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
45031,SRR6466455,SRX3556412,SRS2829760,SRP128941,PRJNA428924,Danio rerio breed:TU Transcriptome or Gene expression,PRJNA428924,Transcriptome Analysis,In order to know about more basic knowledge of none/less gut adhesive strain L. casei BL23 induce on the developmental profile and immunity education in zebrafish,,,pooled of 15 intestine of juveniles  at 35 dpf old.,,Control 35,,breed:TU|age:35 dpf|sex:pooled male and female|tissue:intestine|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvae with or without xxx administration,Ctl 35,Ctl 35,Total RNA were isolated from pooled samples of larvae whole body or juvenile s intestines with TRIzol Tian Gen  Beijing  China following the manufacturer s specifications. The RNA was treated with amplification grade DNase I 1 U/ g RNA; Invitrogen  USA. RNA concentration was measured using Qubit  RNA Assay Kit in Qubit  2.0 Flurometer Life Technologies  CA  USA. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies  CA  USA. All the RNA RIN values were bigger than 9.5 as analyzed by Bioanalyzer 2100 system. For mRNAseq  equal volume and amount 1 g of total RNA from 4 sample pools of each treatment group were mixed as a sequencing sample.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP128941,,,ZFGCK_1.fq.gz ZFGCK_2.fq.gz,fastq fastq,4031784000.0,16127136.0,ZFGCK 2.fq.gz,0:125 1:125,A:1069662566;C:940723613;G:944143624;T:1077192856;N:61341,125,125,,,1069662566,940723613,944143624,1077192856,61341,SRX3556412,SRS2829760,SRA646164,Chinese Academy of Agricultural Sciences|Key Laboratory for Feed Biotechnology of the Minis,Chinese Academy of Agricultural Sciences,2,0.93591,0.9405,0.06779,0.06732,0.72157,0.72372,0.53789,0.52813,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2018-01-12,Juvenile,Juvenile,Gut,Digestive System
45032,SRR6466456,SRX3556411,SRS2829759,SRP128941,PRJNA428924,Danio rerio breed:TU Transcriptome or Gene expression,PRJNA428924,Transcriptome Analysis,In order to know about more basic knowledge of none/less gut adhesive strain L. casei BL23 induce on the developmental profile and immunity education in zebrafish,,,pooled of 15 intestine of juveniles at 35 dpf old with BL23 administration,,BL23 35,,breed:TU|age:35 dpf|sex:pooled male and female|tissue:intestine|treatment:BL23 administration|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvae with or without xxx administration,BL23 35,BL23 35,Total RNA were isolated from pooled samples of larvae whole body or juvenile s intestines with TRIzol Tian Gen  Beijing  China following the manufacturer s specifications. The RNA was treated with amplification grade DNase I 1 U/ g RNA; Invitrogen  USA. RNA concentration was measured using Qubit  RNA Assay Kit in Qubit  2.0 Flurometer Life Technologies  CA  USA. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies  CA  USA. All the RNA RIN values were bigger than 9.5 as analyzed by Bioanalyzer 2100 system. For mRNAseq  equal volume and amount 1 g of total RNA from 4 sample pools of each treatment group were mixed as a sequencing sample.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP128941,,,ZFGBL23_1.fq.gz ZFGBL23_2.fq.gz,fastq fastq,3545702250.0,14182809.0,ZFGBL23 1.fq.gz,0:125 1:125,A:931928697;C:835347026;G:838503871;T:939869548;N:53108,125,125,,,931928697,835347026,838503871,939869548,53108,SRX3556411,SRS2829759,SRA646164,Chinese Academy of Agricultural Sciences|Key Laboratory for Feed Biotechnology of the Minis,Chinese Academy of Agricultural Sciences,2,0.94166,0.94611,0.05678,0.05657,0.71652,0.71894,0.51987,0.53609,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2018-01-12,Juvenile,Juvenile,Gut,Digestive System
