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
28093,SRR26196850,SRX21908248,SRS18993956,SRP463504,PRJNA1021586,Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish,GSE244171,Transcriptome Analysis,Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:38868197,,elipsa mutant  clutch 4,GSM7808262,,source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing,elipsa mutant  clutch 4,Standard processing by BGI.p HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,tissue:whole larvae|genotype: / |treatment:no treatment,GSM7808262,GSM7808262: elipsa mutant  clutch 4; Danio rerio; RNA Seq,GSM7808262 r1,GSM7808262,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP463504,,,ElipsaMUT4_1.fq.gz ElipsaMUT4_2.fq.gz,fastq fastq,4536153000.0,22680765.0,GSM7808262 r1,0:100 1:100,A:1194964224;C:1059904764;G:1074108947;T:1207175065;N:0,100,100,,,1194964224,1059904764,1074108947,1207175065,0,SRX21908248,SRS18993956,SRA1721841,NTNU,NTNU,2,0.93991,0.94735,0.10392,0.10318,0.66434,0.66344,0.48911,0.49311,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-09-27,Larval,Larval,Whole Organism,All anatomical structures
28094,SRR26196851,SRX21908247,SRS18993955,SRP463504,PRJNA1021586,Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish,GSE244171,Transcriptome Analysis,Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:38868197,,elipsa mutant  clutch 3,GSM7808261,,source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing,elipsa mutant  clutch 3,Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,tissue:whole larvae|genotype: / |treatment:no treatment,GSM7808261,GSM7808261: elipsa mutant  clutch 3; Danio rerio; RNA Seq,GSM7808261 r1,GSM7808261,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP463504,,,ElipsaMUT3_1.fq.gz ElipsaMUT3_2.fq.gz,fastq fastq,4547581600.0,22737908.0,GSM7808261 r1,0:100 1:100,A:1183476304;C:1077021222;G:1092963681;T:1194120393;N:0,100,100,,,1183476304,1077021222,1092963681,1194120393,0,SRX21908247,SRS18993955,SRA1721841,NTNU,NTNU,2,0.95029,0.95874,0.09085,0.09059,0.66856,0.66722,0.48534,0.48545,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-09-27,Larval,Larval,Whole Organism,All anatomical structures
28095,SRR26196852,SRX21908246,SRS18993954,SRP463504,PRJNA1021586,Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish,GSE244171,Transcriptome Analysis,Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:38868197,,elipsa mutant  clutch 2,GSM7808260,,source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing,elipsa mutant  clutch 2,Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,tissue:whole larvae|genotype: / |treatment:no treatment,GSM7808260,GSM7808260: elipsa mutant  clutch 2; Danio rerio; RNA Seq,GSM7808260 r1,GSM7808260,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP463504,,,ElipsaMUT2_1.fq.gz ElipsaMUT2_2.fq.gz,fastq fastq,4544444600.0,22722223.0,GSM7808260 r1,0:100 1:100,A:1186329827;C:1072965608;G:1087757513;T:1197391652;N:0,100,100,,,1186329827,1072965608,1087757513,1197391652,0,SRX21908246,SRS18993954,SRA1721841,NTNU,NTNU,2,0.94545,0.95403,0.09705,0.09653,0.66576,0.66466,0.47893,0.47882,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-09-27,Larval,Larval,Whole Organism,All anatomical structures
28096,SRR26196853,SRX21908245,SRS18993953,SRP463504,PRJNA1021586,Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish,GSE244171,Transcriptome Analysis,Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:38868197,,elipsa mutant  clutch 1,GSM7808259,,source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing,elipsa mutant  clutch 1,Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,tissue:whole larvae|genotype: / |treatment:no treatment,GSM7808259,GSM7808259: elipsa mutant  clutch 1; Danio rerio; RNA Seq,GSM7808259 r1,GSM7808259,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP463504,,,ElipsaMUT1_1.fq.gz ElipsaMUT1_2.fq.gz,fastq fastq,4561346400.0,22806732.0,GSM7808259 r1,0:100 1:100,A:1192227498;C:1073309826;G:1091718946;T:1204090130;N:0,100,100,,,1192227498,1073309826,1091718946,1204090130,0,SRX21908245,SRS18993953,SRA1721841,NTNU,NTNU,2,0.94079,0.94928,0.09838,0.09859,0.67093,0.66975,0.47837,0.4824,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-09-27,Larval,Larval,Whole Organism,All anatomical structures
28097,SRR26196854,SRX21908244,SRS18993950,SRP463504,PRJNA1021586,Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish,GSE244171,Transcriptome Analysis,Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:38868197,,elipsa control  clutch 4,GSM7808258,,source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing,elipsa control  clutch 4,Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment,GSM7808258,GSM7808258: elipsa control  clutch 4; Danio rerio; RNA Seq,GSM7808258 r1,GSM7808258,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP463504,,,ElipsaCTRL4_1.fq.gz ElipsaCTRL4_2.fq.gz,fastq fastq,4534543600.0,22672718.0,GSM7808258 r1,0:100 1:100,A:1195456125;C:1060510332;G:1073683545;T:1204893598;N:0,100,100,,,1195456125,1060510332,1073683545,1204893598,0,SRX21908244,SRS18993950,SRA1721841,NTNU,NTNU,2,0.94686,0.95523,0.0948,0.09459,0.66259,0.66093,0.49251,0.49154,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-09-27,Larval,Larval,Whole Organism,All anatomical structures
28098,SRR26196855,SRX21908243,SRS18993952,SRP463504,PRJNA1021586,Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish,GSE244171,Transcriptome Analysis,Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:38868197,,elipsa control  clutch 3,GSM7808257,,source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing,elipsa control  clutch 3,Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment,GSM7808257,GSM7808257: elipsa control  clutch 3; Danio rerio; RNA Seq,GSM7808257 r1,GSM7808257,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP463504,,,ElipsaCTRL3_1.fq.gz ElipsaCTRL3_2.fq.gz,fastq fastq,4546464800.0,22732324.0,GSM7808257 r1,0:100 1:100,A:1192169234;C:1070218166;G:1081895902;T:1202181498;N:0,100,100,,,1192169234,1070218166,1081895902,1202181498,0,SRX21908243,SRS18993952,SRA1721841,NTNU,NTNU,2,0.94937,0.95815,0.09867,0.09825,0.66574,0.66478,0.49056,0.48959,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-09-27,Larval,Larval,Whole Organism,All anatomical structures
28099,SRR26196856,SRX21908242,SRS18993951,SRP463504,PRJNA1021586,Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish,GSE244171,Transcriptome Analysis,Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:38868197,,elipsa control  clutch 2,GSM7808256,,source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing,elipsa control  clutch 2,Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment,GSM7808256,GSM7808256: elipsa control  clutch 2; Danio rerio; RNA Seq,GSM7808256 r1,GSM7808256,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP463504,,,ElipsaCTRL2_1.fq.gz ElipsaCTRL2_2.fq.gz,fastq fastq,4557679200.0,22788396.0,GSM7808256 r1,0:100 1:100,A:1184954651;C:1080955864;G:1098377272;T:1193391413;N:0,100,100,,,1184954651,1080955864,1098377272,1193391413,0,SRX21908242,SRS18993951,SRA1721841,NTNU,NTNU,2,0.94378,0.95076,0.0855,0.0847,0.66604,0.66342,0.48858,0.48404,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-09-27,Larval,Larval,Whole Organism,All anatomical structures
