^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 = GSE158666
!Series_title = Differential expression of Triggering Receptor Expressed on Myeloid Cells (Trem)-2 in tissue eosinophils
!Series_geo_accession = GSE158666
!Series_status = Public on Sep 27 2021
!Series_submission_date = Sep 28 2020
!Series_last_update_date = Sep 27 2021
!Series_summary = No longer regarded as simply end-stage cytotoxic effectors, eosinophils are now recognized as complex cells with unique phenotypes that develop in response to the local microenvironment. In our previous study, we documented eosinophil infiltration in association with characteristic muscle damage in the dystrophin-deficient (mdx) mouse model of Duchenne muscular dystrophy. In this earlier study, we found that eosinophils did not promote formation of muscle lesions, as these persisted in eosinophil-deficient mdx.PHIL mice. To obtain additional insight into these findings, we performed RNA sequencing on eosinophils isolated from muscle tissue of mdx, IL5tg, and mdx.IL5tg mouse strains. We discovered profound up-regulation of classical eosinophil effector proteins (major basic protein-1, eosinophil peroxidase, and eosinophil-associated ribonucleases, or RNases) in eosinophils isolated from lesion-free muscle from IL5tg mice. By contrast, we observed significant upregulation of tissue remodeling genes, including proteases, extracellular matrix components, collagen, and skeletal muscle precursors, as well as the immunomodulatory receptor, TREM2, in eosinophils isolated from skeletal muscle tissue from the dystrophin-deficient mdx mouse strain. The anti-inflammatory properties of TREM2 have been described in the monocyte/macrophage lineage; however, there are no previous studies documenting TREM2 expression in eosinophils. Here we show that TREM2 is critical for full growth and differentiation of bone marrow-derived eosinophil cultures and for full expression of toll-like receptor 4. Immunoreactive TREM2 was also detected on human eosinophils at levels that correlated with donor body mass index. Taken together, our findings provide important insight into the immunomodulatory and remodeling capacity of mouse eosinophils and the flexibility of their gene expression profiles in vivo.
!Series_overall_design = 3 conditions (mdx, mdx+IL5, IL5), 3 biological replicates per condition
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Albert,C,Sek
!Series_contributor = Caroline,M,Percopo
!Series_contributor = Arun,K,Boddapati
!Series_contributor = Michelle,,Ma
!Series_contributor = Wendy,E,Geslewitz
!Series_contributor = Julia,O,Krumholz
!Series_contributor = Justin,B,Lack
!Series_contributor = Helene,F,Rosenberg
!Series_sample_id = GSM4805194
!Series_sample_id = GSM4805195
!Series_sample_id = GSM4805196
!Series_sample_id = GSM4805197
!Series_sample_id = GSM4805198
!Series_sample_id = GSM4805199
!Series_sample_id = GSM4805200
!Series_sample_id = GSM4805201
!Series_sample_id = GSM4805202
!Series_contact_name = Pamela,,Frischmeyer-Guerrerio
!Series_contact_email = pamela.guerrerio@nih.gov
!Series_contact_phone = 301-402-9782
!Series_contact_laboratory = Laboratory of Allergic Diseases
!Series_contact_department = National Institute of Allergy and Infectious Diseases
!Series_contact_institute = National Institutes of Health
!Series_contact_address = Bldg. 10, Rm 11N240B, 10 Center Dr.
