rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
9812,ERR3931362,ERX3938952,ERS4329529,ERP120057,PRJEB36819,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E-MTAB-8800,Transcriptome Analysis,Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,,Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,WKM 7 ED,SAMEA6565186,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565186|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 7 ED|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM7|organism part:head kidney|sample name:E MTAB 8800:WKM 7 ED,,,,,,,,,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E MTAB 8800:WKM 7 ED s,WKM 7 ED s,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,Experimental Factor: stimulus:n1,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,SINGLE,ILLUMINA,NextSeq 500,,ERP120057,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,10_WKM_7_ED.fastq.gz,fastq,3603783627.0,47724788.0,E MTAB 8800:WKM 7 ED,0:75.51 1:0,A:730277817;C:1059558661;G:1006087781;T:807771859;N:87509,75,0,,,730277817,1059558661,1006087781,807771859,87509,ERX3938952,ERS4329529,ERA2383450,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.96114,,0.20335,,0.83798,,0.76524,,76,,B,,usable mapping rate,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,bulk,bulk,,Czech Republic,2021-12-31,Adult,Adult,Multi-tissue,Multi-system
9813,ERR3931361,ERX3938951,ERS4329528,ERP120057,PRJEB36819,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E-MTAB-8800,Transcriptome Analysis,Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,,Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,WKM 7 EaD,SAMEA6565185,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565185|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 7 EaD|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM7|organism part:head kidney|sample name:E MTAB 8800:WKM 7 EaD,,,,,,,,,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E MTAB 8800:WKM 7 EaD s,WKM 7 EaD s,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,Experimental Factor: stimulus:kit ligand,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,SINGLE,ILLUMINA,NextSeq 500,,ERP120057,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,11_WKM_7_EaD_1.fastq.gz,fastq,3127207407.0,41417754.0,E MTAB 8800:WKM 7 EaD,0:75.50 1:0,A:618290483;C:948661192;G:891134088;T:669046822;N:74822,75,0,,,618290483,948661192,891134088,669046822,74822,ERX3938951,ERS4329528,ERA2383450,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.96441,,0.20171,,0.85427,,0.75425,,76,,B,,usable mapping rate,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,bulk,bulk,,Czech Republic,2021-12-31,Adult,Adult,Multi-tissue,Multi-system
9814,ERR3931360,ERX3938950,ERS4329527,ERP120057,PRJEB36819,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E-MTAB-8800,Transcriptome Analysis,Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,,Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,WKM 5 ED,SAMEA6565184,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565184|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 5 ED|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM5|organism part:head kidney|sample name:E MTAB 8800:WKM 5 ED,,,,,,,,,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E MTAB 8800:WKM 5 ED s,WKM 5 ED s,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,Experimental Factor: stimulus:n1,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,SINGLE,ILLUMINA,NextSeq 500,,ERP120057,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,8_WKM_5_ED.fastq.gz,fastq,3762435507.0,49825705.0,E MTAB 8800:WKM 5 ED,0:75.51 1:0,A:760573477;C:1107794761;G:1060998015;T:832975681;N:93573,75,0,,,760573477,1107794761,1060998015,832975681,93573,ERX3938950,ERS4329527,ERA2383450,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.96233,,0.20628,,0.84141,,0.73601,,75,,B,,usable mapping rate,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,bulk,bulk,,Czech Republic,2021-12-31,Adult,Adult,Multi-tissue,Multi-system
9815,ERR3931359,ERX3938949,ERS4329526,ERP120057,PRJEB36819,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E-MTAB-8800,Transcriptome Analysis,Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,,Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,WKM 5 EaD,SAMEA6565183,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565183|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 5 EaD|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM5|organism part:head kidney|sample name:E MTAB 8800:WKM 5 EaD,,,,,,,,,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E MTAB 8800:WKM 5 EaD s,WKM 5 EaD s,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,Experimental Factor: stimulus:kit ligand,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,SINGLE,ILLUMINA,NextSeq 500,,ERP120057,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,9_WKM_5_EaD.fastq.gz,fastq,3602342027.0,47707938.0,E MTAB 8800:WKM 5 EaD,0:75.51 1:0,A:717278291;C:1084375347;G:1027250408;T:773351695;N:86286,75,0,,,717278291,1084375347,1027250408,773351695,86286,ERX3938949,ERS4329526,ERA2383450,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.96461,,0.20281,,0.85303,,0.74553,,75,,B,,usable mapping rate,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,bulk,bulk,,Czech Republic,2021-12-31,Adult,Adult,Multi-tissue,Multi-system