62624,SRR13249700,SRX9681375,SRS7879224,SRP297857,PRJNA685060,Transcriptome of Zebrafish Intestine under Fe'i and Cavendish Banana Diet,GSE163139,Transcriptome Analysis,Fe'i banana Musa troglodytarum fruit is carotenoid rich and has been proposed to be utilized as a functional food. We report the first transcriptome of zebrafish Danio rerio intestine that were subjected to 8 weeks of Fe'i banana and Cavendish Musa acuminata diet. We found that Fe'i consumption in zebrafish modulated genes related to innate immunity. Overall design: Adult healthy zebrafish were divided into 3 diet groups: commercial feed CO  Cavendish CV  and Fe'i banana FE. Zebrafish in commercial feed diet group was used as control and fed Tetramin Tetra  Germany. Ripe Cavendish and Fe'i fruit pulp were mixed with commercial feed into 50% banana containing granule by lyophilization. Treatment lasted for 8 weeks. At day 56  total RNA of intestine from each diet group were sequenced. Transcriptome assembly were done using Tophat Cufflink pipeline.,,,,Zebrafish Intestine   FE,GSM4972509,,tissue:intestine|Stage:Day 56 of diet treatment|treatment:Fe'i diet 50% Tetramin  50% Fe'i fruit pulp|organ:intestine,Zebrafish Intestine   FE,Raw paired end reads were examined for base score  adapter content  and overrepresented sequences with FastQC v0.11.5 Clean reads were aligned to zebrafish genome reference using Tophat2 v2.1.0 with default parameters Transcriptome assembly and gene expression quantification were calculated with Cufflink v2.2.1 in default parameters. Abundance were calculated in fragments per kilobase of transcript per million reads FPKM. Genes were considered differentially expressed if log2FC>1.5 Genome build: Danio rerio GRCz11 GCA 000002035.4 Supplementary files format and content: tab deliminated files containing gene ID  gene short name  locus  and FPKM,intestine,Zebrafish were divided into 3 treatment groups  i.e. control  Cavendish diet  and Fe'i diet. Control zebrafish CO were fed commercial feed Tetramin Tetra  Germany. Zebrafish in Cavendish diet group CV received Cavendish containing granule. Similarly  zebrafish in Fe'i diet group FE were fed Fe'i containing granule. Banana containing granule were prepared from fruit pulp according to Tanaika et al. 2011. The resulting granule contains 50% banana fruit pulp to Tetramin. All feeds were given as much as 4% of body weight per day  divided into three daily feedings.,Zebrafish from each feeding group were fasted for 24 hours. Zebrafish were euthanized with 0.4% MS 222. Intestines were isolated and immersed in RNALater until extraction of RNA. Total RNA was isolated using GeneJET RNA Purification kit according to manufacturer's protocol ThermoFisher Scientific. 1µg of total RNA with RIN values above 7 were used for library preparation. PolyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module. NGS library preparation were constructed with NEBNext Ultra RNA Library Prep Kit for Illumina,Healthy adult zebrafish of 6 mpf 9 mpf were maintained under established protocols Avdesh et al.  2012. Lightning conditions were 14:10 hour light:dark.,Stage:Day 56 of diet treatment|treatment:Fe'i diet 50% Tetramin  50% Fe'i fruit pulp|organ:intestine,GSM4972509,GSM4972509: Zebrafish Intestine   FE; Danio rerio; RNA Seq,GSM4972509,,1,Zebrafish from each feeding group were fasted for 24 hours. Zebrafish were euthanized with 0.4% MS 222. Intestines were isolated and immersed in RNALater until extraction of RNA. Total RNA was isolated using GeneJET RNA Purification kit according to manufacturer's protocol ThermoFisher Scientific. 1µg of total RNA with RIN values above 7 were used for library preparation. PolyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module. NGS library preparation were constructed with NEBNext Ultra RNA Library Prep Kit for Illumina,GEO Accession:GSM4972509,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP297857,,,RNA-FE_1.fq.gz RNA-FE_2.fq.gz,fastq fastq,5800596300.0,19335321.0,GSM4972509 r1,0:150 1:150,A:1554664525;C:1338284097;G:1358262189;T:1549016351;N:369138,150,150,,,1554664525,1338284097,1358262189,1549016351,369138,SRX9681375,SRS7879224,SRA1173924,GEO,"School of Life Sciences and Technology, Institut Teknologi Bandung",2,0.9162,0.9111,0.05227,0.05272,0.76163,0.76974,0.46637,0.47062,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Indonesia,2020-12-14,Juvenile,Juvenile,Gut,Digestive System
