^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 = GSE175839
!Series_title = Decreased  miR-4512 levels in monocytes and macrophages of individuals with systemic lupus erythematosus contribute to innate immune activation and neutrophil NETosis  by targeting TLR4 and CXCL2 [RNA-seq]
!Series_geo_accession = GSE175839
!Series_status = Public on Jun 01 2021
!Series_submission_date = May 31 2021
!Series_last_update_date = Nov 04 2021
!Series_pubmed_id = 34721432
!Series_summary = Peripheral blood mononuclear cells from SLE patients  (n = 5) and healthy controls  (n = 5) were used for miRNA–mRNA co-sequencing to detect miRNAs related to immune abnormalities associated with SLE.
!Series_overall_design = mRNA sequencing was performed on peripheral blood mononuclear cells (PBMCs) from patients with SLE (n=5) and healthy controls
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Binbin,,Yang
!Series_contributor = Danqi,,Deng
!Series_sample_id = GSM5348683
!Series_sample_id = GSM5348684
!Series_sample_id = GSM5348685
!Series_sample_id = GSM5348686
!Series_sample_id = GSM5348687
!Series_sample_id = GSM5348688
!Series_sample_id = GSM5348689
!Series_sample_id = GSM5348690
!Series_sample_id = GSM5348691
!Series_sample_id = GSM5348692
!Series_contact_name = Danqi,,Deng
!Series_contact_email = danqid128@sina.com
!Series_contact_phone = 18314433284
!Series_contact_institute = The Second Affiliated Hospital of Kunming Medical University
!Series_contact_address = 374 Dianmian Road, Wuhua District
!Series_contact_city = Kunming, Yunnan, China
!Series_contact_zip/postal_code = 651000
!Series_contact_country = China
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE175nnn/GSE175839/suppl/GSE175839_Expression.xlsx
!Series_platform_id = GPL11154
!Series_platform_taxid = 9606
!Series_sample_taxid = 9606
!Series_relation = SubSeries of: GSE175841
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA734019
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP322015
^PLATFORM = GPL11154
!Platform_title = Illumina HiSeq 2000 (Homo sapiens)
!Platform_geo_accession = GPL11154
!Platform_status = Public on Nov 02 2010
!Platform_submission_date = Nov 02 2010
!Platform_last_update_date = Mar 27 2019
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Homo sapiens
!Platform_taxid = 9606
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM5348683
!Sample_title = A5
!Sample_geo_accession = GSM5348683
!Sample_status = Public on Jun 01 2021
!Sample_submission_date = May 31 2021
!Sample_last_update_date = Jun 01 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Tibetan SLE patients
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = subject status: Tibetan SLE patients
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cell
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Illumina Casava1.7 software used for basecalling.
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
!Sample_data_processing = Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
!Sample_data_processing = Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
!Sample_data_processing = perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
!Sample_data_processing = Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Danqi,,Deng
!Sample_contact_email = danqid128@sina.com
!Sample_contact_phone = 18314433284
!Sample_contact_institute = The Second Affiliated Hospital of Kunming Medical University
!Sample_contact_address = 374 Dianmian Road, Wuhua District
!Sample_contact_city = Kunming, Yunnan, China
!Sample_contact_zip/postal_code = 651000
!Sample_contact_country = China
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19469018
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11032997
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE175839
!Sample_series_id = GSE175841
!Sample_data_row_count = 0
^SAMPLE = GSM5348684
!Sample_title = A8
!Sample_geo_accession = GSM5348684
!Sample_status = Public on Jun 01 2021
!Sample_submission_date = May 31 2021
!Sample_last_update_date = Jun 01 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Tibetan SLE patients
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = subject status: Tibetan SLE patients
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cell
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Illumina Casava1.7 software used for basecalling.
