^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 = GSE165694
!Series_title = Aspergillus fumigatus-induced transcriptional changes on murine eosinophils
!Series_geo_accession = GSE165694
!Series_status = Public on May 31 2022
!Series_submission_date = Jan 28 2021
!Series_last_update_date = Jun 01 2022
!Series_summary = Eosinophilia is associated with various persisting inflammatory diseases and often coincides with chronic fungal infections or fungal allergy as in case of allergic bronchopulmonary aspergillosis (ABPA). However, the interactions between eosinophils and fungal pathogen leading to release of inflammatory mediators from eosinophils are poorly understood. Therefore, we established a co-culture system of mouse bone marrow derived eosinophils (BMDE) with Aspergillus fumigatus (Af) that we used in part to analyse transcriptional regulation induced by Af.
!Series_overall_design = Transcriptional profile of mouse bone marrow derived eosinophils either cultured alone or co-cultured with Aspergillus fumigatus.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Sebastian,,Schruefer
!Series_contributor = Axel,,Dietschmann
!Series_contributor = Philipp,,Kirchner
!Series_contributor = Arif,,Ekici
!Series_contributor = Daniel,,Radtke
!Series_contributor = Sven,,Krappmann
!Series_contributor = David,,Voehringer
!Series_sample_id = GSM5048309
!Series_sample_id = GSM5048310
!Series_sample_id = GSM5048311
!Series_sample_id = GSM5048312
!Series_sample_id = GSM5048313
!Series_sample_id = GSM5048314
!Series_contact_name = David,,Voehringer
!Series_contact_email = david.voehringer@uk-erlangen.de
!Series_contact_department = Department of Infection Biology
!Series_contact_institute = University Clinic Erlangen
!Series_contact_address = Wasserturmstrasse 3-5
!Series_contact_city = Erlangen
!Series_contact_zip/postal_code = 91054
!Series_contact_country = Germany
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE165nnn/GSE165694/suppl/GSE165694_Dietschmann_et_al_diff_expr_and_norm_counts.xlsx
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE165nnn/GSE165694/suppl/GSE165694_Dietschmann_et_al_raw_counts.txt.gz
!Series_platform_id = GPL17021
!Series_platform_taxid = 10090
!Series_sample_taxid = 10090
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA695469
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP303626
^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 = GSM5048309
!Sample_title = only_BMDE_rep1
!Sample_geo_accession = GSM5048309
!Sample_status = Public on May 31 2022
!Sample_submission_date = Jan 28 2021
!Sample_last_update_date = May 31 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow derived eosinophils (BMDE)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: BALB/c
!Sample_characteristics_ch1 = cell type: bone marrow derived eosinophils (BMDE)
!Sample_characteristics_ch1 = growth protocol: only BMDE
!Sample_treatment_protocol_ch1 = Af conidia (ATCC 46645 WT strain) were pre-grown for 5.5h in RPMI 1640. The medium was removed and eosinophils were added at a conidia-eosinophil ratio of 2:1 and 10 ng/mL rmIL-5. After 6h co-cultivation RNA was isolated.
!Sample_growth_protocol_ch1 = Bone marrow derived eosinophils (BMDE) were generated based on a published protocol (Dyer et al. J Immunol. 2008). Briefly, mouse bone marrow cells from femurs and tibiae were subjected to RBC lysis and adjusted to 10^6/ml in bone marrow medium (BMM), containing 20% FCS, 1% non-essential amino acids, 2 mM L-Glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 100 μg/ml streptomycin, 19.25 μM 2-mercaptoethanol (all Thermo Fisher Scientific, Waltham, MA) and 25 mM HEPES (Carl Roth, Karlsruhe, Germany) in RPMI 1640 (PAN-Biotech, Aidenbach, Germany). For the first four days recombinant mouse SCF and FLT3L (Peprotech, Rocky Hill, NJ) were added to the culture (both 100 ng/ml) and afterwards replaced by recombinant mouse IL-5 (R&D Systems, Minneapolis, MN) (10 ng/ml) until day 14, with medium including fresh cytokine exchanged by half every two days from day 4 on. On day 14 eosinophil culture purity was usually above 90%, assessed by expression of SIGLEC-F and measured via flow cytometry. Bone marrow cells of BALB/c mice were used for BMDE generation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was isolated with the total RNA isolation kit (Fluka, Sigma-Aldrich). 75 mM DTT was added to the lysis buffer to prevent RNA degradation. Samples were treated with RNAse free DNAse set (Qiagen) and RNA integrity was determined with a Bioanalyzer instrument (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Kit (Illumina, San Diego, CA) was used for cDNA library preparation. Libraries were 96 bp single-end sequenced on a HiSeq2500 platform (Illumina).