28100,SRR26196857,SRX21908241,SRS18993949,SRP463504,PRJNA1021586,Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish,GSE244171,Transcriptome Analysis,Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:38868197,,elipsa control  clutch 1,GSM7808255,,source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing,elipsa control  clutch 1,Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment,GSM7808255,GSM7808255: elipsa control  clutch 1; Danio rerio; RNA Seq,GSM7808255 r1,GSM7808255,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP463504,,,ElipsaCTRL1_1.fq.gz ElipsaCTRL1_2.fq.gz,fastq fastq,4566618600.0,22833093.0,GSM7808255 r1,0:100 1:100,A:1193092402;C:1076659586;G:1094193492;T:1202673120;N:0,100,100,,,1193092402,1076659586,1094193492,1202673120,0,SRX21908241,SRS18993949,SRA1721841,NTNU,NTNU,2,0.94269,0.94899,0.09816,0.09712,0.66991,0.66925,0.47671,0.46995,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-09-27,Larval,Larval,Whole Organism,All anatomical structures
28794,SRR26685983,SRX22385777,SRS19431939,SRP470412,PRJNA1036238,RNAseq of Wild Type and  pikfyve?8 zebrafish.,GSE247110,Transcriptome Analysis,Purpose: Phosphoinositide kinase  FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient  pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.,,,,pikfyve3,GSM7883488,,source name:genotype|tissue:genotype|genotype:pikfyve delta8|geo loc name:missing|collection date:missing,pikfyve3,Data filtering  The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5%  postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification  Bowtie2[2] was applied to align the clean reads to the gene set  in which known and novel  coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially  differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype  GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample,genotype,,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products.                                                                            2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair  Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced  while uncyclized linear DNA molecules are digested. 9 Sequencing,,tissue:genotype|genotype:pikfyve delta8,GSM7883488,GSM7883488: pikfyve3; Danio rerio; RNA Seq,GSM7883488 r1,GSM7883488,1,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products.                                                                            2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair  Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced  while uncyclized linear DNA molecules are digested. 9 Sequencing,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP470412,,,pikfyve3_1.fq.gz pikfyve3_2.fq.gz,fastq fastq,6618846900.0,22062823.0,GSM7883488 r1,0:150 1:150,A:1763884594;C:1537497822;G:1533232898;T:1784136042;N:95544,150,150,,,1763884594,1537497822,1533232898,1784136042,95544,SRX22385777,SRS19431939,SRA1746433,"The Second Clinical Medical College, Jinan University","The Second Clinical Medical College, Jinan University",2,0.93396,0.92718,0.09419,0.09305,0.66348,0.66496,0.48704,0.4839,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-06,Undetermined,Undetermined,Undetermined,Undetermined
28795,SRR26685984,SRX22385776,SRS19431938,SRP470412,PRJNA1036238,RNAseq of Wild Type and  pikfyve?8 zebrafish.,GSE247110,Transcriptome Analysis,Purpose: Phosphoinositide kinase  FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient  pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.,,,,pikfyve2,GSM7883487,,source name:genotype|tissue:genotype|genotype:pikfyve delta8|geo loc name:missing|collection date:missing,pikfyve2,Data filtering  The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5%  postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification  Bowtie2[2] was applied to align the clean reads to the gene set  in which known and novel  coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially  differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype  GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample,genotype,,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products.                                                                            2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair  Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced  while uncyclized linear DNA molecules are digested. 9 Sequencing,,tissue:genotype|genotype:pikfyve delta8,GSM7883487,GSM7883487: pikfyve2; Danio rerio; RNA Seq,GSM7883487 r1,GSM7883487,1,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products.                                                                            2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair  Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced  while uncyclized linear DNA molecules are digested. 9 Sequencing,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP470412,,,pikfyve2_1.fq.gz pikfyve2_2.fq.gz,fastq fastq,6640406100.0,22134687.0,GSM7883487 r1,0:150 1:150,A:1765647548;C:1547424271;G:1541609810;T:1785639698;N:84773,150,150,,,1765647548,1547424271,1541609810,1785639698,84773,SRX22385776,SRS19431938,SRA1746433,"The Second Clinical Medical College, Jinan University","The Second Clinical Medical College, Jinan University",2,0.93535,0.92946,0.08654,0.08582,0.67127,0.67298,0.48517,0.48183,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-06,Undetermined,Undetermined,Undetermined,Undetermined
28796,SRR26685985,SRX22385775,SRS19431937,SRP470412,PRJNA1036238,RNAseq of Wild Type and  pikfyve?8 zebrafish.,GSE247110,Transcriptome Analysis,Purpose: Phosphoinositide kinase  FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient  pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.,,,,pikfyve1,GSM7883486,,source name:genotype|tissue:genotype|genotype:pikfyve delta8|geo loc name:missing|collection date:missing,pikfyve1,Data filtering  The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5%  postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification  Bowtie2[2] was applied to align the clean reads to the gene set  in which known and novel  coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially  differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype  GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample,genotype,,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products.                                                                            2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair  Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced  while uncyclized linear DNA molecules are digested. 9 Sequencing,,tissue:genotype|genotype:pikfyve delta8,GSM7883486,GSM7883486: pikfyve1; Danio rerio; RNA Seq,GSM7883486 r1,GSM7883486,1,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products.                                                                            2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair  Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced  while uncyclized linear DNA molecules are digested. 9 Sequencing,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP470412,,,pikfyve1_1.fq.gz pikfyve1_2.fq.gz,fastq fastq,6629613600.0,22098712.0,GSM7883486 r1,0:150 1:150,A:1765377736;C:1543131511;G:1535515864;T:1785505926;N:82563,150,150,,,1765377736,1543131511,1535515864,1785505926,82563,SRX22385775,SRS19431937,SRA1746433,"The Second Clinical Medical College, Jinan University","The Second Clinical Medical College, Jinan University",2,0.93638,0.92994,0.08782,0.08654,0.67138,0.67119,0.47859,0.47753,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-06,Undetermined,Undetermined,Undetermined,Undetermined
