从geo上下载的matrix.txt.gz，解压后打开TXT是如下：

!Series_title"In vitro comparison of CD8+ T cells genetically modified to express CARs containing different intracellular domains"

!Series_geo_accession"GSE145007"

!Series_status"Public on Feb 11 2020"

!Series_submission_date"Feb 10 2020"

!Series_last_update_date"Feb 13 2020"

!Series_summary"CD8+ T cells were genetically modified to express CARs containing three different intracellular domains: ICOS, CD28 and a CD28 mutant (CD28-YMFM). The transcriptome analysis by RNA-sequencing of CAR-T cells six days after in vitro antigen recognition revealed that CD28-YMFM CAR-T cells had only 13 differentially expressed genes (>2- or <2-fold change) compared to CD28 CAR-T cells. By contrast, there were 2173 differentially expressed genes when comparing ICOS and CD28 CAR-T cells."

!Series_overall_design"T cells from two different normal donors were genetically modified to express CARs targeting mesothelin and containing different intracellular domains. At the end of the primary expansion, T cells were stimulated with its cognate antigen in vitro. CD8-T cells were isolated six days after stimulation and their transcriptional profile was analyzed by RNAseq."

!Series_type"Expression profiling by high throughput sequencing"

!Series_contributor"Sonia,,Guedan"

!Series_contributor"Avery,,Posey"

!Series_contributor"Carl,H,June"

!Series_contributor"Regina,M,Young"

!Series_contributor"Aviv,,Madar"

!Series_contributor"Anna,,Wing"

!Series_contributor"Carolyn,,Shaw"

!Series_contributor"Fang,,Liu"

!Series_contributor"Victoria,,Casado-Medrano"

!Series_sample_id"GSM4304197 GSM4304198 GSM4304199 GSM4304200 GSM4304201 GSM4304202 "

!Series_contact_name"Aviv,,Madar"

!Series_contact_email"madaraviv@gmail.com, aviv.madar@novartis.com"

!Series_contact_institute"Novartis Institutes for Biomedical Research"

!Series_contact_address"250 Massachusetts Ave"

!Series_contact_city"Cambridge"

!Series_contact_state"MA"

!Series_contact_zip/postal_code"02139"

!Series_contact_country"USA"

!Series_supplementary_file"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE145nnn/GSE145007/suppl/GSE145007_RAW.tar"

!Series_platform_id"GPL23227"

!Series_platform_taxid"9606"

!Series_sample_taxid"9606"

!Series_relation"BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA605702"

!Series_relation"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP247892"

!Sample_title"CD8CART-ND1-Day6-28z""CD8CART-ND1-Day6-28YMFMz""CD8CART-ND1-Day6-ICOSz""CD8CART-ND2-Day6-28z""CD8CART-ND2-Day6-28YMFMz""CD8CART-ND2-Day6-ICOSz"

!Sample_geo_accession"GSM4304197""GSM4304198""GSM4304199""GSM4304200""GSM4304201""GSM4304202"

!Sample_status"Public on Feb 11 2020""Public on Feb 11 2020""Public on Feb 11 2020""Public on Feb 11 2020""Public on Feb 11 2020""Public on Feb 11 2020"

!Sample_submission_date"Feb 10 2020""Feb 10 2020""Feb 10 2020""Feb 10 2020""Feb 10 2020""Feb 10 2020"

!Sample_last_update_date"Feb 12 2020""Feb 12 2020""Feb 12 2020""Feb 12 2020""Feb 12 2020""Feb 12 2020"

!Sample_type"SRA""SRA""SRA""SRA""SRA""SRA"

!Sample_channel_count"1""1""1""1""1""1"

!Sample_source_name_ch1"CD8+ T cells""CD8+ T cells""CD8+ T cells""CD8+ T cells""CD8+ T cells""CD8+ T cells"

!Sample_organism_ch1"Homo sapiens""Homo sapiens""Homo sapiens""Homo sapiens""Homo sapiens""Homo sapiens"