!Series_contact_city = Bethesda
!Series_contact_state = MD
!Series_contact_zip/postal_code = 20892-1881
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE158nnn/GSE158666/suppl/GSE158666_RawCountFile_RSEM_genes.txt.gz
!Series_platform_id = GPL21103
!Series_platform_taxid = 10090
!Series_sample_taxid = 10090
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA666161
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP285640
^PLATFORM = GPL21103
!Platform_title = Illumina HiSeq 4000 (Mus musculus)
!Platform_geo_accession = GPL21103
!Platform_status = Public on Nov 04 2015
!Platform_submission_date = Nov 04 2015
!Platform_last_update_date = Mar 19 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 = GSM4805194
!Sample_title = replicate 1 of IL5Tg condition
!Sample_geo_accession = GSM4805194
!Sample_status = Public on Sep 27 2021
!Sample_submission_date = Sep 28 2020
!Sample_last_update_date = Sep 27 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = eosinophils isolated from quadricep muscle infiltrates
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: mdx
!Sample_characteristics_ch1 = developmental stage: adult
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Eosinophils from infiltrates in mouse quadriceps muscle were isolated by fluorescence-activated cell sorting (FACS); live eosinophils (CD45+CD11c-Gr1-MHCII-SiglecF+) were sorted directly into TRIZOL-LS (Life Technologies, Frederick, MD, USA) at a 3:1 ratio of TRIZOL-LS to sorted cell sample which was then equilibrated with chloroform. Total RNA was purified from the aqueous phase, combined with equal volumes of 70% ethanol, and purified with the RNeasy Cleanup kit (Qiagen, Germantown, MD, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared using the NEBnext Ultra Low Input Total RNA Library Prep Kit (New England BioLabs, Beverly, MA, USA) following the manufacturer’s instructions.
!Sample_data_processing = Illumina Casava1.8 software used for basecalling.
!Sample_data_processing = Raw fastq files were then trimmed for quality and adapter contamination using Cutadapt v2.10 and trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3 in 2-pass mode.
!Sample_data_processing = Gene-level expression quantification was performed using RSEM v1.3.0
!Sample_data_processing = Prior to differential expression and downstream time course analysis, genes were filtered to include <1 counts per million (CPM) across <3 samples.
!Sample_data_processing = Standard differential expression was performed using the R package limma with voom normalization
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: raw expression (expected counts) text file generated from RSEM
!Sample_platform_id = GPL21103
!Sample_contact_name = Pamela,,Frischmeyer-Guerrerio
!Sample_contact_email = pamela.guerrerio@nih.gov
!Sample_contact_phone = 301-402-9782
!Sample_contact_laboratory = Laboratory of Allergic Diseases
!Sample_contact_department = National Institute of Allergy and Infectious Diseases
!Sample_contact_institute = National Institutes of Health
!Sample_contact_address = Bldg. 10, Rm 11N240B, 10 Center Dr.
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892-1881
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16282192
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9203904
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE158666
!Sample_data_row_count = 0
^SAMPLE = GSM4805195
!Sample_title = replicate 2 of IL5Tg condition
!Sample_geo_accession = GSM4805195
!Sample_status = Public on Sep 27 2021
!Sample_submission_date = Sep 28 2020
!Sample_last_update_date = Sep 27 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = eosinophils isolated from quadricep muscle infiltrates
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: mdx
!Sample_characteristics_ch1 = developmental stage: adult
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Eosinophils from infiltrates in mouse quadriceps muscle were isolated by fluorescence-activated cell sorting (FACS); live eosinophils (CD45+CD11c-Gr1-MHCII-SiglecF+) were sorted directly into TRIZOL-LS (Life Technologies, Frederick, MD, USA) at a 3:1 ratio of TRIZOL-LS to sorted cell sample which was then equilibrated with chloroform. Total RNA was purified from the aqueous phase, combined with equal volumes of 70% ethanol, and purified with the RNeasy Cleanup kit (Qiagen, Germantown, MD, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared using the NEBnext Ultra Low Input Total RNA Library Prep Kit (New England BioLabs, Beverly, MA, USA) following the manufacturer’s instructions.
!Sample_data_processing = Illumina Casava1.8 software used for basecalling.
!Sample_data_processing = Raw fastq files were then trimmed for quality and adapter contamination using Cutadapt v2.10 and trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3 in 2-pass mode.
!Sample_data_processing = Gene-level expression quantification was performed using RSEM v1.3.0
!Sample_data_processing = Prior to differential expression and downstream time course analysis, genes were filtered to include <1 counts per million (CPM) across <3 samples.
!Sample_data_processing = Standard differential expression was performed using the R package limma with voom normalization
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: raw expression (expected counts) text file generated from RSEM
!Sample_platform_id = GPL21103
!Sample_contact_name = Pamela,,Frischmeyer-Guerrerio
!Sample_contact_email = pamela.guerrerio@nih.gov
!Sample_contact_phone = 301-402-9782
!Sample_contact_laboratory = Laboratory of Allergic Diseases
!Sample_contact_department = National Institute of Allergy and Infectious Diseases
!Sample_contact_institute = National Institutes of Health
!Sample_contact_address = Bldg. 10, Rm 11N240B, 10 Center Dr.