28797,SRR26685986,SRX22385774,SRS19431936,SRP470412,PRJNA1036238,RNAseq of Wild Type and  pikfyve?8 zebrafish.,GSE247110,Transcriptome Analysis,Purpose: Phosphoinositide kinase  FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient  pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.,,,,WT3,GSM7883485,,source name:genotype|tissue:genotype|genotype:Wile Type|geo loc name:missing|collection date:missing,WT3,Data filtering  The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5%  postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification  Bowtie2[2] was applied to align the clean reads to the gene set  in which known and novel  coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially  differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype  GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample,genotype,,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products.                                                                            2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair  Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced  while uncyclized linear DNA molecules are digested. 9 Sequencing,,tissue:genotype|genotype:Wile Type,GSM7883485,GSM7883485: WT3; Danio rerio; RNA Seq,GSM7883485 r1,GSM7883485,1,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products.                                                                            2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair  Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced  while uncyclized linear DNA molecules are digested. 9 Sequencing,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP470412,,,WT3_2.fq.gz WT3_1.fq.gz,fastq fastq,6654357000.0,22181190.0,GSM7883485 r1,0:150 1:150,A:1778694761;C:1540249434;G:1534346559;T:1801052542;N:13704,150,150,,,1778694761,1540249434,1534346559,1801052542,13704,SRX22385774,SRS19431936,SRA1746433,"The Second Clinical Medical College, Jinan University","The Second Clinical Medical College, Jinan University",2,0.93688,0.92644,0.09182,0.09071,0.66229,0.66434,0.48313,0.48263,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-06,Undetermined,Undetermined,Undetermined,Undetermined
28798,SRR26685987,SRX22385773,SRS19431935,SRP470412,PRJNA1036238,RNAseq of Wild Type and  pikfyve?8 zebrafish.,GSE247110,Transcriptome Analysis,Purpose: Phosphoinositide kinase  FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient  pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.,,,,WT2,GSM7883484,,source name:genotype|tissue:genotype|genotype:Wile Type|geo loc name:missing|collection date:missing,WT2,Data filtering  The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5%  postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification  Bowtie2[2] was applied to align the clean reads to the gene set  in which known and novel  coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially  differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype  GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample,genotype,,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products.                                                                            2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair  Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced  while uncyclized linear DNA molecules are digested. 9 Sequencing,,tissue:genotype|genotype:Wile Type,GSM7883484,GSM7883484: WT2; Danio rerio; RNA Seq,GSM7883484 r1,GSM7883484,1,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products.                                                                            2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair  Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced  while uncyclized linear DNA molecules are digested. 9 Sequencing,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP470412,,,WT2_1.fq.gz WT2_2.fq.gz,fastq fastq,6661129500.0,22203765.0,GSM7883484 r1,0:150 1:150,A:1774160269;C:1545605554;G:1545211257;T:1796139014;N:13406,150,150,,,1774160269,1545605554,1545211257,1796139014,13406,SRX22385773,SRS19431935,SRA1746433,"The Second Clinical Medical College, Jinan University","The Second Clinical Medical College, Jinan University",2,0.93696,0.9278,0.08665,0.08477,0.66322,0.66498,0.48376,0.48557,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-06,Undetermined,Undetermined,Undetermined,Undetermined
28799,SRR26685988,SRX22385772,SRS19431934,SRP470412,PRJNA1036238,RNAseq of Wild Type and  pikfyve?8 zebrafish.,GSE247110,Transcriptome Analysis,Purpose: Phosphoinositide kinase  FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient  pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.,,,,WT1,GSM7883483,,source name:genotype|tissue:genotype|genotype:Wile Type|geo loc name:missing|collection date:missing,WT1,Data filtering  The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5%  postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification  Bowtie2[2] was applied to align the clean reads to the gene set  in which known and novel  coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially  differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype  GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample,genotype,,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products.                                                                            2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair  Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced  while uncyclized linear DNA molecules are digested. 9 Sequencing,,tissue:genotype|genotype:Wile Type,GSM7883483,GSM7883483: WT1; Danio rerio; RNA Seq,GSM7883483 r1,GSM7883483,1,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products.                                                                            2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair  Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced  while uncyclized linear DNA molecules are digested. 9 Sequencing,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP470412,,,WT1_2.fq.gz WT1_1.fq.gz,fastq fastq,6648386700.0,22161289.0,GSM7883483 r1,0:150 1:150,A:1780975057;C:1536473791;G:1530388485;T:1800462718;N:86649,150,150,,,1780975057,1536473791,1530388485,1800462718,86649,SRX22385772,SRS19431934,SRA1746433,"The Second Clinical Medical College, Jinan University","The Second Clinical Medical College, Jinan University",2,0.93595,0.92974,0.09487,0.09314,0.65969,0.66005,0.48731,0.4845,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-06,Undetermined,Undetermined,Undetermined,Undetermined
30075,SRR27700027,SRX23366859,SRS20229171,SRP485459,PRJNA1068100,Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain,GSE254006,Transcriptome Analysis,The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:39798091,,Smh mutant  clutch 4,GSM8031712,,source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing,Smh mutant  clutch 4,The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,tissue:whole larvae|genotype: / |treatment:no treatment,GSM8031712,GSM8031712: Smh mutant  clutch 4; Danio rerio; RNA Seq,GSM8031712 r1,GSM8031712,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP485459,,,SmhMUT4_1.fq.gz SmhMUT4_2.fq.gz,fastq fastq,4550057400.0,22750287.0,GSM8031712 r1,0:100 1:100,A:1198976754;C:1064190197;G:1077491671;T:1209398778;N:0,100,100,,,1198976754,1064190197,1077491671,1209398778,0,SRX23366859,SRS20229171,SRA1790727,NTNU,NTNU,2,0.94285,0.95266,0.101,0.10096,0.66145,0.65989,0.48209,0.47768,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2024-01-23,Larval,Larval,Whole Organism,All anatomical structures