62625,SRR13249699,SRX9681374,SRS7879223,SRP297857,PRJNA685060,Transcriptome of Zebrafish Intestine under Fe'i and Cavendish Banana Diet,GSE163139,Transcriptome Analysis,Fe'i banana Musa troglodytarum fruit is carotenoid rich and has been proposed to be utilized as a functional food. We report the first transcriptome of zebrafish Danio rerio intestine that were subjected to 8 weeks of Fe'i banana and Cavendish Musa acuminata diet. We found that Fe'i consumption in zebrafish modulated genes related to innate immunity. Overall design: Adult healthy zebrafish were divided into 3 diet groups: commercial feed CO  Cavendish CV  and Fe'i banana FE. Zebrafish in commercial feed diet group was used as control and fed Tetramin Tetra  Germany. Ripe Cavendish and Fe'i fruit pulp were mixed with commercial feed into 50% banana containing granule by lyophilization. Treatment lasted for 8 weeks. At day 56  total RNA of intestine from each diet group were sequenced. Transcriptome assembly were done using Tophat Cufflink pipeline.,,,,Zebrafish Intestine   CV,GSM4972508,,tissue:intestine|Stage:Day 56 of diet treatment|treatment:Cavendish diet 50% Tetramin  50% Cavendish fruit pulp|organ:intestine,Zebrafish Intestine   CV,Raw paired end reads were examined for base score  adapter content  and overrepresented sequences with FastQC v0.11.5 Clean reads were aligned to zebrafish genome reference using Tophat2 v2.1.0 with default parameters Transcriptome assembly and gene expression quantification were calculated with Cufflink v2.2.1 in default parameters. Abundance were calculated in fragments per kilobase of transcript per million reads FPKM. Genes were considered differentially expressed if log2FC>1.5 Genome build: Danio rerio GRCz11 GCA 000002035.4 Supplementary files format and content: tab deliminated files containing gene ID  gene short name  locus  and FPKM,intestine,Zebrafish were divided into 3 treatment groups  i.e. control  Cavendish diet  and Fe'i diet. Control zebrafish CO were fed commercial feed Tetramin Tetra  Germany. Zebrafish in Cavendish diet group CV received Cavendish containing granule. Similarly  zebrafish in Fe'i diet group FE were fed Fe'i containing granule. Banana containing granule were prepared from fruit pulp according to Tanaika et al. 2011. The resulting granule contains 50% banana fruit pulp to Tetramin. All feeds were given as much as 4% of body weight per day  divided into three daily feedings.,Zebrafish from each feeding group were fasted for 24 hours. Zebrafish were euthanized with 0.4% MS 222. Intestines were isolated and immersed in RNALater until extraction of RNA. Total RNA was isolated using GeneJET RNA Purification kit according to manufacturer's protocol ThermoFisher Scientific. 1µg of total RNA with RIN values above 7 were used for library preparation. PolyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module. NGS library preparation were constructed with NEBNext Ultra RNA Library Prep Kit for Illumina,Healthy adult zebrafish of 6 mpf 9 mpf were maintained under established protocols Avdesh et al.  2012. Lightning conditions were 14:10 hour light:dark.,Stage:Day 56 of diet treatment|treatment:Cavendish diet 50% Tetramin  50% Cavendish fruit pulp|organ:intestine,GSM4972508,GSM4972508: Zebrafish Intestine   CV; Danio rerio; RNA Seq,GSM4972508,,1,Zebrafish from each feeding group were fasted for 24 hours. Zebrafish were euthanized with 0.4% MS 222. Intestines were isolated and immersed in RNALater until extraction of RNA. Total RNA was isolated using GeneJET RNA Purification kit according to manufacturer's protocol ThermoFisher Scientific. 