^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 = GSE158241
!Series_title = scRNAseq of DIO-NASH mouse livers
!Series_geo_accession = GSE158241
!Series_status = Public on Sep 19 2020
!Series_submission_date = Sep 18 2020
!Series_last_update_date = Sep 21 2020
!Series_summary = To improve the understanding of the complex biological processes underlying the development of non-alcoholic steatohepatitis (NASH), a multi-omics approach combining bulk RNA-sequencing based transcriptomics, quantitative proteomics and single-cell RNA-sequencing was used to characterize tissue biopsies from histologically validated diet-induced obese (DIO) NASH mice compared to chow-fed controls. Bulk RNA-sequencing and proteomics showed a clear distinction between phenotypes and a good correspondence between mRNA and protein level regulations, apart from specific regulatory events discovered by each technology. Transcriptomics-based gene set enrichment analysis revealed changes associated with key clinical manifestations of NASH, including impaired lipid metabolism, increased extracellular matrix formation/remodeling and pro-inflammatory responses, whereas proteomics-based gene set enrichment analysis pinpointed metabolic pathway perturbations. Integration with single-cell RNA-sequencing data identified key regulated cell types involved in development of NASH demonstrating the cellular heterogeneity and complexity of NASH pathogenesis.
!Series_overall_design = Examination of liver biopsies from 4 healthy and 2 DIO-NASH mice.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Kristoffer,G,Rigbolt
!Series_contributor = Helene,,Ægidius
!Series_sample_id = GSM4795784
!Series_sample_id = GSM4795785
!Series_sample_id = GSM4795786
!Series_sample_id = GSM4795787
!Series_sample_id = GSM4795788
!Series_sample_id = GSM4795789
!Series_contact_name = Kristoffer,G,Rigbolt
!Series_contact_email = kri@gubra.dk
!Series_contact_institute = Gubra
!Series_contact_address = Hørsholm Kongevej 11B
!Series_contact_city = Hørsholm
!Series_contact_zip/postal_code = 2970
!Series_contact_country = Denmark
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE158nnn/GSE158241/suppl/GSE158241_RAW.tar
!Series_platform_id = GPL19057
!Series_platform_taxid = 10090
!Series_sample_taxid = 10090
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA664408
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP283908
^PLATFORM = GPL19057
!Platform_title = Illumina NextSeq 500 (Mus musculus)
!Platform_geo_accession = GPL19057
!Platform_status = Public on Aug 07 2014
!Platform_submission_date = Aug 07 2014
!Platform_last_update_date = Mar 25 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 = GSM4795784
!Sample_title = Lean-chow 1
!Sample_geo_accession = GSM4795784
!Sample_status = Public on Sep 19 2020
!Sample_submission_date = Sep 18 2020
!Sample_last_update_date = Sep 20 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Liver biopsy
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_characteristics_ch1 = tissue: Liver
!Sample_characteristics_ch1 = diagnosis: Healthy
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA extraction was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.
!Sample_extract_protocol_ch1 = Library preparation was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.
!Sample_description = scRNA-seq
!Sample_description = 10x polyA RNA
!Sample_data_processing = Basecalling software: bcl2fastq v2.20.0.422.
!Sample_data_processing = Alignment and preprocessing: CellRanger (v. 1.1.0, 10x Genomics) software.
!Sample_data_processing = Cell filtering and normalization: Seurat R package (v. 3.1.1).
!Sample_data_processing = Genome_build: GRCm38 v89
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Tab-delimited text files include normalized expression values for each sample.
!Sample_platform_id = GPL19057
!Sample_contact_name = Kristoffer,G,Rigbolt
!Sample_contact_email = kri@gubra.dk
!Sample_contact_institute = Gubra
!Sample_contact_address = Hørsholm Kongevej 11B
!Sample_contact_city = Hørsholm
!Sample_contact_zip/postal_code = 2970
!Sample_contact_country = Denmark
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16213524
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9152931
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4795nnn/GSM4795784/suppl/GSM4795784_Lean-chow1.txt.gz
!Sample_series_id = GSE158241
!Sample_data_row_count = 0
^SAMPLE = GSM4795785
!Sample_title = Lean-chow 2
!Sample_geo_accession = GSM4795785
!Sample_status = Public on Sep 19 2020
!Sample_submission_date = Sep 18 2020
!Sample_last_update_date = Sep 20 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Liver biopsy
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_characteristics_ch1 = tissue: Liver
!Sample_characteristics_ch1 = diagnosis: Healthy
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA extraction was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.