!Sample_characteristics_ch1"group: CD28z""group: CD28YMFN-z""group: ICOSz""group: Day6-28z""group: Day6-28YMFMz""group: CD28YMFN-z"

!Sample_characteristics_ch1"cell type: Activated T cells through cognate antigen""cell type: Activated T cells through cognate antigen""cell type: Activated T cells through cognate antigen""cell type: Activated T cells through cognate antigen""cell type: Activated T cells through cognate antigen""cell type: Activated T cells through cognate antigen"

!Sample_treatment_protocol_ch1"We used two donors: ND1 and ND2. T cells were collected 6 days after T cell activation. And three groups: CD28z, ICOSz and CD28YMFN-z. CAR-T cell activation: For each donor, CD4+ and CD8+ T cells were mixed at 1:1 ratio. T cells were activated with magnetic beads coated with recombinant mesothelin-Fc at a 1:3 cell:bead ratio. CD8+ T cells were isolated 6 days following activation by negative selection using microbeads. 1x10^6 CD8+ T cells were pelleted, resuspended in RLT buffer and frozen.""We used two donors: ND1 and ND2. T cells were collected 6 days after T cell activation. And three groups: CD28z, ICOSz and CD28YMFN-z. CAR-T cell activation: For each donor, CD4+ and CD8+ T cells were mixed at 1:1 ratio. T cells were activated with magnetic beads coated with recombinant mesothelin-Fc at a 1:3 cell:bead ratio. CD8+ T cells were isolated 6 days following activation by negative selection using microbeads. 1x10^6 CD8+ T cells were pelleted, resuspended in RLT buffer and frozen.""We used two donors: ND1 and ND2. T cells were collected 6 days after T cell activation. And three groups: CD28z, ICOSz and CD28YMFN-z. CAR-T cell activation: For each donor, CD4+ and CD8+ T cells were mixed at 1:1 ratio. T cells were activated with magnetic beads coated with recombinant mesothelin-Fc at a 1:3 cell:bead ratio. CD8+ T cells were isolated 6 days following activation by negative selection using microbeads. 1x10^6 CD8+ T cells were pelleted, resuspended in RLT buffer and frozen.""We used two donors: ND1 and ND2. T cells were collected 6 days after T cell activation. And three groups: CD28z, ICOSz and CD28YMFN-z. CAR-T cell activation: For each donor, CD4+ and CD8+ T cells were mixed at 1:1 ratio. T cells were activated with magnetic beads coated with recombinant mesothelin-Fc at a 1:3 cell:bead ratio. CD8+ T cells were isolated 6 days following activation by negative selection using microbeads. 1x10^6 CD8+ T cells were pelleted, resuspended in RLT buffer and frozen.""We used two donors: ND1 and ND2. T cells were collected 6 days after T cell activation. And three groups: CD28z, ICOSz and CD28YMFN-z. CAR-T cell activation: For each donor, CD4+ and CD8+ T cells were mixed at 1:1 ratio. T cells were activated with magnetic beads coated with recombinant mesothelin-Fc at a 1:3 cell:bead ratio. CD8+ T cells were isolated 6 days following activation by negative selection using microbeads. 1x10^6 CD8+ T cells were pelleted, resuspended in RLT buffer and frozen.""We used two donors: ND1 and ND2. T cells were collected 6 days after T cell activation. And three groups: CD28z, ICOSz and CD28YMFN-z. CAR-T cell activation: For each donor, CD4+ and CD8+ T cells were mixed at 1:1 ratio. T cells were activated with magnetic beads coated with recombinant mesothelin-Fc at a 1:3 cell:bead ratio. CD8+ T cells were isolated 6 days following activation by negative selection using microbeads. 1x10^6 CD8+ T cells were pelleted, resuspended in RLT buffer and frozen."