1µg of total RNA with RIN values above 7 were used for library preparation. PolyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module. NGS library preparation were constructed with NEBNext Ultra RNA Library Prep Kit for Illumina,GEO Accession:GSM4972508,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP297857,,,RNA-CV_1.fq.gz RNA-CV_2.fq.gz,fastq fastq,8700195600.0,29000652.0,GSM4972508 r1,0:150 1:150,A:2300738433;C:2030008598;G:2063236046;T:2305470240;N:742283,150,150,,,2300738433,2030008598,2063236046,2305470240,742283,SRX9681374,SRS7879223,SRA1173924,GEO,"School of Life Sciences and Technology, Institut Teknologi Bandung",2,0.91916,0.91872,0.04907,0.04902,0.75595,0.76051,0.50144,0.50578,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Indonesia,2020-12-14,Juvenile,Juvenile,Gut,Digestive System
62626,SRR13249698,SRX9681373,SRS7879222,SRP297857,PRJNA685060,Transcriptome of Zebrafish Intestine under Fe'i and Cavendish Banana Diet,GSE163139,Transcriptome Analysis,Fe'i banana Musa troglodytarum fruit is carotenoid rich and has been proposed to be utilized as a functional food. We report the first transcriptome of zebrafish Danio rerio intestine that were subjected to 8 weeks of Fe'i banana and Cavendish Musa acuminata diet. We found that Fe'i consumption in zebrafish modulated genes related to innate immunity. Overall design: Adult healthy zebrafish were divided into 3 diet groups: commercial feed CO  Cavendish CV  and Fe'i banana FE. Zebrafish in commercial feed diet group was used as control and fed Tetramin Tetra  Germany. Ripe Cavendish and Fe'i fruit pulp were mixed with commercial feed into 50% banana containing granule by lyophilization. Treatment lasted for 8 weeks. At day 56  total RNA of intestine from each diet group were sequenced. Transcriptome assembly were done using Tophat Cufflink pipeline.,,,,Zebrafish Intestine   CO,GSM4972507,,tissue:intestine|Stage:Day 56 of diet treatment|treatment:Control Tetramin|organ:intestine,Zebrafish Intestine   CO,Raw paired end reads were examined for base score  adapter content  and overrepresented sequences with FastQC v0.11.5 Clean reads were aligned to zebrafish genome reference using Tophat2 v2.1.0 with default parameters Transcriptome assembly and gene expression quantification were calculated with Cufflink v2.2.1 in default parameters. Abundance were calculated in fragments per kilobase of transcript per million reads FPKM. Genes were considered differentially expressed if log2FC>1.5 Genome build: Danio rerio GRCz11 GCA 000002035.4 Supplementary files format and content: tab deliminated files containing gene ID  gene short name  locus  and FPKM,intestine,Zebrafish were divided into 3 treatment groups  i.e. control  Cavendish diet  and Fe'i diet. Control zebrafish CO were fed commercial feed Tetramin Tetra  Germany. Zebrafish in Cavendish diet group CV received Cavendish containing granule. Similarly  zebrafish in Fe'i diet group FE were fed Fe'i containing granule. Banana containing granule were prepared from fruit pulp according to Tanaika et al. 2011. The resulting granule contains 50% banana fruit pulp to Tetramin. All feeds were given as much as 4% of body weight per day  divided into three daily feedings.,Zebrafish from each feeding group were fasted for 24 hours. Zebrafish were euthanized with 0.4% MS 222. Intestines were isolated and immersed in RNALater until extraction of RNA. Total RNA was isolated using GeneJET RNA Purification kit according to manufacturer's protocol ThermoFisher Scientific. 