35878,SRR33167505,SRX28428347,SRS24751220,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 CC7 S1,GSM8919403,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing,GRC355 CC7 S1,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2,GSM8919403,GSM8919403: GRC355 CC7 S1; Danio rerio; RNA Seq,GSM8919403 r1,GSM8919403,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_CC7_S1_R1_001.fastq.gz,fastq,1602530400.0,21367072.0,GSM8919403 r1,0:75,A:423908384;C:380610264;G:430749077;T:367248932;N:13743,75,,,,423908384,380610264,430749077,367248932,13743,SRX28428347,SRS24751220,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35879,SRR33167506,SRX28428346,SRS24751219,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 CC6 S13,GSM8919402,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing,GRC355 CC6 S13,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2,GSM8919402,GSM8919402: GRC355 CC6 S13; Danio rerio; RNA Seq,GSM8919402 r1,GSM8919402,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_CC6_S13_R1_001.fastq.gz,fastq,2682385275.0,35765137.0,GSM8919402 r1,0:75,A:714420635;C:641843546;G:710142891;T:615939845;N:38358,75,,,,714420635,641843546,710142891,615939845,38358,SRX28428346,SRS24751219,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35880,SRR33167507,SRX28428345,SRS24751218,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 CC5 S9,GSM8919401,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing,GRC355 CC5 S9,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2,GSM8919401,GSM8919401: GRC355 CC5 S9; Danio rerio; RNA Seq,GSM8919401 r1,GSM8919401,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_CC5_S9_R1_001.fastq.gz,fastq,1963794750.0,26183930.0,GSM8919401 r1,0:75,A:526554394;C:453867368;G:498987697;T:484357818;N:27473,75,,,,526554394,453867368,498987697,484357818,27473,SRX28428345,SRS24751218,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35881,SRR33167508,SRX28428344,SRS24751217,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 CC4 S6,GSM8919400,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing,GRC355 CC4 S6,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2,GSM8919400,GSM8919400: GRC355 CC4 S6; Danio rerio; RNA Seq,GSM8919400 r1,GSM8919400,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_CC4_S6_R1_001.fastq.gz,fastq,2337900150.0,31172002.0,GSM8919400 r1,0:75,A:616059883;C:562202412;G:623837969;T:535779947;N:19939,75,,,,616059883,562202412,623837969,535779947,19939,SRX28428344,SRS24751217,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35882,SRR33167509,SRX28428343,SRS24751216,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 CC3 S10,GSM8919399,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing,GRC355 CC3 S10,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2,GSM8919399,GSM8919399: GRC355 CC3 S10; Danio rerio; RNA Seq,GSM8919399 r1,GSM8919399,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_CC3_S10_R1_001.fastq.gz,fastq,2438718375.0,32516245.0,GSM8919399 r1,0:75,A:649883373;C:579588054;G:640815663;T:568410218;N:21067,75,,,,649883373,579588054,640815663,568410218,21067,SRX28428343,SRS24751216,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35883,SRR33167510,SRX28428342,SRS24751215,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 CC2 S12,GSM8919398,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing,GRC355 CC2 S12,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2,GSM8919398,GSM8919398: GRC355 CC2 S12; Danio rerio; RNA Seq,GSM8919398 r1,GSM8919398,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_CC2_S12_R1_001.fastq.gz,fastq,2306185575.0,30749141.0,GSM8919398 r1,0:75,A:618466956;C:553097715;G:596880619;T:537720043;N:20242,75,,,,618466956,553097715,596880619,537720043,20242,SRX28428342,SRS24751215,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35884,SRR33167511,SRX28428341,SRS24751214,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 CC1 S14,GSM8919397,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2|geo loc name:missing|collection date:missing,GRC355 CC1 S14,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:2,GSM8919397,GSM8919397: GRC355 CC1 S14; Danio rerio; RNA Seq,GSM8919397 r1,GSM8919397,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_CC1_S14_R1_001.fastq.gz,fastq,1666975950.0,22226346.0,GSM8919397 r1,0:75,A:444383649;C:378084847;G:409250227;T:435243137;N:14090,75,,,,444383649,378084847,409250227,435243137,14090,SRX28428341,SRS24751214,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35885,SRR33167512,SRX28428340,SRS24751213,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AX7 