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892-1881
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16282191
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9203905
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE158666
!Sample_data_row_count = 0
^SAMPLE = GSM4805196
!Sample_title = replicate 3 of IL5Tg condition
!Sample_geo_accession = GSM4805196
!Sample_status = Public on Sep 27 2021
!Sample_submission_date = Sep 28 2020
!Sample_last_update_date = Sep 27 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = eosinophils isolated from quadricep muscle infiltrates
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: mdx
!Sample_characteristics_ch1 = developmental stage: adult
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Eosinophils from infiltrates in mouse quadriceps muscle were isolated by fluorescence-activated cell sorting (FACS); live eosinophils (CD45+CD11c-Gr1-MHCII-SiglecF+) were sorted directly into TRIZOL-LS (Life Technologies, Frederick, MD, USA) at a 3:1 ratio of TRIZOL-LS to sorted cell sample which was then equilibrated with chloroform. Total RNA was purified from the aqueous phase, combined with equal volumes of 70% ethanol, and purified with the RNeasy Cleanup kit (Qiagen, Germantown, MD, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared using the NEBnext Ultra Low Input Total RNA Library Prep Kit (New England BioLabs, Beverly, MA, USA) following the manufacturer’s instructions.
!Sample_data_processing = Illumina Casava1.8 software used for basecalling.
!Sample_data_processing = Raw fastq files were then trimmed for quality and adapter contamination using Cutadapt v2.10 and trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3 in 2-pass mode.
!Sample_data_processing = Gene-level expression quantification was performed using RSEM v1.3.0
!Sample_data_processing = Prior to differential expression and downstream time course analysis, genes were filtered to include <1 counts per million (CPM) across <3 samples.
!Sample_data_processing = Standard differential expression was performed using the R package limma with voom normalization
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: raw expression (expected counts) text file generated from RSEM
!Sample_platform_id = GPL21103
!Sample_contact_name = Pamela,,Frischmeyer-Guerrerio
!Sample_contact_email = pamela.guerrerio@nih.gov
!Sample_contact_phone = 301-402-9782
!Sample_contact_laboratory = Laboratory of Allergic Diseases
!Sample_contact_department = National Institute of Allergy and Infectious Diseases
!Sample_contact_institute = National Institutes of Health
!Sample_contact_address = Bldg. 10, Rm 11N240B, 10 Center Dr.
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892-1881
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16282190
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9203906
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE158666
!Sample_data_row_count = 0
^SAMPLE = GSM4805197
!Sample_title = replicate 1 of mdx condition
!Sample_geo_accession = GSM4805197
!Sample_status = Public on Sep 27 2021
!Sample_submission_date = Sep 28 2020
!Sample_last_update_date = Sep 27 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = eosinophils isolated from quadricep muscle infiltrates
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: mdx
!Sample_characteristics_ch1 = developmental stage: adult
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Eosinophils from infiltrates in mouse quadriceps muscle were isolated by fluorescence-activated cell sorting (FACS); live eosinophils (CD45+CD11c-Gr1-MHCII-SiglecF+) were sorted directly into TRIZOL-LS (Life Technologies, Frederick, MD, USA) at a 3:1 ratio of TRIZOL-LS to sorted cell sample which was then equilibrated with chloroform. Total RNA was purified from the aqueous phase, combined with equal volumes of 70% ethanol, and purified with the RNeasy Cleanup kit (Qiagen, Germantown, MD, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared using the NEBnext Ultra Low Input Total RNA Library Prep Kit (New England BioLabs, Beverly, MA, USA) following the manufacturer’s instructions.
!Sample_data_processing = Illumina Casava1.8 software used for basecalling.
!Sample_data_processing = Raw fastq files were then trimmed for quality and adapter contamination using Cutadapt v2.10 and trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3 in 2-pass mode.
!Sample_data_processing = Gene-level expression quantification was performed using RSEM v1.3.0
!Sample_data_processing = Prior to differential expression and downstream time course analysis, genes were filtered to include <1 counts per million (CPM) across <3 samples.
