matrix.csv
!Sample_data_processing = QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
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!Sample_data_processing = Gene differential expression analysis were using EdgeR.
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!Sample_platform_id = GPL17021
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!Sample_supplementary_file_1 = NONE
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^SAMPLE = GSM4081543
!Sample_title = 20170926_PM2_XZ4704-1_S5
!Sample_geo_accession = GSM4081543
!Sample_status = Public on May 26 2020
!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 2020
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!Sample_extract_protocol_ch1 = RNA-sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (Illumina Platforms). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and were sequenced with paired-end on an Illumina HiSeq2500.
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!Sample_data_processing = Gene differential expression analysis were using EdgeR.
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!Sample_platform_id = GPL17021
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!Sample_contact_laboratory = Luo's Lab
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!Sample_submission_date = Sep 16 2019
!Sample_last_update_date = May 26 2020
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!Sample_description = processed data file: 2019Granulocyte_bulk_matrix.csv
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!Sample_data_processing = The resulting reads were then mapped to the mouse genome references sequence (GRCm38/mm10 Ensemble release 81) and counted using alignment software STAR2.5.2b.
!Sample_data_processing = Gene differential expression analysis were using EdgeR.
!Sample_data_processing = Genome_build: mm10 (GRCm38)
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!Sample_platform_id = GPL17021
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