1µg of total RNA with RIN values above 7 were used for library preparation. PolyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module. NGS library preparation were constructed with NEBNext Ultra RNA Library Prep Kit for Illumina,Healthy adult zebrafish of 6 mpf 9 mpf were maintained under established protocols Avdesh et al.  2012. Lightning conditions were 14:10 hour light:dark.,Stage:Day 56 of diet treatment|treatment:Control Tetramin|organ:intestine,GSM4972507,GSM4972507: Zebrafish Intestine   CO; Danio rerio; RNA Seq,GSM4972507,,1,Zebrafish from each feeding group were fasted for 24 hours. Zebrafish were euthanized with 0.4% MS 222. Intestines were isolated and immersed in RNALater until extraction of RNA. Total RNA was isolated using GeneJET RNA Purification kit according to manufacturer's protocol ThermoFisher Scientific. 1µg of total RNA with RIN values above 7 were used for library preparation. PolyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module. NGS library preparation were constructed with NEBNext Ultra RNA Library Prep Kit for Illumina,GEO Accession:GSM4972507,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP297857,,,RNA-CO_1.fq.gz RNA-CO_2.fq.gz,fastq fastq,7003647000.0,23345490.0,GSM4972507 r1,0:150 1:150,A:1878060990;C:1612454288;G:1638556904;T:1874134817;N:440001,150,150,,,1878060990,1612454288,1638556904,1874134817,440001,SRX9681373,SRS7879222,SRA1173924,GEO,"School of Life Sciences and Technology, Institut Teknologi Bandung",2,0.91405,0.91527,0.04852,0.04901,0.7624,0.76794,0.47424,0.49842,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Indonesia,2020-12-14,Juvenile,Juvenile,Gut,Digestive System
62742,SRR13360748,SRX9785053,SRS7972286,SRP300470,PRJNA689790,Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish,PRJNA689790,Other,We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.,,,,macrogard,macrogard2,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,PM2,PM2,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP300470,,,pm2_S8_R1_001.fastq.gz,fastq,3517898944.0,46288144.0,pm2 S8 R1 001.fastq.gz,0:76 1:0,A:914616261;C:828363626;G:805674434;T:969167482;N:77141,76,0,,,914616261,828363626,805674434,969167482,77141,SRX9785053,SRS7972286,SRA1180489,Nord University|Faculty of Bioscience,Nord University,1,0.94008,,0.0747,,0.71394,,0.51572,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2021-01-05,Juvenile,Juvenile,Gut,Digestive System
62743,SRR13360749,SRX9785052,SRS7972285,SRP300470,PRJNA689790,Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish,PRJNA689790,Other,We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.,,,,macrogard,macrogard1,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,PM1,PM1,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP300470,,,pm1_S7_R1_001.fastq.gz,fastq,1974822380.0,25984505.0,pm1 S7 R1 001.fastq.gz,0:76 1:0,A:561606319;C:416363486;G:408486827;T:588324386;N:41362,76,0,,,561606319,416363486,408486827,588324386,41362,SRX9785052,SRS7972285,SRA1180489,Nord University|Faculty of Bioscience,Nord University,1,0.9274,,0.16109,,0.74351,,0.57108,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2021-01-05,Juvenile,Juvenile,Gut,Digestive System
62744,SRR13360750,SRX9785051,SRS7972284,SRP300470,PRJNA689790,Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish,PRJNA689790,Other,We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.,,,,soybean,soybean4,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,CP4,CP4,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP300470,,,cp4_S4_R1_001.fastq.gz,fastq,2913402316.0,38334241.0,cp4 S4 R1 001.fastq.gz,0:76 1:0,A:791131658;C:648321809;G:621173454;T:852725371;N:50024,76,0,,,791131658,648321809,621173454,852725371,50024,SRX9785051,SRS7972284,SRA1180489,Nord University|Faculty of Bioscience,Nord University,1,0.93191,,0.1275,,0.7333,,0.55298,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2021-01-05,Juvenile,Juvenile,Gut,Digestive System
62745,SRR13360751,SRX9785050,SRS7972283,SRP300470,PRJNA689790,Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish,PRJNA689790,Other,We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.,,,,soybean,soybean3,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,CP3,CP3,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP300470,,,cp3_S6_R1_001.fastq.gz,fastq,2648220684.0,34845009.0,cp3 S6 R1 001.fastq.gz,0:76 1:0,A:697194378;C:597685138;G:585283565;T:767999519;N:58084,76,0,,,697194378,597685138,585283565,767999519,58084,SRX9785050,SRS7972283,SRA1180489,Nord University|Faculty of Bioscience,Nord University,1,0.93629,,0.1048,,0.7349,,0.54364,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2021-01-05,Juvenile,Juvenile,Gut,Digestive System