S12,GSM8919396,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,GRC355 AX7 S12,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919396,GSM8919396: GRC355 AX7 S12; Danio rerio; RNA Seq,GSM8919396 r1,GSM8919396,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AX7_S12_R1_001.fastq.gz,fastq,2140829850.0,28544398.0,GSM8919396 r1,0:75,A:573637456;C:487537967;G:542176673;T:537445946;N:31808,75,,,,573637456,487537967,542176673,537445946,31808,SRX28428340,SRS24751213,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35886,SRR33167513,SRX28428339,SRS24751212,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AX4 S8,GSM8919395,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,GRC355 AX4 S8,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919395,GSM8919395: GRC355 AX4 S8; Danio rerio; RNA Seq,GSM8919395 r1,GSM8919395,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AX4_S8_R1_001.fastq.gz,fastq,1621849275.0,21624657.0,GSM8919395 r1,0:75,A:427004733;C:380545003;G:418850461;T:395425815;N:23263,75,,,,427004733,380545003,418850461,395425815,23263,SRX28428339,SRS24751212,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35890,SRR33167517,SRX28428335,SRS24751207,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AX3 S5,GSM8919394,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,GRC355 AX3 S5,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919394,GSM8919394: GRC355 AX3 S5; Danio rerio; RNA Seq,GSM8919394 r1,GSM8919394,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AX3_S5_R1_001.fastq.gz,fastq,2554087275.0,34054497.0,GSM8919394 r1,0:75,A:679572493;C:596662581;G:654676127;T:623138913;N:37161,75,,,,679572493,596662581,654676127,623138913,37161,SRX28428335,SRS24751207,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35891,SRR33167518,SRX28428334,SRS24751208,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AX1 S2,GSM8919393,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,GRC355 AX1 S2,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919393,GSM8919393: GRC355 AX1 S2; Danio rerio; RNA Seq,GSM8919393 r1,GSM8919393,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AX1_S2_R1_001.fastq.gz,fastq,2056328850.0,27417718.0,GSM8919393 r1,0:75,A:547609875;C:481406742;G:529530435;T:497753038;N:28760,75,,,,547609875,481406742,529530435,497753038,28760,SRX28428334,SRS24751208,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35892,SRR33167519,SRX28428333,SRS24751206,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AC7 S7,GSM8919392,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing,GRC355 AC7 S7,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2,GSM8919392,GSM8919392: GRC355 AC7 S7; Danio rerio; RNA Seq,GSM8919392 r1,GSM8919392,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AC7_S7_R1_001.fastq.gz,fastq,2227335150.0,29697802.0,GSM8919392 r1,0:75,A:600851630;C:506204586;G:559397063;T:560849750;N:32121,75,,,,600851630,506204586,559397063,560849750,32121,SRX28428333,SRS24751206,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35893,SRR33167520,SRX28428332,SRS24751204,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AC6 S11,GSM8919391,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing,GRC355 AC6 S11,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2,GSM8919391,GSM8919391: GRC355 AC6 S11; Danio rerio; RNA Seq,GSM8919391 r1,GSM8919391,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AC6_S11_R1_001.fastq.gz,fastq,2585681925.0,34475759.0,GSM8919391 r1,0:75,A:689801171;C:608098568;G:666027069;T:621732490;N:22627,75,,,,689801171,608098568,666027069,621732490,22627,SRX28428332,SRS24751204,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35894,SRR33167521,SRX28428331,SRS24751205,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AC5 S14,GSM8919390,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing,GRC355 AC5 S14,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2,GSM8919390,GSM8919390: GRC355 AC5 S14; Danio rerio; RNA Seq,GSM8919390 r1,GSM8919390,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AC5_S14_R1_001.fastq.gz,fastq,2494451250.0,33259350.0,GSM8919390 r1,0:75,A:663836714;C:570411156;G:619148577;T:641019188;N:35615,75,,,,663836714,570411156,619148577,641019188,35615,SRX28428331,SRS24751205,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35895,SRR33167522,SRX28428330,SRS24751203,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AC4 S16,GSM8919389,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing,GRC355 AC4 S16,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2,GSM8919389,GSM8919389: GRC355 AC4 S16; Danio rerio; RNA Seq,GSM8919389 r1,GSM8919389,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AC4_S16_R1_001.fastq.gz,fastq,2318944500.0,30919260.0,GSM8919389 