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
!Sample_data_processing = Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
!Sample_data_processing = Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
!Sample_data_processing = perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
!Sample_data_processing = Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Danqi,,Deng
!Sample_contact_email = danqid128@sina.com
!Sample_contact_phone = 18314433284
!Sample_contact_institute = The Second Affiliated Hospital of Kunming Medical University
!Sample_contact_address = 374 Dianmian Road, Wuhua District
!Sample_contact_city = Kunming, Yunnan, China
!Sample_contact_zip/postal_code = 651000
!Sample_contact_country = China
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19469017
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11032998
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE175839
!Sample_series_id = GSE175841
!Sample_data_row_count = 0
^SAMPLE = GSM5348685
!Sample_title = A11
!Sample_geo_accession = GSM5348685
!Sample_status = Public on Jun 01 2021
!Sample_submission_date = May 31 2021
!Sample_last_update_date = Jun 01 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Tibetan SLE patients
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = subject status: Tibetan SLE patients
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cell
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Illumina Casava1.7 software used for basecalling.
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
!Sample_data_processing = Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
!Sample_data_processing = Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
!Sample_data_processing = perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
!Sample_data_processing = Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Danqi,,Deng
!Sample_contact_email = danqid128@sina.com
!Sample_contact_phone = 18314433284
!Sample_contact_institute = The Second Affiliated Hospital of Kunming Medical University
!Sample_contact_address = 374 Dianmian Road, Wuhua District
!Sample_contact_city = Kunming, Yunnan, China
!Sample_contact_zip/postal_code = 651000
!Sample_contact_country = China
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19469016
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11032999
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE175839
!Sample_series_id = GSE175841
!Sample_data_row_count = 0
^SAMPLE = GSM5348686
!Sample_title = A12
!Sample_geo_accession = GSM5348686
!Sample_status = Public on Jun 01 2021
!Sample_submission_date = May 31 2021
!Sample_last_update_date = Jun 01 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Tibetan SLE patients
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = subject status: Tibetan SLE patients
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cell
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Illumina Casava1.7 software used for basecalling.
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
!Sample_data_processing = Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
!Sample_data_processing = Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
!Sample_data_processing = perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
!Sample_data_processing = Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Danqi,,Deng
!Sample_contact_email = danqid128@sina.com
!Sample_contact_phone = 18314433284
!Sample_contact_institute = The Second Affiliated Hospital of Kunming Medical University
!Sample_contact_address = 374 Dianmian Road, Wuhua District
!Sample_contact_city = Kunming, Yunnan, China
!Sample_contact_zip/postal_code = 651000
!Sample_contact_country = China
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19469015
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11033000
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE175839
!Sample_series_id = GSE175841
!Sample_data_row_count = 0
^SAMPLE = GSM5348687
!Sample_title = A14
!Sample_geo_accession = GSM5348687
!Sample_status = Public on Jun 01 2021
!Sample_submission_date = May 31 2021
!Sample_last_update_date = Jun 01 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Tibetan SLE patients
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = subject status: Tibetan SLE patients
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cell
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Illumina Casava1.7 software used for basecalling.
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
!Sample_data_processing = Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
!Sample_data_processing = Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
!Sample_data_processing = perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
!Sample_data_processing = Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Danqi,,Deng
!Sample_contact_email = danqid128@sina.com
!Sample_contact_phone = 18314433284
!Sample_contact_institute = The Second Affiliated Hospital of Kunming Medical University
!Sample_contact_address = 374 Dianmian Road, Wuhua District
!Sample_contact_city = Kunming, Yunnan, China
!Sample_contact_zip/postal_code = 651000
!Sample_contact_country = China
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19469014
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11033001
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE175839
!Sample_series_id = GSE175841
!Sample_data_row_count = 0
^SAMPLE = GSM5348688
!Sample_title = B7
!Sample_geo_accession = GSM5348688
!Sample_status = Public on Jun 01 2021
!Sample_submission_date = May 31 2021
!Sample_last_update_date = Jun 01 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Tibetan health control
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = subject status: Tibetan health control
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cell
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Illumina Casava1.7 software used for basecalling.
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
!Sample_data_processing = Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
!Sample_data_processing = Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
!Sample_data_processing = perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
!Sample_data_processing = Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Danqi,,Deng
!Sample_contact_email = danqid128@sina.com
!Sample_contact_phone = 18314433284
!Sample_contact_institute = The Second Affiliated Hospital of Kunming Medical University
!Sample_contact_address = 374 Dianmian Road, Wuhua District
!Sample_contact_city = Kunming, Yunnan, China
!Sample_contact_zip/postal_code = 651000
!Sample_contact_country = China
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19469013
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11033002
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE175839
!Sample_series_id = GSE175841
!Sample_data_row_count = 0
^SAMPLE = GSM5348689
!Sample_title = B8
!Sample_geo_accession = GSM5348689
!Sample_status = Public on Jun 01 2021
!Sample_submission_date = May 31 2021
!Sample_last_update_date = Jun 01 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Tibetan health control
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = subject status: Tibetan health control
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cell
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Illumina Casava1.7 software used for basecalling.