!Sample_extract_protocol_ch1 = TruSeq Stranded mRNA Kit (Illumina)
!Sample_description = HU.231978_naive_4
!Sample_data_processing = Conversion raw data to reads (bcl2fastq v2.17)
!Sample_data_processing = Trimmed of adapters and discarded reads < 60bp (cutadapt v1.18)
!Sample_data_processing = Determined read quality (fastqc v0.11.8)
!Sample_data_processing = Aligned to GRCm38 with GENCODE annotation M23 (STAR v2.6.1c). A.fumigatus genome ASM265 was added to catch and remove Af reads.
!Sample_data_processing = Quality check (RNAseQC v2.3.4)
!Sample_data_processing = Read counts for non overlapping exons were generated (samtools v1.8, subread v1.6.1)
!Sample_data_processing = Genome_build: GRCm38
!Sample_data_processing = Supplementary_files_format_and_content: Dietschmann_raw_counts.txt, Dietschmann_et_al_diff_expr_and_norm_counts.xlsx
!Sample_platform_id = GPL17021
!Sample_contact_name = David,,Voehringer
!Sample_contact_email = david.voehringer@uk-erlangen.de
!Sample_contact_department = Department of Infection Biology
!Sample_contact_institute = University Clinic Erlangen
!Sample_contact_address = Wasserturmstrasse 3-5
!Sample_contact_city = Erlangen
!Sample_contact_zip/postal_code = 91054
!Sample_contact_country = Germany
!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/SAMN17615138
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9969173
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE165694
!Sample_data_row_count = 0
^SAMPLE = GSM5048310
!Sample_title = only_BMDE_rep2
!Sample_geo_accession = GSM5048310
!Sample_status = Public on May 31 2022
!Sample_submission_date = Jan 28 2021
!Sample_last_update_date = May 31 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow derived eosinophils (BMDE)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: BALB/c
!Sample_characteristics_ch1 = cell type: bone marrow derived eosinophils (BMDE)
!Sample_characteristics_ch1 = growth protocol: only BMDE
!Sample_treatment_protocol_ch1 = Af conidia (ATCC 46645 WT strain) were pre-grown for 5.5h in RPMI 1640. The medium was removed and eosinophils were added at a conidia-eosinophil ratio of 2:1 and 10 ng/mL rmIL-5. After 6h co-cultivation RNA was isolated.
!Sample_growth_protocol_ch1 = Bone marrow derived eosinophils (BMDE) were generated based on a published protocol (Dyer et al. J Immunol. 2008). Briefly, mouse bone marrow cells from femurs and tibiae were subjected to RBC lysis and adjusted to 10^6/ml in bone marrow medium (BMM), containing 20% FCS, 1% non-essential amino acids, 2 mM L-Glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 100 μg/ml streptomycin, 19.25 μM 2-mercaptoethanol (all Thermo Fisher Scientific, Waltham, MA) and 25 mM HEPES (Carl Roth, Karlsruhe, Germany) in RPMI 1640 (PAN-Biotech, Aidenbach, Germany). For the first four days recombinant mouse SCF and FLT3L (Peprotech, Rocky Hill, NJ) were added to the culture (both 100 ng/ml) and afterwards replaced by recombinant mouse IL-5 (R&D Systems, Minneapolis, MN) (10 ng/ml) until day 14, with medium including fresh cytokine exchanged by half every two days from day 4 on. On day 14 eosinophil culture purity was usually above 90%, assessed by expression of SIGLEC-F and measured via flow cytometry. Bone marrow cells of BALB/c mice were used for BMDE generation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was isolated with the total RNA isolation kit (Fluka, Sigma-Aldrich). 75 mM DTT was added to the lysis buffer to prevent RNA degradation. Samples were treated with RNAse free DNAse set (Qiagen) and RNA integrity was determined with a Bioanalyzer instrument (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Kit (Illumina, San Diego, CA) was used for cDNA library preparation. Libraries were 96 bp single-end sequenced on a HiSeq2500 platform (Illumina).