!Sample_extract_protocol_ch1 = Library preparation was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.
!Sample_description = scRNA-seq
!Sample_description = 10x polyA RNA
!Sample_data_processing = Basecalling software: bcl2fastq v2.20.0.422.
!Sample_data_processing = Alignment and preprocessing: CellRanger (v. 1.1.0, 10x Genomics) software.
!Sample_data_processing = Cell filtering and normalization: Seurat R package (v. 3.1.1).
!Sample_data_processing = Genome_build: GRCm38 v89
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Tab-delimited text files include normalized expression values for each sample.
!Sample_platform_id = GPL19057
!Sample_contact_name = Kristoffer,G,Rigbolt
!Sample_contact_email = kri@gubra.dk
!Sample_contact_institute = Gubra
!Sample_contact_address = Hørsholm Kongevej 11B
!Sample_contact_city = Hørsholm
!Sample_contact_zip/postal_code = 2970
!Sample_contact_country = Denmark
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16213523
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9152932
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4795nnn/GSM4795785/suppl/GSM4795785_Lean-chow2.txt.gz
!Sample_series_id = GSE158241
!Sample_data_row_count = 0
^SAMPLE = GSM4795786
!Sample_title = Lean-chow 3
!Sample_geo_accession = GSM4795786
!Sample_status = Public on Sep 19 2020
!Sample_submission_date = Sep 18 2020
!Sample_last_update_date = Sep 20 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Liver biopsy
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_characteristics_ch1 = tissue: Liver
!Sample_characteristics_ch1 = diagnosis: Healthy
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA extraction was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.
!Sample_extract_protocol_ch1 = Library preparation was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.
!Sample_description = scRNA-seq
!Sample_description = 10x polyA RNA
!Sample_data_processing = Basecalling software: bcl2fastq v2.20.0.422.
!Sample_data_processing = Alignment and preprocessing: CellRanger (v. 1.1.0, 10x Genomics) software.
!Sample_data_processing = Cell filtering and normalization: Seurat R package (v. 3.1.1).
!Sample_data_processing = Genome_build: GRCm38 v89
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Tab-delimited text files include normalized expression values for each sample.
!Sample_platform_id = GPL19057
!Sample_contact_name = Kristoffer,G,Rigbolt
!Sample_contact_email = kri@gubra.dk
!Sample_contact_institute = Gubra
!Sample_contact_address = Hørsholm Kongevej 11B
!Sample_contact_city = Hørsholm
!Sample_contact_zip/postal_code = 2970
!Sample_contact_country = Denmark
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16213522
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9152933
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4795nnn/GSM4795786/suppl/GSM4795786_Lean-chow3.txt.gz
!Sample_series_id = GSE158241
!Sample_data_row_count = 0
^SAMPLE = GSM4795787
!Sample_title = Lean-chow 4
!Sample_geo_accession = GSM4795787
!Sample_status = Public on Sep 19 2020
!Sample_submission_date = Sep 18 2020
!Sample_last_update_date = Sep 20 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Liver biopsy
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_characteristics_ch1 = tissue: Liver
!Sample_characteristics_ch1 = diagnosis: Healthy
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA extraction was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.
!Sample_extract_protocol_ch1 = Library preparation was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.
!Sample_description = scRNA-seq
!Sample_description = 10x polyA RNA
!Sample_data_processing = Basecalling software: bcl2fastq v2.20.0.422.
!Sample_data_processing = Alignment and preprocessing: CellRanger (v. 1.1.0, 10x Genomics) software.
!Sample_data_processing = Cell filtering and normalization: Seurat R package (v. 3.1.1).