30076,SRR27700028,SRX23366858,SRS20229175,SRP485459,PRJNA1068100,Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain,GSE254006,Transcriptome Analysis,The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:39798091,,Smh mutant  clutch 3,GSM8031711,,source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing,Smh mutant  clutch 3,The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,tissue:whole larvae|genotype: / |treatment:no treatment,GSM8031711,GSM8031711: Smh mutant  clutch 3; Danio rerio; RNA Seq,GSM8031711 r1,GSM8031711,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP485459,,,SmhMUT3_1.fq.gz SmhMUT3_2.fq.gz,fastq fastq,4545452600.0,22727263.0,GSM8031711 r1,0:100 1:100,A:1188958937;C:1071903723;G:1087032258;T:1197557682;N:0,100,100,,,1188958937,1071903723,1087032258,1197557682,0,SRX23366858,SRS20229175,SRA1790727,NTNU,NTNU,2,0.94501,0.95409,0.09005,0.08947,0.66149,0.66062,0.46824,0.48019,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2024-01-23,Larval,Larval,Whole Organism,All anatomical structures
30077,SRR27700029,SRX23366857,SRS20229173,SRP485459,PRJNA1068100,Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain,GSE254006,Transcriptome Analysis,The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:39798091,,Smh mutant  clutch 2,GSM8031710,,source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing,Smh mutant  clutch 2,The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,tissue:whole larvae|genotype: / |treatment:no treatment,GSM8031710,GSM8031710: Smh mutant  clutch 2; Danio rerio; RNA Seq,GSM8031710 r1,GSM8031710,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP485459,,,SmhMUT2_1.fq.gz SmhMUT2_2.fq.gz,fastq fastq,4548042000.0,22740210.0,GSM8031710 r1,0:100 1:100,A:1184618587;C:1077947166;G:1089628929;T:1195847318;N:0,100,100,,,1184618587,1077947166,1089628929,1195847318,0,SRX23366857,SRS20229173,SRA1790727,NTNU,NTNU,2,0.94502,0.95416,0.09209,0.092,0.66407,0.66214,0.48538,0.48509,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2024-01-23,Larval,Larval,Whole Organism,All anatomical structures
30078,SRR27700030,SRX23366856,SRS20229174,SRP485459,PRJNA1068100,Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain,GSE254006,Transcriptome Analysis,The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:39798091,,Smh mutant  clutch 1,GSM8031709,,source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing,Smh mutant  clutch 1,The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,tissue:whole larvae|genotype: / |treatment:no treatment,GSM8031709,GSM8031709: Smh mutant  clutch 1; Danio rerio; RNA Seq,GSM8031709 r1,GSM8031709,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP485459,,,SmhMUT1_1.fq.gz SmhMUT1_2.fq.gz,fastq fastq,4544759600.0,22723798.0,GSM8031709 r1,0:100 1:100,A:1194011331;C:1066502346;G:1077923006;T:1206322917;N:0,100,100,,,1194011331,1066502346,1077923006,1206322917,0,SRX23366856,SRS20229174,SRA1790727,NTNU,NTNU,2,0.945,0.95433,0.09733,0.09796,0.66034,0.65951,0.477,0.47705,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2024-01-23,Larval,Larval,Whole Organism,All anatomical structures
30079,SRR27700031,SRX23366855,SRS20229172,SRP485459,PRJNA1068100,Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain,GSE254006,Transcriptome Analysis,The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:39798091,,Smh control  clutch 4,GSM8031708,,source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing,Smh control  clutch 4,The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment,GSM8031708,GSM8031708: Smh control  clutch 4; Danio rerio; RNA Seq,GSM8031708 r1,GSM8031708,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP485459,,,SmhCTRL4_1.fq.gz SmhCTRL4_2.fq.gz,fastq fastq,4536141000.0,22680705.0,GSM8031708 r1,0:100 1:100,A:1196842043;C:1059535727;G:1071488375;T:1208274855;N:0,100,100,,,1196842043,1059535727,1071488375,1208274855,0,SRX23366855,SRS20229172,SRA1790727,NTNU,NTNU,2,0.94102,0.95093,0.09453,0.09431,0.66403,0.6631,0.49804,0.49818,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2024-01-23,Larval,Larval,Whole Organism,All anatomical structures
30080,SRR27700032,SRX23366854,SRS20229170,SRP485459,PRJNA1068100,Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain,GSE254006,Transcriptome Analysis,The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:39798091,,Smh control  clutch 3,GSM8031707,,source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing,Smh control  clutch 3,The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment,GSM8031707,GSM8031707: Smh control  clutch 3; Danio rerio; RNA Seq,GSM8031707 r1,GSM8031707,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP485459,,,SmhCTRL3_1.fq.gz SmhCTRL3_2.fq.gz,fastq fastq,4543416000.0,22717080.0,GSM8031707 r1,0:100 1:100,A:1189755812;C:1071666785;G:1082665579;T:1199327824;N:0,100,100,,,1189755812,1071666785,1082665579,1199327824,0,SRX23366854,SRS20229170,SRA1790727,NTNU,NTNU,2,0.94571,0.95506,0.08989,0.09005,0.6632,0.66107,0.49631,0.49649,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2024-01-23,Larval,Larval,Whole Organism,All anatomical structures
30081,SRR27700033,SRX23366853,SRS20229169,SRP485459,PRJNA1068100,Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain,GSE254006,Transcriptome Analysis,The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:39798091,,Smh control  clutch 2,GSM8031706,,source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing,Smh control  clutch 2,The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment,GSM8031706,GSM8031706: Smh control  clutch 2; Danio rerio; RNA Seq,GSM8031706 r1,GSM8031706,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP485459,,,SmhCTRL2_2.fq.gz SmhCTRL2_1.fq.gz,fastq fastq,4536576000.0,22682880.0,GSM8031706 r1,0:100 1:100,A:1180961957;C:1074391564;G:1088552770;T:1192669709;N:0,100,100,,,1180961957,1074391564,1088552770,1192669709,0,SRX23366853,SRS20229169,SRA1790727,NTNU,NTNU,2,0.94324,0.95313,0.08618,0.08685,0.66399,0.66216,0.49362,0.49644,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2024-01-23,Larval,Larval,Whole Organism,All anatomical structures
30082,SRR27700034,SRX23366852,SRS20229168,SRP485459,PRJNA1068100,Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain,GSE254006,Transcriptome Analysis,The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.,,pubmed:39798091,,Smh control  clutch 1,GSM8031705,,source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing,Smh control  clutch 1,The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx,whole larvae,,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment,GSM8031705,GSM8031705: Smh control  clutch 1; Danio rerio; RNA Seq,GSM8031705 r1,GSM8031705,1,To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation  350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters：  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version：v2.2.5  Parameters： q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version：v1.2.8  Parameters： p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,MGISEQ-2000RS,,SRP485459,,,SmhCTRL1_1.fq.gz SmhCTRL1_2.fq.gz,fastq fastq,4546026800.0,22730134.0,GSM8031705 r1,0:100 1:100,A:1201447089;C:1060722844;G:1073012718;T:1210844149;N:0,100,100,,,1201447089,1060722844,1073012718,1210844149,0,SRX23366852,SRS20229168,SRA1790727,NTNU,NTNU,2,0.94554,0.95419,0.09192,0.09168,0.66436,0.66222,0.4762,0.48114,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2024-01-23,Larval,Larval,Whole Organism,All anatomical structures