r1,0:75,A:622730628;C:558676778;G:600421168;T:537095873;N:20053,75,,,,622730628,558676778,600421168,537095873,20053,SRX28428330,SRS24751203,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35896,SRR33167523,SRX28428329,SRS24751201,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AC3 S10,GSM8919388,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing,GRC355 AC3 S10,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2,GSM8919388,GSM8919388: GRC355 AC3 S10; Danio rerio; RNA Seq,GSM8919388 r1,GSM8919388,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AC3_S10_R1_001.fastq.gz,fastq,2294756475.0,30596753.0,GSM8919388 r1,0:75,A:602530943;C:536584842;G:585162453;T:570445286;N:32951,75,,,,602530943,536584842,585162453,570445286,32951,SRX28428329,SRS24751201,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35897,SRR33167524,SRX28428328,SRS24751202,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AC2 S1,GSM8919387,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing,GRC355 AC2 S1,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2,GSM8919387,GSM8919387: GRC355 AC2 S1; Danio rerio; RNA Seq,GSM8919387 r1,GSM8919387,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AC2_S1_R1_001.fastq.gz,fastq,2339756250.0,31196750.0,GSM8919387 r1,0:75,A:612473749;C:554816637;G:611772519;T:560660557;N:32788,75,,,,612473749,554816637,611772519,560660557,32788,SRX28428328,SRS24751202,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35906,SRR33167533,SRX28428319,SRS24751193,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AC1 S4,GSM8919386,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing,GRC355 AC1 S4,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2,GSM8919386,GSM8919386: GRC355 AC1 S4; Danio rerio; RNA Seq,GSM8919386 r1,GSM8919386,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AC1_S4_R1_001.fastq.gz,fastq,2063624400.0,27514992.0,GSM8919386 r1,0:75,A:560729563;C:466634352;G:528754548;T:507475626;N:30311,75,,,,560729563,466634352,528754548,507475626,30311,SRX28428319,SRS24751193,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
36017,SRR33397788,SRX28640389,SRS24910746,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,5IRDGN 1726,GSM8965491,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:red fluorescent macrophages from infected larvae|geo loc name:missing|collection date:missing,5IRDGN 1726,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:red fluorescent macrophages from infected larvae,GSM8965491,GSM8965491: 5IRDGN 1726; Danio rerio; RNA Seq,GSM8965491 r1,GSM8965491,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,5IRDGN_1726.fastq.gz,fastq,1418064486.0,27805186.0,GSM8965491 r1,0:51,A:391531980;C:314713052;G:316733094;T:395075392;N:10968,51,,,,391531980,314713052,316733094,395075392,10968,SRX28640389,SRS24910746,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36018,SRR33397789,SRX28640388,SRS24910745,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,5irdgn 1358,GSM8965490,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:red fluorescent macrophages from infected larvae|geo loc name:missing|collection date:missing,5irdgn 1358,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:red fluorescent macrophages from infected larvae,GSM8965490,GSM8965490: 5irdgn 1358; Danio rerio; RNA Seq,GSM8965490 r1,GSM8965490,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,5irdgn_1358.fastq.gz,fastq,1615867578.0,31683678.0,GSM8965490 r1,0:51,A:443495782;C:364518673;G:367459501;T:440313305;N:80317,51,,,,443495782,364518673,367459501,440313305,80317,SRX28640388,SRS24910745,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36019,SRR33397790,SRX28640387,SRS24910744,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,5IRDGN 1140mfap4infect,GSM8965489,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:red fluorescent macrophages from infected larvae|geo loc name:missing|collection date:missing,5IRDGN 1140mfap4infect,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:red fluorescent macrophages from infected larvae,GSM8965489,GSM8965489: 5IRDGN 1140mfap4infect; Danio rerio; RNA Seq,GSM8965489 r1,GSM8965489,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,5IRDGN_1140mfap4infect.fastq.gz,fastq,1198028403.0,23490753.0,GSM8965489 r1,0:51,A:337163959;C:263381934;G:263010311;T:334256631;N:215568,51,,,,337163959,263381934,263010311,334256631,215568,SRX28640387,SRS24910744,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36020,SRR33397791,SRX28640386,SRS24910743,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,4IRD 1726,GSM8965488,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:red fluorescent macrophages from infected larvae|geo loc name:missing|collection date:missing,4IRD 1726,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:red fluorescent macrophages from infected larvae,GSM8965488,GSM8965488: 4IRD 1726; Danio rerio; RNA Seq,GSM8965488 r1,GSM8965488,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,4IRD_1726.fastq.gz,fastq,1608899907.0,31547057.0,GSM8965488 