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
!Sample_data_processing = Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
!Sample_data_processing = Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
!Sample_data_processing = perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
!Sample_data_processing = Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Danqi,,Deng
!Sample_contact_email = danqid128@sina.com
!Sample_contact_phone = 18314433284
!Sample_contact_institute = The Second Affiliated Hospital of Kunming Medical University
!Sample_contact_address = 374 Dianmian Road, Wuhua District
!Sample_contact_city = Kunming, Yunnan, China
!Sample_contact_zip/postal_code = 651000
!Sample_contact_country = China
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19469012
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11033003
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE175839
!Sample_series_id = GSE175841
!Sample_data_row_count = 0
^SAMPLE = GSM5348690
!Sample_title = B9
!Sample_geo_accession = GSM5348690
!Sample_status = Public on Jun 01 2021
!Sample_submission_date = May 31 2021
!Sample_last_update_date = Jun 01 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Tibetan health control
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = subject status: Tibetan health control
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cell
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Illumina Casava1.7 software used for basecalling.
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
!Sample_data_processing = Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
!Sample_data_processing = Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
!Sample_data_processing = perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
!Sample_data_processing = Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Danqi,,Deng
!Sample_contact_email = danqid128@sina.com
!Sample_contact_phone = 18314433284
!Sample_contact_institute = The Second Affiliated Hospital of Kunming Medical University
!Sample_contact_address = 374 Dianmian Road, Wuhua District
!Sample_contact_city = Kunming, Yunnan, China
!Sample_contact_zip/postal_code = 651000
!Sample_contact_country = China
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19469011
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11033004
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE175839
!Sample_series_id = GSE175841
!Sample_data_row_count = 0
^SAMPLE = GSM5348691
!Sample_title = B10
!Sample_geo_accession = GSM5348691
!Sample_status = Public on Jun 01 2021
!Sample_submission_date = May 31 2021
!Sample_last_update_date = Jun 01 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Tibetan health control
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = subject status: Tibetan health control
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cell
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Illumina Casava1.7 software used for basecalling.
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
!Sample_data_processing = Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
!Sample_data_processing = Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
!Sample_data_processing = perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
!Sample_data_processing = Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Danqi,,Deng
!Sample_contact_email = danqid128@sina.com
!Sample_contact_phone = 18314433284
!Sample_contact_institute = The Second Affiliated Hospital of Kunming Medical University
!Sample_contact_address = 374 Dianmian Road, Wuhua District
!Sample_contact_city = Kunming, Yunnan, China
!Sample_contact_zip/postal_code = 651000
!Sample_contact_country = China
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19469010
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11033005
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE175839
!Sample_series_id = GSE175841
!Sample_data_row_count = 0
^SAMPLE = GSM5348692
!Sample_title = B12
!Sample_geo_accession = GSM5348692
!Sample_status = Public on Jun 01 2021
!Sample_submission_date = May 31 2021
!Sample_last_update_date = Jun 01 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Tibetan health control
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = subject status: Tibetan health control
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cell
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Illumina Casava1.7 software used for basecalling.
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
!Sample_data_processing = Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
!Sample_data_processing = Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
!Sample_data_processing = perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
!Sample_data_processing = Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Danqi,,Deng
!Sample_contact_email = danqid128@sina.com
!Sample_contact_phone = 18314433284
!Sample_contact_institute = The Second Affiliated Hospital of Kunming Medical University
!Sample_contact_address = 374 Dianmian Road, Wuhua District
!Sample_contact_city = Kunming, Yunnan, China
!Sample_contact_zip/postal_code = 651000
!Sample_contact_country = China
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19469009
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11033006
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE175839
!Sample_series_id = GSE175841
!Sample_data_row_count = 0