33164,SRR29809736,SRX25309007,SRS21984115,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 20mM STS 5,GSM8393514,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 20mM STS 5,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS,GSM8393514,GSM8393514: pdx1 morpholino + 20mM STS 5; Danio rerio; RNA Seq,GSM8393514 r1,GSM8393514,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,6_2.fq.gz 6_1.fq.gz,fastq fastq,4827420200.0,24137101.0,GSM8393514 r1,0:100 1:100,A:1278807278;C:1130198430;G:1150325506;T:1268088986;N:0,100,100,,,1278807278,1130198430,1150325506,1268088986,0,SRX25309007,SRS21984115,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.9409,0.94542,0.08059,0.07981,0.69021,0.68887,0.47275,0.47095,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33165,SRR29809737,SRX25309006,SRS21984114,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 20mM STS 4,GSM8393513,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 20mM STS 4,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS,GSM8393513,GSM8393513: pdx1 morpholino + 20mM STS 4; Danio rerio; RNA Seq,GSM8393513 r1,GSM8393513,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,30_2.fq.gz 30_1.fq.gz,fastq fastq,4240862400.0,21204312.0,GSM8393513 r1,0:100 1:100,A:1146088921;C:972830110;G:990127288;T:1131816081;N:0,100,100,,,1146088921,972830110,990127288,1131816081,0,SRX25309006,SRS21984114,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.93888,0.9444,0.08826,0.08671,0.70431,0.70212,0.48083,0.48199,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33166,SRR29809738,SRX25309005,SRS21984113,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 20mM STS 3,GSM8393512,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 20mM STS 3,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS,GSM8393512,GSM8393512: pdx1 morpholino + 20mM STS 3; Danio rerio; RNA Seq,GSM8393512 r1,GSM8393512,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,24_2.fq.gz 24_1.fq.gz,fastq fastq,4822516400.0,24112582.0,GSM8393512 r1,0:100 1:100,A:1276866727;C:1130641795;G:1148897951;T:1266109927;N:0,100,100,,,1276866727,1130641795,1148897951,1266109927,0,SRX25309005,SRS21984113,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94126,0.94446,0.07837,0.07762,0.6911,0.69037,0.46251,0.4642,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33167,SRR29809739,SRX25309004,SRS21984112,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 20mM STS 2,GSM8393511,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 20mM STS 2,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS,GSM8393511,GSM8393511: pdx1 morpholino + 20mM STS 2; Danio rerio; RNA Seq,GSM8393511 r1,GSM8393511,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,18_2.fq.gz 18_1.fq.gz,fastq fastq,4820332000.0,24101660.0,GSM8393511 r1,0:100 1:100,A:1306037553;C:1103383630;G:1122255994;T:1288654823;N:0,100,100,,,1306037553,1103383630,1122255994,1288654823,0,SRX25309004,SRS21984112,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94035,0.9445,0.08468,0.08417,0.71106,0.70897,0.47897,0.47969,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33168,SRR29809740,SRX25309003,SRS21984111,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 20mM STS 1,GSM8393510,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 20mM STS 1,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS,GSM8393510,GSM8393510: pdx1 morpholino + 20mM STS 1; Danio rerio; RNA Seq,GSM8393510 r1,GSM8393510,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,12_1.fq.gz 12_2.fq.gz,fastq fastq,4825742600.0,24128713.0,GSM8393510 r1,0:100 1:100,A:1264457552;C:1145133600;G:1160084092;T:1256067356;N:0,100,100,,,1264457552,1145133600,1160084092,1256067356,0,SRX25309003,SRS21984111,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94613,0.9501,0.06915,0.06812,0.68941,0.68852,0.45659,0.45507,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33169,SRR29809741,SRX25309002,SRS21984110,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 15mM STS 5,GSM8393509,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 15mM STS 5,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS,GSM8393509,GSM8393509: pdx1 morpholino + 15mM STS 5; Danio rerio; RNA Seq,GSM8393509 r1,GSM8393509,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,5_2.fq.gz 5_1.fq.gz,fastq fastq,4816068800.0,24080344.0,GSM8393509 r1,0:100 1:100,A:1278638535;C:1126555210;G:1141985166;T:1268889889;N:0,100,100,,,1278638535,1126555210,1141985166,1268889889,0,SRX25309002,SRS21984110,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.9414,0.94516,0.08012,0.07915,0.69284,0.69185,0.46526,0.46882,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33170,SRR29809742,SRX25309001,SRS21984109,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 15mM STS 4,GSM8393508,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 15mM STS 4,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS,GSM8393508,GSM8393508: pdx1 morpholino + 15mM STS 4; Danio rerio; RNA Seq,GSM8393508 r1,GSM8393508,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,29_2.fq.gz 29_1.fq.gz,fastq fastq,4386218400.0,21931092.0,GSM8393508 r1,0:100 1:100,A:1181773341;C:1011246416;G:1025789654;T:1167408989;N:0,100,100,,,1181773341,1011246416,1025789654,1167408989,0,SRX25309001,SRS21984109,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94168,0.94587,0.08215,0.08003,0.69682,0.69544,0.47251,0.47607,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33171,SRR29809743,SRX25309000,SRS21984108,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 15mM STS 3,GSM8393507,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 15mM STS 3,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS,GSM8393507,GSM8393507: pdx1 morpholino + 15mM STS 3; Danio rerio; RNA Seq,GSM8393507 r1,GSM8393507,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,23_2.fq.gz 23_1.fq.gz,fastq fastq,4808808800.0,24044044.0,GSM8393507 r1,0:100 1:100,A:1269564907;C:1132101674;G:1149286214;T:1257856005;N:0,100,100,,,1269564907,1132101674,1149286214,1257856005,0,SRX25309000,SRS21984108,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.9434,0.94774,0.07109,0.0703,0.69264,0.69183,0.45908,0.46455,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33172,SRR29809744,SRX25308999,SRS21984107,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 15mM STS 2,GSM8393506,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 15mM STS 2,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS,GSM8393506,GSM8393506: pdx1 morpholino + 15mM STS 2; Danio rerio; RNA Seq,GSM8393506 r1,GSM8393506,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,17_1.fq.gz 17_2.fq.gz,fastq fastq,4805883400.0,24029417.0,GSM8393506 r1,0:100 1:100,A:1299291748;C:1102517917;G:1122450422;T:1281623313;N:0,100,100,,,1299291748,1102517917,1122450422,1281623313,0,SRX25308999,SRS21984107,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94253,0.9461,0.08371,0.08155,0.70589,0.70423,0.4853,0.47925,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33173,SRR29809745,SRX25308998,SRS21984106,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 15mM STS 1,GSM8393505,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 15mM STS 1,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS,GSM8393505,GSM8393505: pdx1 morpholino + 15mM STS 1; Danio rerio; RNA Seq,GSM8393505 r1,GSM8393505,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,11_1.fq.gz 11_2.fq.gz,fastq fastq,4812111600.0,24060558.0,GSM8393505 r1,0:100 1:100,A:1269803704;C:1133657948;G:1150461915;T:1258188033;N:0,100,100,,,1269803704,1133657948,1150461915,1258188033,0,SRX25308998,SRS21984106,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94311,0.94708,0.07444,0.07235,0.69266,0.69158,0.46689,0.46584,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33174,SRR29809746,SRX25308997,SRS21984105,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 0mM STS 5,GSM8393504,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 0mM STS 