r1,0:51,A:440123176;C:362892104;G:362919613;T:442952498;N:12516,51,,,,440123176,362892104,362919613,442952498,12516,SRX28640386,SRS24910743,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36021,SRR33397792,SRX28640385,SRS24910742,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,4ird 1358,GSM8965487,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:red fluorescent macrophages from infected larvae|geo loc name:missing|collection date:missing,4ird 1358,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:red fluorescent macrophages from infected larvae,GSM8965487,GSM8965487: 4ird 1358; Danio rerio; RNA Seq,GSM8965487 r1,GSM8965487,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,4ird_1358.fastq.gz,fastq,1918656006.0,37620706.0,GSM8965487 r1,0:51,A:523353788;C:437243796;G:437111630;T:520844757;N:102035,51,,,,523353788,437243796,437111630,520844757,102035,SRX28640385,SRS24910742,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36022,SRR33397793,SRX28640384,SRS24910741,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,4IRD 1140mfap4infect,GSM8965486,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:red fluorescent macrophages from infected larvae|geo loc name:missing|collection date:missing,4IRD 1140mfap4infect,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:red fluorescent macrophages from infected larvae,GSM8965486,GSM8965486: 4IRD 1140mfap4infect; Danio rerio; RNA Seq,GSM8965486 r1,GSM8965486,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,4IRD_1140mfap4infect.fastq.gz,fastq,2065124181.0,40492631.0,GSM8965486 r1,0:51,A:575599448;C:457995578;G:456794039;T:574364307;N:370809,51,,,,575599448,457995578,456794039,574364307,370809,SRX28640384,SRS24910741,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36023,SRR33397794,SRX28640383,SRS24910740,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,3I 1726,GSM8965485,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:nonfluorescent cells from infected larvae|geo loc name:missing|collection date:missing,3I 1726,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:nonfluorescent cells from infected larvae,GSM8965485,GSM8965485: 3I 1726; Danio rerio; RNA Seq,GSM8965485 r1,GSM8965485,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,3I_1726.fastq.gz,fastq,2079030147.0,40765297.0,GSM8965485 r1,0:51,A:573828792;C:463441412;G:462345628;T:579398386;N:15929,51,,,,573828792,463441412,462345628,579398386,15929,SRX28640383,SRS24910740,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36024,SRR33397795,SRX28640382,SRS24910739,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,3i 1358,GSM8965484,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:nonfluorescent cells from infected larvae|geo loc name:missing|collection date:missing,3i 1358,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:nonfluorescent cells from infected larvae,GSM8965484,GSM8965484: 3i 1358; Danio rerio; RNA Seq,GSM8965484 r1,GSM8965484,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,3i_1358.fastq.gz,fastq,1875951870.0,36783370.0,GSM8965484 r1,0:51,A:517454713;C:417324032;G:419934573;T:521137218;N:101334,51,,,,517454713,417324032,419934573,521137218,101334,SRX28640382,SRS24910739,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36025,SRR33397796,SRX28640381,SRS24910738,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,3I 1140mfap4infect,GSM8965483,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:nonfluorescent cells from infected larvae|geo loc name:missing|collection date:missing,3I 1140mfap4infect,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Infected|treatment:nonfluorescent cells from infected larvae,GSM8965483,GSM8965483: 3I 1140mfap4infect; Danio rerio; RNA Seq,GSM8965483 r1,GSM8965483,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,3I_1140mfap4infect.fastq.gz,fastq,2287673136.0,44856336.0,GSM8965483 r1,0:51,A:640600430;C:506279148;G:505458087;T:634930103;N:405368,51,,,,640600430,506279148,505458087,634930103,405368,SRX28640381,SRS24910738,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36026,SRR33397797,SRX28640380,SRS24910737,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,2CRD 1726,GSM8965482,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:red fluorescent macrophages from uninfected larvae|geo loc name:missing|collection date:missing,2CRD 1726,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:red fluorescent macrophages from uninfected larvae,GSM8965482,GSM8965482: 2CRD 1726; Danio rerio; RNA Seq,GSM8965482 r1,GSM8965482,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,2CRD_1726.fastq.gz,fastq,1714227708.0,33612308.0,GSM8965482 r1,0:51,A:469735292;C:384334472;G:384797565;T:475347080;N:13299,51,,,,469735292,384334472,384797565,475347080,13299,SRX28640380,SRS24910737,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36027,SRR33397798,SRX28640379,SRS24910736,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,2crd 1358,GSM8965481,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:red