!Sample_extract_protocol_ch1 = TruSeq Stranded mRNA Kit (Illumina)
!Sample_description = HU.231980_naive_1
!Sample_data_processing = Conversion raw data to reads (bcl2fastq v2.17)
!Sample_data_processing = Trimmed of adapters and discarded reads < 60bp (cutadapt v1.18)
!Sample_data_processing = Determined read quality (fastqc v0.11.8)
!Sample_data_processing = Aligned to GRCm38 with GENCODE annotation M23 (STAR v2.6.1c). A.fumigatus genome ASM265 was added to catch and remove Af reads.
!Sample_data_processing = Quality check (RNAseQC v2.3.4)
!Sample_data_processing = Read counts for non overlapping exons were generated (samtools v1.8, subread v1.6.1)
!Sample_data_processing = Genome_build: GRCm38
!Sample_data_processing = Supplementary_files_format_and_content: Dietschmann_raw_counts.txt, Dietschmann_et_al_diff_expr_and_norm_counts.xlsx
!Sample_platform_id = GPL17021
!Sample_contact_name = David,,Voehringer
!Sample_contact_email = david.voehringer@uk-erlangen.de
!Sample_contact_department = Department of Infection Biology
!Sample_contact_institute = University Clinic Erlangen
!Sample_contact_address = Wasserturmstrasse 3-5
!Sample_contact_city = Erlangen
!Sample_contact_zip/postal_code = 91054
!Sample_contact_country = Germany
!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/SAMN17615137
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9969174
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE165694
!Sample_data_row_count = 0
^SAMPLE = GSM5048311
!Sample_title = only_BMDE_rep3
!Sample_geo_accession = GSM5048311
!Sample_status = Public on May 31 2022
!Sample_submission_date = Jan 28 2021
!Sample_last_update_date = May 31 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow derived eosinophils (BMDE)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: BALB/c
!Sample_characteristics_ch1 = cell type: bone marrow derived eosinophils (BMDE)
!Sample_characteristics_ch1 = growth protocol: only BMDE
!Sample_treatment_protocol_ch1 = Af conidia (ATCC 46645 WT strain) were pre-grown for 5.5h in RPMI 1640. The medium was removed and eosinophils were added at a conidia-eosinophil ratio of 2:1 and 10 ng/mL rmIL-5. After 6h co-cultivation RNA was isolated.
!Sample_growth_protocol_ch1 = Bone marrow derived eosinophils (BMDE) were generated based on a published protocol (Dyer et al. J Immunol. 2008). Briefly, mouse bone marrow cells from femurs and tibiae were subjected to RBC lysis and adjusted to 10^6/ml in bone marrow medium (BMM), containing 20% FCS, 1% non-essential amino acids, 2 mM L-Glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 100 μg/ml streptomycin, 19.25 μM 2-mercaptoethanol (all Thermo Fisher Scientific, Waltham, MA) and 25 mM HEPES (Carl Roth, Karlsruhe, Germany) in RPMI 1640 (PAN-Biotech, Aidenbach, Germany). For the first four days recombinant mouse SCF and FLT3L (Peprotech, Rocky Hill, NJ) were added to the culture (both 100 ng/ml) and afterwards replaced by recombinant mouse IL-5 (R&D Systems, Minneapolis, MN) (10 ng/ml) until day 14, with medium including fresh cytokine exchanged by half every two days from day 4 on. On day 14 eosinophil culture purity was usually above 90%, assessed by expression of SIGLEC-F and measured via flow cytometry. Bone marrow cells of BALB/c mice were used for BMDE generation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was isolated with the total RNA isolation kit (Fluka, Sigma-Aldrich). 75 mM DTT was added to the lysis buffer to prevent RNA degradation. Samples were treated with RNAse free DNAse set (Qiagen) and RNA integrity was determined with a Bioanalyzer instrument (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Kit (Illumina, San Diego, CA) was used for cDNA library preparation. Libraries were 96 bp single-end sequenced on a HiSeq2500 platform (Illumina).
!Sample_extract_protocol_ch1 = TruSeq Stranded mRNA Kit (Illumina)
!Sample_description = HU.231981_naive_2
!Sample_data_processing = Conversion raw data to reads (bcl2fastq v2.17)
!Sample_data_processing = Trimmed of adapters and discarded reads < 60bp (cutadapt v1.18)
!Sample_data_processing = Determined read quality (fastqc v0.11.8)
!Sample_data_processing = Aligned to GRCm38 with GENCODE annotation M23 (STAR v2.6.1c). A.fumigatus genome ASM265 was added to catch and remove Af reads.