!Sample_data_processing = Standard differential expression was performed using the R package limma with voom normalization
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: raw expression (expected counts) text file generated from RSEM
!Sample_platform_id = GPL21103
!Sample_contact_name = Pamela,,Frischmeyer-Guerrerio
!Sample_contact_email = pamela.guerrerio@nih.gov
!Sample_contact_phone = 301-402-9782
!Sample_contact_laboratory = Laboratory of Allergic Diseases
!Sample_contact_department = National Institute of Allergy and Infectious Diseases
!Sample_contact_institute = National Institutes of Health
!Sample_contact_address = Bldg. 10, Rm 11N240B, 10 Center Dr.
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892-1881
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16282189
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9203907
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE158666
!Sample_data_row_count = 0
^SAMPLE = GSM4805198
!Sample_title = replicate 2 of mdx condition
!Sample_geo_accession = GSM4805198
!Sample_status = Public on Sep 27 2021
!Sample_submission_date = Sep 28 2020
!Sample_last_update_date = Sep 27 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = eosinophils isolated from quadricep muscle infiltrates
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: mdx
!Sample_characteristics_ch1 = developmental stage: adult
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Eosinophils from infiltrates in mouse quadriceps muscle were isolated by fluorescence-activated cell sorting (FACS); live eosinophils (CD45+CD11c-Gr1-MHCII-SiglecF+) were sorted directly into TRIZOL-LS (Life Technologies, Frederick, MD, USA) at a 3:1 ratio of TRIZOL-LS to sorted cell sample which was then equilibrated with chloroform. Total RNA was purified from the aqueous phase, combined with equal volumes of 70% ethanol, and purified with the RNeasy Cleanup kit (Qiagen, Germantown, MD, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared using the NEBnext Ultra Low Input Total RNA Library Prep Kit (New England BioLabs, Beverly, MA, USA) following the manufacturer’s instructions.
!Sample_data_processing = Illumina Casava1.8 software used for basecalling.
!Sample_data_processing = Raw fastq files were then trimmed for quality and adapter contamination using Cutadapt v2.10 and trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3 in 2-pass mode.
!Sample_data_processing = Gene-level expression quantification was performed using RSEM v1.3.0
!Sample_data_processing = Prior to differential expression and downstream time course analysis, genes were filtered to include <1 counts per million (CPM) across <3 samples.
!Sample_data_processing = Standard differential expression was performed using the R package limma with voom normalization
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: raw expression (expected counts) text file generated from RSEM
!Sample_platform_id = GPL21103
!Sample_contact_name = Pamela,,Frischmeyer-Guerrerio
!Sample_contact_email = pamela.guerrerio@nih.gov
!Sample_contact_phone = 301-402-9782
!Sample_contact_laboratory = Laboratory of Allergic Diseases
!Sample_contact_department = National Institute of Allergy and Infectious Diseases
!Sample_contact_institute = National Institutes of Health
!Sample_contact_address = Bldg. 10, Rm 11N240B, 10 Center Dr.
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892-1881
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16282188
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9203908
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE158666
!Sample_data_row_count = 0
^SAMPLE = GSM4805199
!Sample_title = replicate 3 of mdx condition
!Sample_geo_accession = GSM4805199
!Sample_status = Public on Sep 27 2021
!Sample_submission_date = Sep 28 2020
!Sample_last_update_date = Sep 27 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = eosinophils isolated from quadricep muscle infiltrates
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: mdx
!Sample_characteristics_ch1 = developmental stage: adult
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Eosinophils from infiltrates in mouse quadriceps muscle were isolated by fluorescence-activated cell sorting (FACS); live eosinophils (CD45+CD11c-Gr1-MHCII-SiglecF+) were sorted directly into TRIZOL-LS (Life Technologies, Frederick, MD, USA) at a 3:1 ratio of TRIZOL-LS to sorted cell sample which was then equilibrated with chloroform. Total RNA was purified from the aqueous phase, combined with equal volumes of 70% ethanol, and purified with the RNeasy Cleanup kit (Qiagen, Germantown, MD, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared using the NEBnext Ultra Low Input Total RNA Library Prep Kit (New England BioLabs, Beverly, MA, USA) following the manufacturer’s instructions.