fluorescent macrophages from uninfected larvae|geo loc name:missing|collection date:missing,2crd 1358,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:red fluorescent macrophages from uninfected larvae,GSM8965481,GSM8965481: 2crd 1358; Danio rerio; RNA Seq,GSM8965481 r1,GSM8965481,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,2crd_1358.fastq.gz,fastq,1351675950.0,26503450.0,GSM8965481 r1,0:51,A:372863619;C:299416281;G:306620686;T:372717432;N:57932,51,,,,372863619,299416281,306620686,372717432,57932,SRX28640379,SRS24910736,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36028,SRR33397799,SRX28640378,SRS24910735,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,2CRD 1140mfap4infect,GSM8965480,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:red fluorescent macrophages from uninfected larvae|geo loc name:missing|collection date:missing,2CRD 1140mfap4infect,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:red fluorescent macrophages from uninfected larvae,GSM8965480,GSM8965480: 2CRD 1140mfap4infect; Danio rerio; RNA Seq,GSM8965480 r1,GSM8965480,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,2CRD_1140mfap4infect.fastq.gz,fastq,1870366299.0,36673849.0,GSM8965480 r1,0:51,A:522034016;C:412925534;G:413693089;T:521379784;N:333876,51,,,,522034016,412925534,413693089,521379784,333876,SRX28640378,SRS24910735,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36029,SRR33397800,SRX28640377,SRS24910734,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,1C 1726,GSM8965479,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:nonfluorescent cells from uninfected larvae|geo loc name:missing|collection date:missing,1C 1726,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:nonfluorescent cells from uninfected larvae,GSM8965479,GSM8965479: 1C 1726; Danio rerio; RNA Seq,GSM8965479 r1,GSM8965479,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,1C_1726.fastq.gz,fastq,2116510506.0,41500206.0,GSM8965479 r1,0:51,A:580244434;C:475940957;G:474848964;T:585459729;N:16422,51,,,,580244434,475940957,474848964,585459729,16422,SRX28640377,SRS24910734,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36030,SRR33397801,SRX28640376,SRS24910733,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,1c 1358,GSM8965478,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:nonfluorescent cells from uninfected larvae|geo loc name:missing|collection date:missing,1c 1358,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:nonfluorescent cells from uninfected larvae,GSM8965478,GSM8965478: 1c 1358; Danio rerio; RNA Seq,GSM8965478 r1,GSM8965478,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,1c_1358.fastq.gz,fastq,1745512893.0,34225743.0,GSM8965478 r1,0:51,A:470456301;C:396221813;G:401458508;T:477287506;N:88765,51,,,,470456301,396221813,401458508,477287506,88765,SRX28640376,SRS24910733,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
36031,SRR33397802,SRX28640375,SRS24910732,SRP582598,PRJNA1257824,Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish,GSE296119,Transcriptome Analysis,Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.,,,,1C 1140mfap4infect,GSM8965477,,source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:nonfluorescent cells from uninfected larvae|geo loc name:missing|collection date:missing,1C 1140mfap4infect,RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon,Larval,Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 μg/mL.,tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:nonfluorescent cells from uninfected larvae,GSM8965477,GSM8965477: 1C 1140mfap4infect; Danio rerio; RNA Seq,GSM8965477 r1,GSM8965477,1,RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP582598,,,1C_1140mfap4infect.fastq.gz,fastq,1492422690.0,29263190.0,GSM8965477 r1,0:51,A:421145406;C:327412398;G:328273236;T:415327504;N:264146,51,,,,421145406,327412398,328273236,415327504,264146,SRX28640375,SRS24910732,SRA2148962,Duke University,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2025-05-01,Larval,Larval,Multi-tissue,Multi-system
71536,SRR21659017,SRX17658775,SRS15191042,SRP398439,PRJNA882818,Defining function of wild type and three patient specific TP53 mutations in a zebrafish model of embryonal rhabdomyosarcoma,GSE213869,Transcriptome Analysis,RNAseq analyses comparing gene expression in zebrafish embryonal rhabdomyosarcoma tumors expressing kRASG12D/tp53 / /GFP or /kRASG12Dtp53 /  + TP53 P153?/GFP Overall design: The RNAseq samples being submitted are of zebrafish  embryonal rhabdomyosarcoma tumors generated in th CG1 syngeneic background expressing kRASG12D/tp53 / /GFP and /kRASG12Dtp53 /  + TP53 P153?