!Sample_growth_protocol_ch1"Blood samples were obtained from the Human Immunology Core of the University of Pennsylvania. Peripheral blood CD4+ and CD8+ T cells from two different normal donors were negatively isolated using RosetteSep Kits (Stem cell Technologies). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 100-U/ml penicillin, 100 g/ml streptomycin sulfate, 10 mM HEPES in a 37°C and 5% CO2 incubator.  For stimulation, CD4+ and CD8+ T cells were cultured with activating beads coated with antibodies to CD3 and CD28 at a 1:3 cell to bead ratio. Approximately 24 h after activation, T cells were transduced with lentiviral vectors at an MOI of 5. Lentiviral vectors encoded CAR constructs targeting mesothelin with the SS1 scFv and costimulated by CD28, ICOS and CD28-YMFM (a CD28 mutant with a substitution of an asparagine to phenylalanine in the YMNM motif). For CD8+ T cells, human IL-2 (Chiron) was added every other day to a final concentration of 50 IU/ml. Cells were counted and fed every 2 days and once T cells appeared to rest down, as determined by both decreased growth kinetics and cell size, they were cryopreserved.""Blood samples were obtained from the Human Immunology Core of the University of Pennsylvania. Peripheral blood CD4+ and CD8+ T cells from two different normal donors were negatively isolated using RosetteSep Kits (Stem cell Technologies). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 100-U/ml penicillin, 100 g/ml streptomycin sulfate, 10 mM HEPES in a 37°C and 5% CO2 incubator.  For stimulation, CD4+ and CD8+ T cells were cultured with activating beads coated with antibodies to CD3 and CD28 at a 1:3 cell to bead ratio. Approximately 24 h after activation, T cells were transduced with lentiviral vectors at an MOI of 5. Lentiviral vectors encoded CAR constructs targeting mesothelin with the SS1 scFv and costimulated by CD28, ICOS and CD28-YMFM (a CD28 mutant with a substitution of an asparagine to phenylalanine in the YMNM motif). For CD8+ T cells, human IL-2 (Chiron) was added every other day to a final concentration of 50 IU/ml. Cells were counted and fed every 2 days and once T cells appeared to rest down, as determined by both decreased growth kinetics and cell size, they were cryopreserved.""Blood samples were obtained from the Human Immunology Core of the University of Pennsylvania. Peripheral blood CD4+ and CD8+ T cells from two different normal donors were negatively isolated using RosetteSep Kits (Stem cell Technologies). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 100-U/ml penicillin, 100 g/ml streptomycin sulfate, 10 mM HEPES in a 37°C and 5% CO2 incubator.  For stimulation, CD4+ and CD8+ T cells were cultured with activating beads coated with antibodies to CD3 and CD28 at a 1:3 cell to bead ratio. Approximately 24 h after activation, T cells were transduced with lentiviral vectors at an MOI of 5. Lentiviral vectors encoded CAR constructs targeting mesothelin with the SS1 scFv and costimulated by CD28, ICOS and CD28-YMFM (a CD28 mutant with a substitution of an asparagine to phenylalanine in the YMNM motif). For CD8+ T cells, human IL-2 (Chiron) was added every other day to a final concentration of 50 IU/ml. Cells were counted and fed every 2 days and once T cells appeared to rest down, as determined by both decreased growth kinetics and cell size, they were cryopreserved.""Blood samples were obtained from the Human Immunology Core of the University of Pennsylvania. Peripheral blood CD4+ and CD8+ T cells from two different normal donors were negatively isolated using RosetteSep Kits (Stem cell Technologies). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 100-U/ml penicillin, 100 g/ml streptomycin sulfate, 10 mM HEPES in a 37°C and 5% CO2 incubator.  For stimulation, CD4+ and CD8+ T cells were cultured with activating beads coated with antibodies to CD3 and CD28 at a 1:3 cell to bead ratio. Approximately 24 h after activation, T cells were transduced with lentiviral vectors at an MOI of 5. Lentiviral vectors encoded CAR constructs targeting mesothelin with the SS1 scFv and costimulated by CD28, ICOS and CD28-YMFM (a CD28 mutant with a substitution of an asparagine to phenylalanine in the YMNM motif). For CD8+ T cells, human IL-2 (Chiron) was added every other day to a final concentration of 50 IU/ml. Cells were counted and fed every 2 days and once T cells appeared to rest down, as determined by both decreased growth kinetics and cell size, they were cryopreserved.""Blood samples were obtained from the Human Immunology Core of the University of Pennsylvania. Peripheral blood CD4+ and CD8+ T cells from two different normal donors were negatively isolated using RosetteSep Kits (Stem cell Technologies). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 100-U/ml penicillin, 100 g/ml streptomycin sulfate, 10 mM HEPES in a 37°C and 5% CO2 incubator.  For stimulation, CD4+ and CD8+ T cells were cultured with activating beads coated with antibodies to CD3 and CD28 at a 1:3 cell to bead ratio. Approximately 24 h after activation, T cells were transduced with lentiviral vectors at an MOI of 5. Lentiviral vectors encoded CAR constructs targeting mesothelin with the SS1 scFv and costimulated by CD28, ICOS and CD28-YMFM (a CD28 mutant with a substitution of an asparagine to phenylalanine in the YMNM motif). For CD8+ T cells, human IL-2 (Chiron) was added every other day to a final concentration of 50 IU/ml. Cells were counted and fed every 2 days and once T cells appeared to rest down, as determined by both decreased growth kinetics and cell size, they were cryopreserved.""Blood samples were obtained from the Human Immunology Core of the University of Pennsylvania. Peripheral blood CD4+ and CD8+ T cells from two different normal donors were negatively isolated using RosetteSep Kits (Stem cell Technologies). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 100-U/ml penicillin, 100 g/ml streptomycin sulfate, 10 mM HEPES in a 37°C and 5% CO2 incubator.  For stimulation, CD4+ and CD8+ T cells were cultured with activating beads coated with antibodies to CD3 and CD28 at a 1:3 cell to bead ratio. Approximately 24 h after activation, T cells were transduced with lentiviral vectors at an MOI of 5. Lentiviral vectors encoded CAR constructs targeting mesothelin with the SS1 scFv and costimulated by CD28, ICOS and CD28-YMFM (a CD28 mutant with a substitution of an asparagine to phenylalanine in the YMNM motif). For CD8+ T cells, human IL-2 (Chiron) was added every other day to a final concentration of 50 IU/ml. Cells were counted and fed every 2 days and once T cells appeared to rest down, as determined by both decreased growth kinetics and cell size, they were cryopreserved."