!Sample_data_processing = Quality check (RNAseQC v2.3.4)
!Sample_data_processing = Read counts for non overlapping exons were generated (samtools v1.8, subread v1.6.1)
!Sample_data_processing = Genome_build: GRCm38
!Sample_data_processing = Supplementary_files_format_and_content: Dietschmann_raw_counts.txt, Dietschmann_et_al_diff_expr_and_norm_counts.xlsx
!Sample_platform_id = GPL17021
!Sample_contact_name = David,,Voehringer
!Sample_contact_email = david.voehringer@uk-erlangen.de
!Sample_contact_department = Department of Infection Biology
!Sample_contact_institute = University Clinic Erlangen
!Sample_contact_address = Wasserturmstrasse 3-5
!Sample_contact_city = Erlangen
!Sample_contact_zip/postal_code = 91054
!Sample_contact_country = Germany
!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/SAMN17615136
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9969175
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE165694
!Sample_data_row_count = 0
^SAMPLE = GSM5048312
!Sample_title = BMDE_Af_co_culture_rep1
!Sample_geo_accession = GSM5048312
!Sample_status = Public on May 31 2022
!Sample_submission_date = Jan 28 2021
!Sample_last_update_date = May 31 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow derived eosinophils (BMDE)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: BALB/c
!Sample_characteristics_ch1 = cell type: bone marrow derived eosinophils (BMDE)
!Sample_characteristics_ch1 = growth protocol: Co-culture BMDE and Aspergillus fumigatus
!Sample_treatment_protocol_ch1 = Af conidia (ATCC 46645 WT strain) were pre-grown for 5.5h in RPMI 1640. The medium was removed and eosinophils were added at a conidia-eosinophil ratio of 2:1 and 10 ng/mL rmIL-5. After 6h co-cultivation RNA was isolated.
!Sample_growth_protocol_ch1 = Bone marrow derived eosinophils (BMDE) were generated based on a published protocol (Dyer et al. J Immunol. 2008). Briefly, mouse bone marrow cells from femurs and tibiae were subjected to RBC lysis and adjusted to 10^6/ml in bone marrow medium (BMM), containing 20% FCS, 1% non-essential amino acids, 2 mM L-Glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 100 μg/ml streptomycin, 19.25 μM 2-mercaptoethanol (all Thermo Fisher Scientific, Waltham, MA) and 25 mM HEPES (Carl Roth, Karlsruhe, Germany) in RPMI 1640 (PAN-Biotech, Aidenbach, Germany). For the first four days recombinant mouse SCF and FLT3L (Peprotech, Rocky Hill, NJ) were added to the culture (both 100 ng/ml) and afterwards replaced by recombinant mouse IL-5 (R&D Systems, Minneapolis, MN) (10 ng/ml) until day 14, with medium including fresh cytokine exchanged by half every two days from day 4 on. On day 14 eosinophil culture purity was usually above 90%, assessed by expression of SIGLEC-F and measured via flow cytometry. Bone marrow cells of BALB/c mice were used for BMDE generation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was isolated with the total RNA isolation kit (Fluka, Sigma-Aldrich). 75 mM DTT was added to the lysis buffer to prevent RNA degradation. Samples were treated with RNAse free DNAse set (Qiagen) and RNA integrity was determined with a Bioanalyzer instrument (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Kit (Illumina, San Diego, CA) was used for cDNA library preparation. Libraries were 96 bp single-end sequenced on a HiSeq2500 platform (Illumina).
!Sample_extract_protocol_ch1 = TruSeq Stranded mRNA Kit (Illumina)
!Sample_description = HU.231983_co.culture_1
!Sample_data_processing = Conversion raw data to reads (bcl2fastq v2.17)
!Sample_data_processing = Trimmed of adapters and discarded reads < 60bp (cutadapt v1.18)
!Sample_data_processing = Determined read quality (fastqc v0.11.8)
!Sample_data_processing = Aligned to GRCm38 with GENCODE annotation M23 (STAR v2.6.1c). A.fumigatus genome ASM265 was added to catch and remove Af reads.