!Sample_data_processing = Illumina Casava1.8 software used for basecalling.
!Sample_data_processing = Raw fastq files were then trimmed for quality and adapter contamination using Cutadapt v2.10 and trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3 in 2-pass mode.
!Sample_data_processing = Gene-level expression quantification was performed using RSEM v1.3.0
!Sample_data_processing = Prior to differential expression and downstream time course analysis, genes were filtered to include <1 counts per million (CPM) across <3 samples.
!Sample_data_processing = Standard differential expression was performed using the R package limma with voom normalization
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: raw expression (expected counts) text file generated from RSEM
!Sample_platform_id = GPL21103
!Sample_contact_name = Pamela,,Frischmeyer-Guerrerio
!Sample_contact_email = pamela.guerrerio@nih.gov
!Sample_contact_phone = 301-402-9782
!Sample_contact_laboratory = Laboratory of Allergic Diseases
!Sample_contact_department = National Institute of Allergy and Infectious Diseases
!Sample_contact_institute = National Institutes of Health
!Sample_contact_address = Bldg. 10, Rm 11N240B, 10 Center Dr.
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892-1881
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16282187
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9203909
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE158666
!Sample_data_row_count = 0
^SAMPLE = GSM4805200
!Sample_title = replicate 1 of mdx_IL5Tg condition
!Sample_geo_accession = GSM4805200
!Sample_status = Public on Sep 27 2021
!Sample_submission_date = Sep 28 2020
!Sample_last_update_date = Sep 27 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = eosinophils isolated from quadricep muscle infiltrates
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: mdx
!Sample_characteristics_ch1 = developmental stage: adult
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Eosinophils from infiltrates in mouse quadriceps muscle were isolated by fluorescence-activated cell sorting (FACS); live eosinophils (CD45+CD11c-Gr1-MHCII-SiglecF+) were sorted directly into TRIZOL-LS (Life Technologies, Frederick, MD, USA) at a 3:1 ratio of TRIZOL-LS to sorted cell sample which was then equilibrated with chloroform. Total RNA was purified from the aqueous phase, combined with equal volumes of 70% ethanol, and purified with the RNeasy Cleanup kit (Qiagen, Germantown, MD, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared using the NEBnext Ultra Low Input Total RNA Library Prep Kit (New England BioLabs, Beverly, MA, USA) following the manufacturer’s instructions.
!Sample_data_processing = Illumina Casava1.8 software used for basecalling.
!Sample_data_processing = Raw fastq files were then trimmed for quality and adapter contamination using Cutadapt v2.10 and trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3 in 2-pass mode.
!Sample_data_processing = Gene-level expression quantification was performed using RSEM v1.3.0
!Sample_data_processing = Prior to differential expression and downstream time course analysis, genes were filtered to include <1 counts per million (CPM) across <3 samples.
!Sample_data_processing = Standard differential expression was performed using the R package limma with voom normalization
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: raw expression (expected counts) text file generated from RSEM
!Sample_platform_id = GPL21103
!Sample_contact_name = Pamela,,Frischmeyer-Guerrerio
!Sample_contact_email = pamela.guerrerio@nih.gov
!Sample_contact_phone = 301-402-9782
!Sample_contact_laboratory = Laboratory of Allergic Diseases
!Sample_contact_department = National Institute of Allergy and Infectious Diseases
!Sample_contact_institute = National Institutes of Health
!Sample_contact_address = Bldg. 10, Rm 11N240B, 10 Center Dr.
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892-1881
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16282186
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9203910
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE158666
!Sample_data_row_count = 0
^SAMPLE = GSM4805201
!Sample_title = replicate 2 of mdx_IL5Tg condition
!Sample_geo_accession = GSM4805201
!Sample_status = Public on Sep 27 2021
!Sample_submission_date = Sep 28 2020
!Sample_last_update_date = Sep 27 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = eosinophils isolated from quadricep muscle infiltrates
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: mdx
!Sample_characteristics_ch1 = developmental stage: adult
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Eosinophils from infiltrates in mouse quadriceps muscle were isolated by fluorescence-activated cell sorting (FACS); live eosinophils (CD45+CD11c-Gr1-MHCII-SiglecF+) were sorted directly into TRIZOL-LS (Life Technologies, Frederick, MD, USA) at a 3:1 ratio of TRIZOL-LS to sorted cell sample which was then equilibrated with chloroform. Total RNA was purified from the aqueous phase, combined with equal volumes of 70% ethanol, and purified with the RNeasy Cleanup kit (Qiagen, Germantown, MD, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared using the NEBnext Ultra Low Input Total RNA Library Prep Kit (New England BioLabs, Beverly, MA, USA) following the manufacturer’s instructions.