!Sample_molecule_ch1"polyA RNA""polyA RNA""polyA RNA""polyA RNA""polyA RNA""polyA RNA"

!Sample_extract_protocol_ch1"Frozen CD8+ T cells in RLT buffer were sent to BGI Genomics for RNA extraction, library preparation and sequencing.""Frozen CD8+ T cells in RLT buffer were sent to BGI Genomics for RNA extraction, library preparation and sequencing.""Frozen CD8+ T cells in RLT buffer were sent to BGI Genomics for RNA extraction, library preparation and sequencing.""Frozen CD8+ T cells in RLT buffer were sent to BGI Genomics for RNA extraction, library preparation and sequencing.""Frozen CD8+ T cells in RLT buffer were sent to BGI Genomics for RNA extraction, library preparation and sequencing.""Frozen CD8+ T cells in RLT buffer were sent to BGI Genomics for RNA extraction, library preparation and sequencing."

!Sample_extract_protocol_ch1"1) There are two methods to treat total RNA. Oligo (dT) magnetic beads are used to select mRNA with polyA tail,  or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library.""1) There are two methods to treat total RNA. Oligo (dT) magnetic beads are used to select mRNA with polyA tail,  or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library.""1) There are two methods to treat total RNA. Oligo (dT) magnetic beads are used to select mRNA with polyA tail,  or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library.""1) There are two methods to treat total RNA. Oligo (dT) magnetic beads are used to select mRNA with polyA tail,  or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library.""1) There are two methods to treat total RNA. Oligo (dT) magnetic beads are used to select mRNA with polyA tail,  or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library.""1) There are two methods to treat total RNA. Oligo (dT) magnetic beads are used to select mRNA with polyA tail,  or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library."