!Sample_data_processing = Quality check (RNAseQC v2.3.4)
!Sample_data_processing = Read counts for non overlapping exons were generated (samtools v1.8, subread v1.6.1)
!Sample_data_processing = Genome_build: GRCm38
!Sample_data_processing = Supplementary_files_format_and_content: Dietschmann_raw_counts.txt, Dietschmann_et_al_diff_expr_and_norm_counts.xlsx
!Sample_platform_id = GPL17021
!Sample_contact_name = David,,Voehringer
!Sample_contact_email = david.voehringer@uk-erlangen.de
!Sample_contact_department = Department of Infection Biology
!Sample_contact_institute = University Clinic Erlangen
!Sample_contact_address = Wasserturmstrasse 3-5
!Sample_contact_city = Erlangen
!Sample_contact_zip/postal_code = 91054
!Sample_contact_country = Germany
!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/SAMN17615135
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9969176
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE165694
!Sample_data_row_count = 0
^SAMPLE = GSM5048313
!Sample_title = BMDE_Af_co_culture_rep2
!Sample_geo_accession = GSM5048313
!Sample_status = Public on May 31 2022
!Sample_submission_date = Jan 28 2021
!Sample_last_update_date = May 31 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow derived eosinophils (BMDE)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: BALB/c
!Sample_characteristics_ch1 = cell type: bone marrow derived eosinophils (BMDE)
!Sample_characteristics_ch1 = growth protocol: Co-culture BMDE and Aspergillus fumigatus
!Sample_treatment_protocol_ch1 = Af conidia (ATCC 46645 WT strain) were pre-grown for 5.5h in RPMI 1640. The medium was removed and eosinophils were added at a conidia-eosinophil ratio of 2:1 and 10 ng/mL rmIL-5. After 6h co-cultivation RNA was isolated.
!Sample_growth_protocol_ch1 = Bone marrow derived eosinophils (BMDE) were generated based on a published protocol (Dyer et al. J Immunol. 2008). Briefly, mouse bone marrow cells from femurs and tibiae were subjected to RBC lysis and adjusted to 10^6/ml in bone marrow medium (BMM), containing 20% FCS, 1% non-essential amino acids, 2 mM L-Glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 100 μg/ml streptomycin, 19.25 μM 2-mercaptoethanol (all Thermo Fisher Scientific, Waltham, MA) and 25 mM HEPES (Carl Roth, Karlsruhe, Germany) in RPMI 1640 (PAN-Biotech, Aidenbach, Germany). For the first four days recombinant mouse SCF and FLT3L (Peprotech, Rocky Hill, NJ) were added to the culture (both 100 ng/ml) and afterwards replaced by recombinant mouse IL-5 (R&D Systems, Minneapolis, MN) (10 ng/ml) until day 14, with medium including fresh cytokine exchanged by half every two days from day 4 on. On day 14 eosinophil culture purity was usually above 90%, assessed by expression of SIGLEC-F and measured via flow cytometry. Bone marrow cells of BALB/c mice were used for BMDE generation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was isolated with the total RNA isolation kit (Fluka, Sigma-Aldrich). 75 mM DTT was added to the lysis buffer to prevent RNA degradation. Samples were treated with RNAse free DNAse set (Qiagen) and RNA integrity was determined with a Bioanalyzer instrument (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Kit (Illumina, San Diego, CA) was used for cDNA library preparation. Libraries were 96 bp single-end sequenced on a HiSeq2500 platform (Illumina).
!Sample_extract_protocol_ch1 = TruSeq Stranded mRNA Kit (Illumina)
!Sample_description = HU.231985_co.culture_2
!Sample_data_processing = Conversion raw data to reads (bcl2fastq v2.17)
!Sample_data_processing = Trimmed of adapters and discarded reads < 60bp (cutadapt v1.18)
!Sample_data_processing = Determined read quality (fastqc v0.11.8)
!Sample_data_processing = Aligned to GRCm38 with GENCODE annotation M23 (STAR v2.6.1c). A.fumigatus genome ASM265 was added to catch and remove Af reads.