!Sample_data_processing = Illumina Casava1.8 software used for basecalling.
!Sample_data_processing = Raw fastq files were then trimmed for quality and adapter contamination using Cutadapt v2.10 and trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3 in 2-pass mode.
!Sample_data_processing = Gene-level expression quantification was performed using RSEM v1.3.0
!Sample_data_processing = Prior to differential expression and downstream time course analysis, genes were filtered to include <1 counts per million (CPM) across <3 samples.
!Sample_data_processing = Standard differential expression was performed using the R package limma with voom normalization
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: raw expression (expected counts) text file generated from RSEM
!Sample_platform_id = GPL21103
!Sample_contact_name = Pamela,,Frischmeyer-Guerrerio
!Sample_contact_email = pamela.guerrerio@nih.gov
!Sample_contact_phone = 301-402-9782
!Sample_contact_laboratory = Laboratory of Allergic Diseases
!Sample_contact_department = National Institute of Allergy and Infectious Diseases
!Sample_contact_institute = National Institutes of Health
!Sample_contact_address = Bldg. 10, Rm 11N240B, 10 Center Dr.
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892-1881
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16282184
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9203911
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE158666
!Sample_data_row_count = 0
^SAMPLE = GSM4805202
!Sample_title = replicate 3 of mdx_IL5Tg condition
!Sample_geo_accession = GSM4805202
!Sample_status = Public on Sep 27 2021
!Sample_submission_date = Sep 28 2020
!Sample_last_update_date = Sep 27 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = eosinophils isolated from quadricep muscle infiltrates
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: mdx
!Sample_characteristics_ch1 = developmental stage: adult
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Eosinophils from infiltrates in mouse quadriceps muscle were isolated by fluorescence-activated cell sorting (FACS); live eosinophils (CD45+CD11c-Gr1-MHCII-SiglecF+) were sorted directly into TRIZOL-LS (Life Technologies, Frederick, MD, USA) at a 3:1 ratio of TRIZOL-LS to sorted cell sample which was then equilibrated with chloroform. Total RNA was purified from the aqueous phase, combined with equal volumes of 70% ethanol, and purified with the RNeasy Cleanup kit (Qiagen, Germantown, MD, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared using the NEBnext Ultra Low Input Total RNA Library Prep Kit (New England BioLabs, Beverly, MA, USA) following the manufacturer’s instructions.
!Sample_data_processing = Illumina Casava1.8 software used for basecalling.
!Sample_data_processing = Raw fastq files were then trimmed for quality and adapter contamination using Cutadapt v2.10 and trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3 in 2-pass mode.
!Sample_data_processing = Gene-level expression quantification was performed using RSEM v1.3.0
!Sample_data_processing = Prior to differential expression and downstream time course analysis, genes were filtered to include <1 counts per million (CPM) across <3 samples.
!Sample_data_processing = Standard differential expression was performed using the R package limma with voom normalization
!Sample_data_processing = Genome_build: mm10
!Sample_data_processing = Supplementary_files_format_and_content: raw expression (expected counts) text file generated from RSEM
!Sample_platform_id = GPL21103
!Sample_contact_name = Pamela,,Frischmeyer-Guerrerio
!Sample_contact_email = pamela.guerrerio@nih.gov
!Sample_contact_phone = 301-402-9782
!Sample_contact_laboratory = Laboratory of Allergic Diseases
!Sample_contact_department = National Institute of Allergy and Infectious Diseases
!Sample_contact_institute = National Institutes of Health
!Sample_contact_address = Bldg. 10, Rm 11N240B, 10 Center Dr.
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892-1881
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16282183
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9203912
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE158666
!Sample_data_row_count = 0