!Sample_taxid_ch1"9606""9606""9606""9606""9606""9606"

!Sample_description"Genetically modified to express chimeric antigen receptors""Genetically modified to express chimeric antigen receptors""Genetically modified to express chimeric antigen receptors""Genetically modified to express chimeric antigen receptors""Genetically modified to express chimeric antigen receptors""Genetically modified to express chimeric antigen receptors"

!Sample_data_processing"Starting with raw data. Filtering step: We define ""dirty"" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads. They need to be removed before downstream analysis to decrease data noise. Filtering steps are as follows:  1) Remove reads with adaptors;  2) Remove reads in which unknown bases are more than 10%;  3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).""Starting with raw data. Filtering step: We define ""dirty"" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads. They need to be removed before downstream analysis to decrease data noise. Filtering steps are as follows:  1) Remove reads with adaptors;  2) Remove reads in which unknown bases are more than 10%;  3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).""Starting with raw data. Filtering step: We define ""dirty"" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads. They need to be removed before downstream analysis to decrease data noise. Filtering steps are as follows:  1) Remove reads with adaptors;  2) Remove reads in which unknown bases are more than 10%;  3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).""Starting with raw data. Filtering step: We define ""dirty"" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads. They need to be removed before downstream analysis to decrease data noise. Filtering steps are as follows:  1) Remove reads with adaptors;  2) Remove reads in which unknown bases are more than 10%;  3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).""Starting with raw data. Filtering step: We define ""dirty"" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads. They need to be removed before downstream analysis to decrease data noise. Filtering steps are as follows:  1) Remove reads with adaptors;  2) Remove reads in which unknown bases are more than 10%;  3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).""Starting with raw data. Filtering step: We define ""dirty"" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads. They need to be removed before downstream analysis to decrease data noise. Filtering steps are as follows:  1) Remove reads with adaptors;  2) Remove reads in which unknown bases are more than 10%;  3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5)."

!Sample_data_processing"After filtering, the remaining reads are called ""clean reads"" and stored as FASTQ format""After filtering, the remaining reads are called ""clean reads"" and stored as FASTQ format""After filtering, the remaining reads are called ""clean reads"" and stored as FASTQ format""After filtering, the remaining reads are called ""clean reads"" and stored as FASTQ format""After filtering, the remaining reads are called ""clean reads"" and stored as FASTQ format""After filtering, the remaining reads are called ""clean reads"" and stored as FASTQ format"

!Sample_data_processing"Reads Mapping: We used Bowtie2 to map clean reads to reference gene. Bowtie2 parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200""Reads Mapping: We used Bowtie2 to map clean reads to reference gene. Bowtie2 parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200""Reads Mapping: We used Bowtie2 to map clean reads to reference gene. Bowtie2 parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200""Reads Mapping: We used Bowtie2 to map clean reads to reference gene. Bowtie2 parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200""Reads Mapping: We used Bowtie2 to map clean reads to reference gene. Bowtie2 parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200""Reads Mapping: We used Bowtie2 to map clean reads to reference gene. Bowtie2 parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200"

!Sample_data_processing"FPKM were calculated using RSEM""FPKM were calculated using RSEM""FPKM were calculated using RSEM""FPKM were calculated using RSEM""FPKM were calculated using RSEM""FPKM were calculated using RSEM"

!Sample_data_processing"Genome_build: GRCh38.p13""Genome_build: GRCh38.p13""Genome_build: GRCh38.p13""Genome_build: GRCh38.p13""Genome_build: GRCh38.p13""Genome_build: GRCh38.p13"