5,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS,GSM8393504,GSM8393504: pdx1 morpholino + 0mM STS 5; Danio rerio; RNA Seq,GSM8393504 r1,GSM8393504,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,4_2.fq.gz 4_1.fq.gz,fastq fastq,4804978800.0,24024894.0,GSM8393504 r1,0:100 1:100,A:1266882676;C:1131396187;G:1149418875;T:1257281062;N:0,100,100,,,1266882676,1131396187,1149418875,1257281062,0,SRX25308997,SRS21984105,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94345,0.94707,0.07428,0.0741,0.6898,0.68856,0.4653,0.46918,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33175,SRR29809747,SRX25308996,SRS21984104,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 0mM STS 4,GSM8393503,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 0mM STS 4,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS,GSM8393503,GSM8393503: pdx1 morpholino + 0mM STS 4; Danio rerio; RNA Seq,GSM8393503 r1,GSM8393503,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,28_1.fq.gz 28_2.fq.gz,fastq fastq,4464066400.0,22320332.0,GSM8393503 r1,0:100 1:100,A:1209155509;C:1023407835;G:1040239673;T:1191263383;N:0,100,100,,,1209155509,1023407835,1040239673,1191263383,0,SRX25308996,SRS21984104,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.934,0.93723,0.08814,0.08601,0.69834,0.69798,0.47533,0.47611,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33176,SRR29809748,SRX25308995,SRS21984103,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 0mM STS 3,GSM8393502,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 0mM STS 3,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS,GSM8393502,GSM8393502: pdx1 morpholino + 0mM STS 3; Danio rerio; RNA Seq,GSM8393502 r1,GSM8393502,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,22_1.fq.gz 22_2.fq.gz,fastq fastq,4613819800.0,23069099.0,GSM8393502 r1,0:100 1:100,A:1218890904;C:1084874278;G:1104087523;T:1205967095;N:0,100,100,,,1218890904,1084874278,1104087523,1205967095,0,SRX25308995,SRS21984103,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.9426,0.94852,0.07601,0.07487,0.69197,0.69075,0.45872,0.45856,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33177,SRR29809749,SRX25308994,SRS21984102,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 0mM STS 2,GSM8393501,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 0mM STS 2,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS,GSM8393501,GSM8393501: pdx1 morpholino + 0mM STS 2; Danio rerio; RNA Seq,GSM8393501 r1,GSM8393501,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,16_1.fq.gz 16_2.fq.gz,fastq fastq,4818005000.0,24090025.0,GSM8393501 r1,0:100 1:100,A:1291680744;C:1114433015;G:1134463270;T:1277427971;N:0,100,100,,,1291680744,1114433015,1134463270,1277427971,0,SRX25308994,SRS21984102,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.93988,0.94257,0.08614,0.08554,0.69376,0.69367,0.47178,0.47111,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33178,SRR29809750,SRX25308993,SRS21984101,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 0mM STS 1,GSM8393500,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 0mM STS 1,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS,GSM8393500,GSM8393500: pdx1 morpholino + 0mM STS 1; Danio rerio; RNA Seq,GSM8393500 r1,GSM8393500,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,10_2.fq.gz 10_1.fq.gz,fastq fastq,4827935800.0,24139679.0,GSM8393500 r1,0:100 1:100,A:1267823750;C:1143323623;G:1156194469;T:1260593958;N:0,100,100,,,1267823750,1143323623,1156194469,1260593958,0,SRX25308993,SRS21984101,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94483,0.94829,0.07178,0.07025,0.69077,0.69025,0.46181,0.45982,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33179,SRR29809751,SRX25308992,SRS21984100,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 20mM STS 5,GSM8393499,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 20mM STS 5,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS,GSM8393499,GSM8393499: Control morpholino + 20mM STS 5; Danio rerio; RNA Seq,GSM8393499 r1,GSM8393499,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,9_1.fq.gz 9_2.fq.gz,fastq fastq,4822379000.0,24111895.0,GSM8393499 r1,0:100 1:100,A:1262977318;C:1145277730;G:1159167028;T:1254956924;N:0,100,100,,,1262977318,1145277730,1159167028,1254956924,0,SRX25308992,SRS21984100,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94642,0.94964,0.06863,0.0674,0.69288,0.69252,0.4574,0.44372,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33180,SRR29809752,SRX25308991,SRS21984099,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 20mM STS 4,GSM8393498,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 20mM STS 4,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS,GSM8393498,GSM8393498: Control morpholino + 20mM STS 4; Danio rerio; RNA Seq,GSM8393498 r1,GSM8393498,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,3_1.fq.gz 3_2.fq.gz,fastq fastq,4803150200.0,24015751.0,GSM8393498 r1,0:100 1:100,A:1253239300;C:1144350399;G:1158671984;T:1246888517;N:0,100,100,,,1253239300,1144350399,1158671984,1246888517,0,SRX25308991,SRS21984099,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94606,0.95015,0.06543,0.06441,0.68676,0.68611,0.44857,0.44396,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33181,SRR29809753,SRX25308990,SRS21984098,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 20mM STS 3,GSM8393497,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 20mM STS 3,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS,GSM8393497,GSM8393497: Control morpholino + 20mM STS 3; Danio rerio; RNA Seq,GSM8393497 r1,GSM8393497,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,27_1.fq.gz 27_2.fq.gz,fastq fastq,4277827200.0,21389136.0,GSM8393497 r1,0:100 1:100,A:1142589086;C:997230367;G:1005771965;T:1132235782;N:0,100,100,,,1142589086,997230367,1005771965,1132235782,0,SRX25308990,SRS21984098,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94201,0.94596,0.07754,0.07484,0.69794,0.69617,0.46286,0.45985,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33182,SRR29809754,SRX25308989,SRS21984097,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 20mM STS 2,GSM8393496,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 20mM STS 2,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS,GSM8393496,GSM8393496: Control morpholino + 20mM STS 2; Danio rerio; RNA Seq,GSM8393496 r1,GSM8393496,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,21_2.fq.gz 21_1.fq.gz,fastq fastq,4019456600.0,20097283.0,GSM8393496 r1,0:100 1:100,A:1053249649;C:953992221;G:968100759;T:1044113971;N:0,100,100,,,1053249649,953992221,968100759,1044113971,0,SRX25308989,SRS21984097,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94377,0.95125,0.06861,0.06745,0.68676,0.68523,0.45049,0.45168,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33183,SRR29809755,SRX25308988,SRS21984096,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 20mM STS 1,GSM8393495,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 20mM STS 1,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS,GSM8393495,GSM8393495: Control morpholino + 20mM STS 1; Danio rerio; RNA Seq,GSM8393495 r1,GSM8393495,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,15_1.fq.gz 15_2.fq.gz,fastq fastq,4829679200.0,24148396.0,GSM8393495 r1,0:100 1:100,A:1292193191;C:1119414896;G:1140502241;T:1277568872;N:0,100,100,,,1292193191,1119414896,1140502241,1277568872,0,SRX25308988,SRS21984096,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.9423,0.9467,0.07958,0.07808,0.69763,0.69658,0.46406,0.46623,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33184,SRR29809756,SRX25308987,SRS21984095,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 