62746,SRR13360752,SRX9785049,SRS7972282,SRP300470,PRJNA689790,Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish,PRJNA689790,Other,We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.,,,,soybean,soybean2,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,CP2,CP2,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP300470,,,cp2_S5_R1_001.fastq.gz,fastq,2339410872.0,30781722.0,cp2 S5 R1 001.fastq.gz,0:76 1:0,A:620056592;C:539298564;G:520500416;T:659503250;N:52050,76,0,,,620056592,539298564,520500416,659503250,52050,SRX9785049,SRS7972282,SRA1180489,Nord University|Faculty of Bioscience,Nord University,1,0.93909,,0.0916,,0.70942,,0.51709,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2021-01-05,Juvenile,Juvenile,Gut,Digestive System
62747,SRR13360753,SRX9785048,SRS7972281,SRP300470,PRJNA689790,Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish,PRJNA689790,Other,We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.,,,,soybean,soybean1,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:soybeanCP replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,CP1,CP1,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP300470,,,cp1_S4_R1_001.fastq.gz,fastq,2271445592.0,29887442.0,cp1 S4 R1 001.fastq.gz,0:76 1:0,A:620595380;C:508382666;G:499686333;T:642731924;N:49289,76,0,,,620595380,508382666,499686333,642731924,49289,SRX9785048,SRS7972281,SRA1180489,Nord University|Faculty of Bioscience,Nord University,1,0.93497,,0.1129,,0.71127,,0.50787,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2021-01-05,Juvenile,Juvenile,Gut,Digestive System
62748,SRR13360754,SRX9785047,SRS7972280,SRP300470,PRJNA689790,Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish,PRJNA689790,Other,We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.,,,,control,control4,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,CZ4,CZ4,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP300470,,,cz4_S1_R1_001.fastq.gz,fastq,2772612848.0,36481748.0,cz4 S1 R1 001.fastq.gz,0:76 1:0,A:753409223;C:625962831;G:590503241;T:802690640;N:46913,76,0,,,753409223,625962831,590503241,802690640,46913,SRX9785047,SRS7972280,SRA1180489,Nord University|Faculty of Bioscience,Nord University,1,0.92942,,0.15362,,0.62889,,0.51867,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2021-01-05,Juvenile,Juvenile,Gut,Digestive System
62749,SRR13360755,SRX9785046,SRS7972279,SRP300470,PRJNA689790,Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish,PRJNA689790,Other,We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.,,,,control,control3,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,CZ3,CZ3,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP300470,,,cz3_S3_R1_001.fastq.gz,fastq,2424287672.0,31898522.0,cz3 S3 R1 001.fastq.gz,0:76 1:0,A:629966430;C:571438897;G:558947157;T:663881953;N:53235,76,0,,,629966430,571438897,558947157,663881953,53235,SRX9785046,SRS7972279,SRA1180489,Nord University|Faculty of Bioscience,Nord University,1,0.94199,,0.04836,,0.72218,,0.48478,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2021-01-05,Juvenile,Juvenile,Gut,Digestive System
62750,SRR13360756,SRX9785045,SRS7972278,SRP300470,PRJNA689790,Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish,PRJNA689790,Other,We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.,,,,macrogard,macrogard4,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,PM4,PM4,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP300470,,,pm4_S7_R1_001.fastq.gz,fastq,2901513560.0,38177810.0,pm4 S7 R1 001.fastq.gz,0:76 1:0,A:737189471;C:698799076;G:664901115;T:800575145;N:48753,76,0,,,737189471,698799076,664901115,800575145,48753,SRX9785045,SRS7972278,SRA1180489,Nord University|Faculty of Bioscience,Nord University,1,0.95173,,0.04367,,0.74089,,0.50116,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2021-01-05,Juvenile,Juvenile,Gut,Digestive System