!Sample_data_processing = Genome_build: GRCm38 v89
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Tab-delimited text files include normalized expression values for each sample.
!Sample_platform_id = GPL19057
!Sample_contact_name = Kristoffer,G,Rigbolt
!Sample_contact_email = kri@gubra.dk
!Sample_contact_institute = Gubra
!Sample_contact_address = Hørsholm Kongevej 11B
!Sample_contact_city = Hørsholm
!Sample_contact_zip/postal_code = 2970
!Sample_contact_country = Denmark
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16213521
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9152934
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4795nnn/GSM4795787/suppl/GSM4795787_Lean-chow4.txt.gz
!Sample_series_id = GSE158241
!Sample_data_row_count = 0
^SAMPLE = GSM4795788
!Sample_title = DIO-NASH 1
!Sample_geo_accession = GSM4795788
!Sample_status = Public on Sep 19 2020
!Sample_submission_date = Sep 18 2020
!Sample_last_update_date = Sep 20 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Liver biopsy
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_characteristics_ch1 = tissue: Liver
!Sample_characteristics_ch1 = diagnosis: DIO-NASH
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA extraction was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.
!Sample_extract_protocol_ch1 = Library preparation was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.
!Sample_description = scRNA-seq
!Sample_description = 10x polyA RNA
!Sample_data_processing = Basecalling software: bcl2fastq v2.20.0.422.
!Sample_data_processing = Alignment and preprocessing: CellRanger (v. 1.1.0, 10x Genomics) software.
!Sample_data_processing = Cell filtering and normalization: Seurat R package (v. 3.1.1).
!Sample_data_processing = Genome_build: GRCm38 v89
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Tab-delimited text files include normalized expression values for each sample.
!Sample_platform_id = GPL19057
!Sample_contact_name = Kristoffer,G,Rigbolt
!Sample_contact_email = kri@gubra.dk
!Sample_contact_institute = Gubra
!Sample_contact_address = Hørsholm Kongevej 11B
!Sample_contact_city = Hørsholm
!Sample_contact_zip/postal_code = 2970
!Sample_contact_country = Denmark
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16213520
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9152935
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4795nnn/GSM4795788/suppl/GSM4795788_DIO-NASH1.txt.gz
!Sample_series_id = GSE158241
!Sample_data_row_count = 0
^SAMPLE = GSM4795789
!Sample_title = DIO-NASH 2
!Sample_geo_accession = GSM4795789
!Sample_status = Public on Sep 19 2020
!Sample_submission_date = Sep 18 2020
!Sample_last_update_date = Sep 20 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Liver biopsy
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = strain: C57BL/6
!Sample_characteristics_ch1 = tissue: Liver
!Sample_characteristics_ch1 = diagnosis: DIO-NASH
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = RNA extraction was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.
!Sample_extract_protocol_ch1 = Library preparation was performed using the 10x Genomics Single-cell 3′ v2 Reagent Kit.
!Sample_description = scRNA-seq
!Sample_description = 10x polyA RNA
!Sample_data_processing = Basecalling software: bcl2fastq v2.20.0.422.
!Sample_data_processing = Alignment and preprocessing: CellRanger (v. 1.1.0, 10x Genomics) software.
!Sample_data_processing = Cell filtering and normalization: Seurat R package (v. 3.1.1).
!Sample_data_processing = Genome_build: GRCm38 v89
!Sample_data_processing = Supplementary_files_format_and_content: *.txt: Tab-delimited text files include normalized expression values for each sample.
!Sample_platform_id = GPL19057
!Sample_contact_name = Kristoffer,G,Rigbolt
!Sample_contact_email = kri@gubra.dk
!Sample_contact_institute = Gubra
!Sample_contact_address = Hørsholm Kongevej 11B
!Sample_contact_city = Hørsholm
!Sample_contact_zip/postal_code = 2970
!Sample_contact_country = Denmark
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16213519
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9152936
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4795nnn/GSM4795789/suppl/GSM4795789_DIO-NASH2.txt.gz
!Sample_series_id = GSE158241
!Sample_data_row_count = 0