/GFP,,pubmed:37266578,,p53LOF3 C,GSM6595570,,source name:rhabdomyosarcoma tumors in zebrafish|tissue:zebrafish|geo loc name:missing|collection date:missing,p53LOF3 C,Illumina Casava v1.8.2 software used for base calling All RNA seq FastQ reads were aligned with the reference genome danRer11 using TopHat2 default settings. The aligned BAM files sorted SAMTools and then processed using HTSeq count to obtain the counts per gene gene count measurements were obtained using HTSeq count Assembly: danRer11 Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq count.,rhabdomyosarcoma tumors in zebrafish,,post tissue grinding and homogenization in RNA lysis buffer  total RNA was isolated from harvested tumors using the RNAeasy Kit Qiagen; Valencia  CA according to the manufacturer’s recommendation. post quantification with Nanodrop Thermo Scientific; Rockford  IL  RNA was stored at  80ºC. Total RNA was used for RNA Seq library preparation by following the KAPA Stranded RNA Seq Kit,For expression of mutant human TP53 experiments  tumors were generated by injecting XhoI linearized rag2 kRASG12D and rag2 GFP along with Xmn1 linearized rag2 TP53 P153△  35 ng/ml of rag2 kRASG12D  15 ng/ml rag2 GFP or mutant TP53 and 10 ng/ml of rag2 GFP into the one cell stage of syngeneic zebrafish CG1/tp53 /  embryos <1 hpf Ignatius et al.  2012. Animals were monitored for tumor onset beginning at 10 dpf by scoring for GFP fluorescence under an Olympus MVX10 stereomicroscope with an X Cite series 120Q fluorescence illuminator. Scoring for tumor initiation was conducted for 60 days. 3 tumors each expressing kRASG12D/GFP/tp53 /   or kRASG12D/GFP/tp53 /  +TP53 P153△ were transplanted into secondary CG1 recipients and engrafted tumors were isolated  prepared as single cell suspensions and sorted by flowcytometry. Tumor cells were then processed to isolate RNA which was then submitted for RNAseq analyses Ignatius et al.  2012.,tissue:zebrafish|tp53 / |trunk tumor,GSM6595570,GSM6595570: p53LOF3 C; Danio rerio; RNA Seq,GSM6595570 r1,GSM6595570,1,post tissue grinding and homogenization in RNA lysis buffer  total RNA was isolated from harvested tumors using the RNAeasy Kit Qiagen; Valencia  CA according to the manufacturer's recommendation. post quantification with Nanodrop Thermo Scientific; Rockford  IL  RNA was stored at  80ºC. Total RNA was used for RNA Seq library preparation by following the KAPA Stranded RNA Seq Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP398439,,,p53LOF3_C_S40_R1.fastq,fastq,1557586665.0,30540915.0,GSM6595570 r1,0:51 1:0,A:366005467;C:370627473;G:374745850;T:445748688;N:459187,51,0,,,366005467,370627473,374745850,445748688,459187,SRX17658775,SRS15191042,SRA1503133,"Population Health Sciences, UT Health Science Center at San Antonio","Population Health Sciences, UT Health Science Center at San Antonio",1,0.92663,,0.08635,,0.70364,,0.49219,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2022-09-21,Multi-stage,Multi-stage,Multi-tissue,Multi-system
71537,SRR21659018,SRX17658774,SRS15191041,SRP398439,PRJNA882818,Defining function of wild type and three patient specific TP53 mutations in a zebrafish model of embryonal rhabdomyosarcoma,GSE213869,Transcriptome Analysis,RNAseq analyses comparing gene expression in zebrafish embryonal rhabdomyosarcoma tumors expressing kRASG12D/tp53 / /GFP or /kRASG12Dtp53 /  + TP53 P153?/GFP Overall design: The RNAseq samples being submitted are of zebrafish  embryonal rhabdomyosarcoma tumors generated in th CG1 syngeneic background expressing kRASG12D/tp53 / /GFP and /kRASG12Dtp53 /  + TP53 P153?/GFP,,pubmed:37266578,,p53LOF2 B,GSM6595569,,source name:rhabdomyosarcoma tumors in zebrafish|tissue:zebrafish|geo loc name:missing|collection date:missing,p53LOF2 B,Illumina Casava v1.8.2 software used for base calling All RNA seq FastQ reads were aligned with the reference genome danRer11 using TopHat2 default settings. The aligned BAM files sorted SAMTools and then processed using HTSeq count to obtain the counts per gene gene count measurements were obtained using HTSeq count Assembly: danRer11 Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq count.,rhabdomyosarcoma tumors in zebrafish,,post tissue grinding and homogenization in RNA lysis buffer  total RNA was isolated from harvested tumors using the RNAeasy Kit Qiagen; Valencia  CA according to the manufacturer’s recommendation. post quantification with Nanodrop Thermo Scientific; Rockford  IL  RNA was stored at  80ºC. Total RNA was used for RNA Seq library preparation by following the KAPA Stranded RNA Seq Kit,For expression of mutant human TP53 experiments  tumors were generated by injecting XhoI linearized rag2 kRASG12D and rag2 GFP along with Xmn1 linearized rag2 TP53 P153△  35 ng/ml of rag2 kRASG12D  15 ng/ml rag2 GFP or mutant TP53 and 10 ng/ml of rag2 GFP into the one cell stage of syngeneic zebrafish CG1/tp53 /  embryos <1 hpf Ignatius et al.  2012. Animals were monitored for tumor onset beginning at 10 dpf by scoring for GFP fluorescence under an Olympus MVX10 stereomicroscope with an X Cite series 120Q fluorescence illuminator. Scoring for tumor initiation was conducted for 60 days. 3 tumors each expressing kRASG12D/GFP/tp53 /   or kRASG12D/GFP/tp53 /  +TP53 P153△ were transplanted into secondary CG1 recipients and engrafted tumors were isolated  prepared as single cell suspensions and sorted by flowcytometry. Tumor cells were then processed to isolate RNA which was then submitted for RNAseq analyses Ignatius et al.  2012.,tissue:zebrafish|tp53 / |head tumor,GSM6595569,GSM6595569: p53LOF2 B; Danio rerio; RNA Seq,GSM6595569 r1,GSM6595569,1,post tissue grinding and homogenization in RNA lysis buffer  total RNA was isolated from harvested tumors using the RNAeasy Kit Qiagen; Valencia  CA according to the manufacturer's recommendation. post quantification with Nanodrop Thermo Scientific; Rockford  IL  RNA was stored at  80ºC. Total RNA was used for RNA Seq library preparation by following the KAPA Stranded RNA Seq Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP398439,,,p53LOF2_B_S43_R1.fastq,fastq,2176596615.0,42678365.0,GSM6595569 r1,0:51 1:0,A:527590046;C:499969347;G:517464206;T:630928221;N:644795,51,0,,,527590046,499969347,517464206,630928221,644795,SRX17658774,SRS15191041,SRA1503133,"Population Health Sciences, UT Health Science Center at San Antonio","Population Health Sciences, UT Health Science Center at San Antonio",1,0.92023,,0.11082,,0.71407,,0.51435,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2022-09-21,Multi-stage,Multi-stage,Multi-tissue,Multi-system
71538,SRR21659019,SRX17658773,SRS15191040,SRP398439,PRJNA882818,Defining function of wild type and three patient specific TP53 mutations in a zebrafish model of embryonal rhabdomyosarcoma,GSE213869,Transcriptome Analysis,RNAseq analyses comparing gene expression in zebrafish embryonal rhabdomyosarcoma tumors expressing kRASG12D/tp53 / /GFP or /kRASG12Dtp53 /  + TP53 P153?/GFP Overall design: The RNAseq samples being submitted are of zebrafish  embryonal rhabdomyosarcoma tumors generated in th CG1 syngeneic background expressing kRASG12D/tp53 / /GFP and /kRASG12Dtp53 /  + TP53 P153?/GFP,,pubmed:37266578,,p53LOF1 A,GSM6595568,,source name:rhabdomyosarcoma tumors in zebrafish|tissue:zebrafish|geo loc name:missing|collection date:missing,p53LOF1 A,Illumina Casava v1.8.2 software used for base calling All RNA seq FastQ reads were aligned with the reference genome danRer11 using TopHat2 default settings. The aligned BAM files sorted SAMTools and then processed using HTSeq count to obtain the counts per gene gene count measurements were obtained using HTSeq count Assembly: danRer11 Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq count.,rhabdomyosarcoma tumors in zebrafish,,post tissue grinding and homogenization in RNA lysis buffer  total RNA was isolated from harvested tumors using the RNAeasy Kit Qiagen; Valencia  CA according to the manufacturer’s recommendation. post quantification with Nanodrop Thermo Scientific; Rockford  IL  RNA was stored at  80ºC. Total RNA was used for RNA Seq library preparation by following the KAPA Stranded RNA Seq Kit,For expression of mutant human TP53 experiments  tumors were generated by injecting XhoI linearized rag2 kRASG12D and rag2 GFP along with Xmn1 linearized rag2 TP53 P153△  35 ng/ml of rag2 kRASG12D  15 ng/ml rag2 GFP or mutant TP53 and 10 ng/ml of rag2 GFP into the one cell stage of syngeneic zebrafish CG1/tp53 /  embryos <1 hpf Ignatius et al.  2012. Animals were monitored for tumor onset beginning at 10 dpf by scoring for GFP fluorescence under an Olympus MVX10 stereomicroscope with an X Cite series 120Q fluorescence illuminator. Scoring for tumor initiation was conducted for 60 days. 3 tumors each expressing kRASG12D/GFP/tp53 /   or kRASG12D/GFP/tp53 /  +TP53 P153△ were transplanted into secondary CG1 recipients and engrafted tumors were isolated  prepared as single cell suspensions and sorted by flowcytometry. Tumor cells were then processed to isolate RNA which was then submitted for RNAseq analyses Ignatius et al.  2012.,tissue:zebrafish|tp53 / |trunk tumor,GSM6595568,GSM6595568: p53LOF1 A; Danio rerio; RNA Seq,GSM6595568 r1,GSM6595568,1,post tissue grinding and homogenization in RNA lysis buffer  total RNA was isolated from harvested tumors using the RNAeasy Kit Qiagen; Valencia  CA according to the manufacturer's recommendation. post quantification with Nanodrop Thermo Scientific; Rockford  IL  RNA was stored at  80ºC. Total RNA was used for RNA Seq library preparation by following the KAPA Stranded RNA Seq Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP398439,,,p53LOF1_A_S38_R1.fastq,fastq,2113237224.0,41436024.0,GSM6595568 r1,0:51 1:0,A:497086214;C:509743114;G:493698505;T:612086517;N:622874,51,0,,,497086214,509743114,493698505,612086517,622874,SRX17658773,SRS15191040,SRA1503133,"Population Health Sciences, UT Health Science Center at San Antonio","Population Health Sciences, UT Health Science Center at San Antonio",1,0.9059,,0.08436,,0.7149,,0.51685,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2022-09-21,Multi-stage,Multi-stage,Multi-tissue,Multi-system