62751,SRR13360757,SRX9785044,SRS7972277,SRP300470,PRJNA689790,Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish,PRJNA689790,Other,We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.,,,,macrogard,macrogard3,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:macrogardPM replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,PM3,PM3,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP300470,,,pm3_S9_R1_001.fastq.gz,fastq,3148390744.0,41426194.0,pm3 S9 R1 001.fastq.gz,0:76 1:0,A:834545372;C:725073648;G:704241250;T:884462724;N:67750,76,0,,,834545372,725073648,704241250,884462724,67750,SRX9785044,SRS7972277,SRA1180489,Nord University|Faculty of Bioscience,Nord University,1,0.94256,,0.09248,,0.72099,,0.52303,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2021-01-05,Juvenile,Juvenile,Gut,Digestive System
62752,SRR13360758,SRX9785043,SRS7972276,SRP300470,PRJNA689790,Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish,PRJNA689790,Other,We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.,,,,control,control2,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,CZ2,CZ2,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP300470,,,cz2_S2_R1_001.fastq,fastq,2207708116.0,29048791.0,cz2 S2 R1 001.fastq,0:76 1:0,A:614048827;C:488071931;G:474165427;T:631372646;N:49285,76,0,,,614048827,488071931,474165427,631372646,49285,SRX9785043,SRS7972276,SRA1180489,Nord University|Faculty of Bioscience,Nord University,1,0.93271,,0.12538,,0.71733,,0.53166,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2021-01-05,Juvenile,Juvenile,Gut,Digestive System
62753,SRR13360759,SRX9785042,SRS7972275,SRP300470,PRJNA689790,Elucidating the effects of microbe derived glucans on the gut microbiota and the immune system of zebrafish,PRJNA689790,Other,We present a holistic picture of soybean induced changes in the intestine of juvenile zebrafish and the effect of yeast beta glucan through a transcriptomic approach. Dietary soybean altered the expression of specific GTP binding genes which are known to initiate inflammatory responses in the intestinal tissue. The intestinal barrier function appears to be affected by the modulation of mucin genes and genes linked to junction proteins. Furthermore  the inclusion of soybean meal affected metabolic genes that are related to oxidative stress and genes related to lipid metabolism  namely arl4ca and elovl6 in the intestinal tissue. Genes that counter inflammation were also upregulated in the soybean fed group. Our study also explains the plausible effect of yeast beta glucan on the intestinal barrier through regulation of immune responses and autophagy  and strengthening of the mucosal barrier. Our findings indicate a subdued inflammation in juvenile zebrafish fed soybean meal and a strengthened mucosal barrier in the fish fed yeast beta glucan.,,,,control,control1,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:50 days|dev stage:Juvenile|sex:not applicable|tissue:intestine|collected by:Saima Nord University|collection date:2019 11|treatment:controlCZ replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,CZ1,CZ1,PCR enrichment of adaptor ligated DNA,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP300470,,,cz1_S1_R1_001.fastq.gz,fastq,2264115696.0,29790996.0,cz1 S1 R1 001.fastq.gz,0:76 1:0,A:619936364;C:496981021;G:501038961;T:646109550;N:49800,76,0,,,619936364,496981021,501038961,646109550,49800,SRX9785042,SRS7972275,SRA1180489,Nord University|Faculty of Bioscience,Nord University,1,0.93737,,0.1307,,0.73003,,0.55416,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2021-01-05,Juvenile,Juvenile,Gut,Digestive System