!Sample_data_processing = Quality check (RNAseQC v2.3.4)
!Sample_data_processing = Read counts for non overlapping exons were generated (samtools v1.8, subread v1.6.1)
!Sample_data_processing = Genome_build: GRCm38
!Sample_data_processing = Supplementary_files_format_and_content: Dietschmann_raw_counts.txt, Dietschmann_et_al_diff_expr_and_norm_counts.xlsx
!Sample_platform_id = GPL17021
!Sample_contact_name = David,,Voehringer
!Sample_contact_email = david.voehringer@uk-erlangen.de
!Sample_contact_department = Department of Infection Biology
!Sample_contact_institute = University Clinic Erlangen
!Sample_contact_address = Wasserturmstrasse 3-5
!Sample_contact_city = Erlangen
!Sample_contact_zip/postal_code = 91054
!Sample_contact_country = Germany
!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/SAMN17615134
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9969177
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE165694
!Sample_data_row_count = 0
^SAMPLE = GSM5048314
!Sample_title = BMDE_Af_co_culture_rep3
!Sample_geo_accession = GSM5048314
!Sample_status = Public on May 31 2022
!Sample_submission_date = Jan 28 2021
!Sample_last_update_date = May 31 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = bone marrow derived eosinophils (BMDE)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: BALB/c
!Sample_characteristics_ch1 = cell type: bone marrow derived eosinophils (BMDE)
!Sample_characteristics_ch1 = growth protocol: Co-culture BMDE and Aspergillus fumigatus
!Sample_treatment_protocol_ch1 = Af conidia (ATCC 46645 WT strain) were pre-grown for 5.5h in RPMI 1640. The medium was removed and eosinophils were added at a conidia-eosinophil ratio of 2:1 and 10 ng/mL rmIL-5. After 6h co-cultivation RNA was isolated.
!Sample_growth_protocol_ch1 = Bone marrow derived eosinophils (BMDE) were generated based on a published protocol (Dyer et al. J Immunol. 2008). Briefly, mouse bone marrow cells from femurs and tibiae were subjected to RBC lysis and adjusted to 10^6/ml in bone marrow medium (BMM), containing 20% FCS, 1% non-essential amino acids, 2 mM L-Glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 100 μg/ml streptomycin, 19.25 μM 2-mercaptoethanol (all Thermo Fisher Scientific, Waltham, MA) and 25 mM HEPES (Carl Roth, Karlsruhe, Germany) in RPMI 1640 (PAN-Biotech, Aidenbach, Germany). For the first four days recombinant mouse SCF and FLT3L (Peprotech, Rocky Hill, NJ) were added to the culture (both 100 ng/ml) and afterwards replaced by recombinant mouse IL-5 (R&D Systems, Minneapolis, MN) (10 ng/ml) until day 14, with medium including fresh cytokine exchanged by half every two days from day 4 on. On day 14 eosinophil culture purity was usually above 90%, assessed by expression of SIGLEC-F and measured via flow cytometry. Bone marrow cells of BALB/c mice were used for BMDE generation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA was isolated with the total RNA isolation kit (Fluka, Sigma-Aldrich). 75 mM DTT was added to the lysis buffer to prevent RNA degradation. Samples were treated with RNAse free DNAse set (Qiagen) and RNA integrity was determined with a Bioanalyzer instrument (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Kit (Illumina, San Diego, CA) was used for cDNA library preparation. Libraries were 96 bp single-end sequenced on a HiSeq2500 platform (Illumina).
!Sample_extract_protocol_ch1 = TruSeq Stranded mRNA Kit (Illumina)
!Sample_description = HU.231987_co.culture_4
!Sample_data_processing = Conversion raw data to reads (bcl2fastq v2.17)
!Sample_data_processing = Trimmed of adapters and discarded reads < 60bp (cutadapt v1.18)
!Sample_data_processing = Determined read quality (fastqc v0.11.8)
!Sample_data_processing = Aligned to GRCm38 with GENCODE annotation M23 (STAR v2.6.1c). A.fumigatus genome ASM265 was added to catch and remove Af reads.
!Sample_data_processing = Quality check (RNAseQC v2.3.4)
!Sample_data_processing = Read counts for non overlapping exons were generated (samtools v1.8, subread v1.6.1)
!Sample_data_processing = Genome_build: GRCm38
!Sample_data_processing = Supplementary_files_format_and_content: Dietschmann_raw_counts.txt, Dietschmann_et_al_diff_expr_and_norm_counts.xlsx
!Sample_platform_id = GPL17021
!Sample_contact_name = David,,Voehringer
!Sample_contact_email = david.voehringer@uk-erlangen.de
!Sample_contact_department = Department of Infection Biology
!Sample_contact_institute = University Clinic Erlangen
!Sample_contact_address = Wasserturmstrasse 3-5
!Sample_contact_city = Erlangen
!Sample_contact_zip/postal_code = 91054
!Sample_contact_country = Germany
!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/SAMN17615133
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9969178
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE165694
!Sample_data_row_count = 0