!Sample_data_processing"Supplementary_files_format_and_content: Tab Separated Values containing genes FPKM values""Supplementary_files_format_and_content: Tab Separated Values containing genes FPKM values""Supplementary_files_format_and_content: Tab Separated Values containing genes FPKM values""Supplementary_files_format_and_content: Tab Separated Values containing genes FPKM values""Supplementary_files_format_and_content: Tab Separated Values containing genes FPKM values""Supplementary_files_format_and_content: Tab Separated Values containing genes FPKM values"

!Sample_platform_id"GPL23227""GPL23227""GPL23227""GPL23227""GPL23227""GPL23227"

!Sample_contact_name"Aviv,,Madar""Aviv,,Madar""Aviv,,Madar""Aviv,,Madar""Aviv,,Madar""Aviv,,Madar"

!Sample_contact_email"madaraviv@gmail.com, aviv.madar@novartis.com""madaraviv@gmail.com, aviv.madar@novartis.com""madaraviv@gmail.com, aviv.madar@novartis.com""madaraviv@gmail.com, aviv.madar@novartis.com""madaraviv@gmail.com, aviv.madar@novartis.com""madaraviv@gmail.com, aviv.madar@novartis.com"

!Sample_contact_institute"Novartis Institutes for Biomedical Research""Novartis Institutes for Biomedical Research""Novartis Institutes for Biomedical Research""Novartis Institutes for Biomedical Research""Novartis Institutes for Biomedical Research""Novartis Institutes for Biomedical Research"

!Sample_contact_address"250 Massachusetts Ave""250 Massachusetts Ave""250 Massachusetts Ave""250 Massachusetts Ave""250 Massachusetts Ave""250 Massachusetts Ave"

!Sample_contact_city"Cambridge""Cambridge""Cambridge""Cambridge""Cambridge""Cambridge"

!Sample_contact_state"MA""MA""MA""MA""MA""MA"

!Sample_contact_zip/postal_code"02139""02139""02139""02139""02139""02139"

!Sample_contact_country"USA""USA""USA""USA""USA""USA"

!Sample_data_row_count"0""0""0""0""0""0"

!Sample_instrument_model"BGISEQ-500""BGISEQ-500""BGISEQ-500""BGISEQ-500""BGISEQ-500""BGISEQ-500"

!Sample_library_selection"cDNA""cDNA""cDNA""cDNA""cDNA""cDNA"

!Sample_library_source"transcriptomic""transcriptomic""transcriptomic""transcriptomic""transcriptomic""transcriptomic"

!Sample_library_strategy"RNA-Seq""RNA-Seq""RNA-Seq""RNA-Seq""RNA-Seq""RNA-Seq"

!Sample_relation"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14074491""BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14074490""BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14074489""BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14074488""BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14074487""BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14074486"

!Sample_relation"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7700692""SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7700693""SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7700688""SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7700689""SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7700690""SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7700691"

!Sample_supplementary_file_1"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4304nnn/GSM4304197/suppl/GSM4304197_Day6_ND1_28zA.gene.FPKM.txt.gz""ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4304nnn/GSM4304198/suppl/GSM4304198_Day6_ND1_28z-YMFMA.gene.FPKM.txt.gz""ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4304nnn/GSM4304199/suppl/GSM4304199_Day6_ND1_ICOSzA.gene.FPKM.txt.gz""ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4304nnn/GSM4304200/suppl/GSM4304200_Day6_ND2_28zA.gene.FPKM.txt.gz""ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4304nnn/GSM4304201/suppl/GSM4304201_Day6_ND2_28z-YMFMA.gene.FPKM.txt.gz""ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4304nnn/GSM4304202/suppl/GSM4304202_Day6_ND2_ICOSzA.gene.FPKM.txt.gz"

!series_matrix_table_begin

"ID_REF""GSM4304197""GSM4304198""GSM4304199""GSM4304200""GSM4304201""GSM4304202"

!series_matrix_table_end