15mM STS 5,GSM8393494,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 15mM STS 5,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS,GSM8393494,GSM8393494: Control morpholino + 15mM STS 5; Danio rerio; RNA Seq,GSM8393494 r1,GSM8393494,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,8_2.fq.gz 8_1.fq.gz,fastq fastq,4803709800.0,24018549.0,GSM8393494 r1,0:100 1:100,A:1253733589;C:1143748058;G:1158768340;T:1247459813;N:0,100,100,,,1253733589,1143748058,1158768340,1247459813,0,SRX25308987,SRS21984095,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94718,0.94926,0.06582,0.06461,0.68791,0.68738,0.44759,0.44517,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33185,SRR29809757,SRX25308986,SRS21984094,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 15mM STS 4,GSM8393493,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 15mM STS 4,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS,GSM8393493,GSM8393493: Control morpholino + 15mM STS 4; Danio rerio; RNA Seq,GSM8393493 r1,GSM8393493,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,26_1.fq.gz 26_2.fq.gz,fastq fastq,4816718000.0,24083590.0,GSM8393493 r1,0:100 1:100,A:1278966223;C:1129131703;G:1144234415;T:1264385659;N:0,100,100,,,1278966223,1129131703,1144234415,1264385659,0,SRX25308986,SRS21984094,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94278,0.94713,0.07235,0.0704,0.69895,0.698,0.4536,0.45416,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33186,SRR29809758,SRX25308985,SRS21984093,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 15mM STS 3,GSM8393492,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 15mM STS 3,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS,GSM8393492,GSM8393492: Control morpholino + 15mM STS 3; Danio rerio; RNA Seq,GSM8393492 r1,GSM8393492,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,20_2.fq.gz 20_1.fq.gz,fastq fastq,4825880400.0,24129402.0,GSM8393492 r1,0:100 1:100,A:1263053657;C:1147908238;G:1161094243;T:1253824262;N:0,100,100,,,1263053657,1147908238,1161094243,1253824262,0,SRX25308985,SRS21984093,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94642,0.95164,0.06472,0.06312,0.69035,0.68909,0.44854,0.44216,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33187,SRR29809759,SRX25308984,SRS21984092,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 15mM STS 2,GSM8393491,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 15mM STS 2,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS,GSM8393491,GSM8393491: Control morpholino + 15mM STS 2; Danio rerio; RNA Seq,GSM8393491 r1,GSM8393491,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,2_1.fq.gz 2_2.fq.gz,fastq fastq,4805985200.0,24029926.0,GSM8393491 r1,0:100 1:100,A:1255841114;C:1143278337;G:1157783615;T:1249082134;N:0,100,100,,,1255841114,1143278337,1157783615,1249082134,0,SRX25308984,SRS21984092,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94666,0.94794,0.06553,0.06456,0.69181,0.69175,0.4359,0.44559,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33188,SRR29809760,SRX25308983,SRS21984091,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 15mM STS 1,GSM8393490,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 15mM STS 1,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS,GSM8393490,GSM8393490: Control morpholino + 15mM STS 1; Danio rerio; RNA Seq,GSM8393490 r1,GSM8393490,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,14_1.fq.gz 14_2.fq.gz,fastq fastq,4553465000.0,22767325.0,GSM8393490 r1,0:100 1:100,A:1209891078;C:1063666819;G:1082075995;T:1197831108;N:0,100,100,,,1209891078,1063666819,1082075995,1197831108,0,SRX25308983,SRS21984091,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.9432,0.94661,0.07696,0.07599,0.69763,0.69721,0.46463,0.46425,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33189,SRR29809761,SRX25308982,SRS21984090,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 0mM STS 5,GSM8393489,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 0mM STS 5,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS,GSM8393489,GSM8393489: Control morpholino + 0mM STS 5; Danio rerio; RNA Seq,GSM8393489 r1,GSM8393489,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,7_1.fq.gz 7_2.fq.gz,fastq fastq,4813770200.0,24068851.0,GSM8393489 r1,0:100 1:100,A:1251918123;C:1151936172;G:1164458418;T:1245457487;N:0,100,100,,,1251918123,1151936172,1164458418,1245457487,0,SRX25308982,SRS21984090,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.95021,0.95271,0.06538,0.06376,0.69171,0.68996,0.44317,0.4435,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33190,SRR29809762,SRX25308981,SRS21984089,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 0mM STS 4,GSM8393488,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 0mM STS 4,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS,GSM8393488,GSM8393488: Control morpholino + 0mM STS 4; Danio rerio; RNA Seq,GSM8393488 r1,GSM8393488,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,25_1.fq.gz 25_2.fq.gz,fastq fastq,4810346800.0,24051734.0,GSM8393488 r1,0:100 1:100,A:1275301780;C:1127999390;G:1144547869;T:1262497761;N:0,100,100,,,1275301780,1127999390,1144547869,1262497761,0,SRX25308981,SRS21984089,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94519,0.94834,0.06949,0.06803,0.69552,0.69524,0.44741,0.45052,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33191,SRR29809763,SRX25308980,SRS21984088,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 0mM STS 3,GSM8393487,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 0mM STS 3,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS,GSM8393487,GSM8393487: Control morpholino + 0mM STS 3; Danio rerio; RNA Seq,GSM8393487 r1,GSM8393487,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,19_1.fq.gz 19_2.fq.gz,fastq fastq,4811704200.0,24058521.0,GSM8393487 r1,0:100 1:100,A:1257129134;C:1146835083;G:1160663520;T:1247076463;N:0,100,100,,,1257129134,1146835083,1160663520,1247076463,0,SRX25308980,SRS21984088,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94691,0.95082,0.06344,0.06212,0.69014,0.69059,0.45386,0.43864,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33192,SRR29809764,SRX25308979,SRS21984087,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 0mM STS 2,GSM8393486,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 0mM STS 2,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS,GSM8393486,GSM8393486: Control morpholino + 0mM STS 2; Danio rerio; RNA Seq,GSM8393486 r1,GSM8393486,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,13_1.fq.gz 13_2.fq.gz,fastq fastq,4616178800.0,23080894.0,GSM8393486 r1,0:100 1:100,A:1225429879;C:1079094541;G:1096304865;T:1215349515;N:0,100,100,,,1225429879,1079094541,1096304865,1215349515,0,SRX25308979,SRS21984087,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94498,0.9498,0.07635,0.075,0.69319,0.6927,0.46598,0.466,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
33193,SRR29809765,SRX25308978,SRS21984086,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 0mM STS 1,GSM8393485,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 0mM STS 1,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS,GSM8393485,GSM8393485: Control morpholino + 0mM STS 1; Danio rerio; RNA Seq,GSM8393485 r1,GSM8393485,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,1_1.fq.gz 1_2.fq.gz,fastq fastq,4823953400.0,24119767.0,GSM8393485 r1,0:100 1:100,A:1270954678;C:1137736456;G:1155516940;T:1259745326;N:0,100,100,,,1270954678,1137736456,1155516940,1259745326,0,SRX25308978,SRS21984086,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94325,0.94699,0.06928,0.06864,0.69372,0.69307,0.44844,0.45647,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure
34182,SRR31399561,SRX26768859,SRS23256160,SRP546207,PRJNA1188114,Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome,GSE282310,Transcriptome Analysis,Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.,,,,eif6 3,GSM8641203,,source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO|geo loc name:missing|collection date:missing,eif6 3,Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3’ adapter sequence  2 were 5’ 3’ adapter ligation products  3 were 5’ 5’ adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values,whole larvae,5 dpf,RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform,,tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO,GSM8641203,GSM8641203: eif6 3; Danio rerio; RNA Seq,GSM8641203 r1,GSM8641203,1,RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP546207,,,eif6_3_1.fq.gz eif6_3_2.fq.gz,fastq fastq,6955801200.0,34779006.0,GSM8641203 r1,0:100 1:100,A:1784502248;C:1653592398;G:1716091635;T:1801614919;N:0,100,100,,,1784502248,1653592398,1716091635,1801614919,0,SRX26768859,SRS23256160,SRA2017777,Cleveland Clinic,Cleveland Clinic,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2024-11-19,Larval,Larval,Whole Organism,All anatomical structures
34183,SRR31399562,SRX26768858,SRS23256161,SRP546207,PRJNA1188114,Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome,GSE282310,Transcriptome Analysis,Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.,,,,eif6 2,GSM8641202,,source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO|geo loc name:missing|collection date:missing,eif6 2,Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3’ adapter sequence  2 were 5’ 3’ adapter ligation products  3 were 5’ 5’ adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values,whole larvae,5 dpf,RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform,,tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO,GSM8641202,GSM8641202: eif6 2; Danio rerio; RNA Seq,GSM8641202 r1,GSM8641202,1,RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP546207,,,eif6_2_1.fq.gz eif6_2_2.fq.gz,fastq fastq,6968721400.0,34843607.0,GSM8641202 r1,0:100 1:100,A:1798630009;C:1650901437;G:1708195694;T:1810994260;N:0,100,100,,,1798630009,1650901437,1708195694,1810994260,0,SRX26768858,SRS23256161,SRA2017777,Cleveland Clinic,Cleveland Clinic,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2024-11-19,Larval,Larval,Whole Organism,All anatomical structures
34184,SRR31399563,SRX26768857,SRS23256159,SRP546207,PRJNA1188114,Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome,GSE282310,Transcriptome Analysis,Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.,,,,eif6 1,GSM8641201,,source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO|geo loc name:missing|collection date:missing,eif6 1,Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3’ adapter sequence  2 were 5’ 3’ adapter ligation products  3 were 5’ 5’ adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values,whole larvae,5 dpf,RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform,,tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO,GSM8641201,GSM8641201: eif6 1; Danio rerio; RNA Seq,GSM8641201 r1,GSM8641201,1,RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP546207,,,eif6_1_1.fq.gz eif6_1_2.fq.gz,fastq fastq,6976474200.0,34882371.0,GSM8641201 r1,0:100 1:100,A:1819387431;C:1630709320;G:1698463303;T:1827914146;N:0,100,100,,,1819387431,1630709320,1698463303,1827914146,0,SRX26768857,SRS23256159,SRA2017777,Cleveland Clinic,Cleveland Clinic,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2024-11-19,Larval,Larval,Whole Organism,All anatomical structures
34185,SRR31399564,SRX26768856,SRS23256158,SRP546207,PRJNA1188114,Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome,GSE282310,Transcriptome Analysis,Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.,,,,wt3,GSM8641200,,source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype|geo loc name:missing|collection date:missing,wt3,Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3’ adapter sequence  2 were 5’ 3’ adapter ligation products  3 were 5’ 5’ adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values,whole larvae,5 dpf,RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform,,tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype,GSM8641200,GSM8641200: wt3; Danio rerio; RNA Seq,GSM8641200 r1,GSM8641200,1,RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP546207,,,wt3_1.fq.gz wt3_2.fq.gz,fastq fastq,6990771600.0,34953858.0,GSM8641200 r1,0:100 1:100,A:1823561732;C:1639273273;G:1691098287;T:1836838308;N:0,100,100,,,1823561732,1639273273,1691098287,1836838308,0,SRX26768856,SRS23256158,SRA2017777,Cleveland Clinic,Cleveland Clinic,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2024-11-19,Larval,Larval,Whole Organism,All anatomical structures
34186,SRR31399565,SRX26768855,SRS23256157,SRP546207,PRJNA1188114,Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome,GSE282310,Transcriptome Analysis,Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.,,,,wt2,GSM8641199,,source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype|geo loc name:missing|collection date:missing,wt2,Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3’ adapter sequence  2 were 5’ 3’ adapter ligation products  3 were 5’ 5’ adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values,whole larvae,5 dpf,RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform,,tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype,GSM8641199,GSM8641199: wt2; Danio rerio; RNA Seq,GSM8641199 r1,GSM8641199,1,RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP546207,,,wt2_1.fq.gz wt2_2.fq.gz,fastq fastq,6996780600.0,34983903.0,GSM8641199 r1,0:100 1:100,A:1819793027;C:1646550105;G:1701161650;T:1829275818;N:0,100,100,,,1819793027,1646550105,1701161650,1829275818,0,SRX26768855,SRS23256157,SRA2017777,Cleveland Clinic,Cleveland Clinic,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2024-11-19,Larval,Larval,Whole Organism,All anatomical structures
34187,SRR31399566,SRX26768854,SRS23256156,SRP546207,PRJNA1188114,Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome,GSE282310,Transcriptome Analysis,Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.,,,,wt1,GSM8641198,,source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype|geo loc name:missing|collection date:missing,wt1,Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3’ adapter sequence  2 were 5’ 3’ adapter ligation products  3 were 5’ 5’ adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values,whole larvae,5 dpf,RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform,,tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype,GSM8641198,GSM8641198: wt1; Danio rerio; RNA Seq,GSM8641198 r1,GSM8641198,1,RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP546207,,,wt1_1.fq.gz wt1_2.fq.gz,fastq fastq,6976844600.0,34884223.0,GSM8641198 r1,0:100 1:100,A:1807619362;C:1649374675;G:1693243894;T:1826606669;N:0,100,100,,,1807619362,1649374675,1693243894,1826606669,0,SRX26768854,SRS23256156,SRA2017777,Cleveland Clinic,Cleveland Clinic,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2024-11-19,Larval,Larval,Whole Organism,All anatomical structures
55373,SRR10322141,SRX7032952,SRS5553012,SRP226571,PRJNA578840,RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4,GSE139226,Transcriptome Analysis,RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter.  Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation.   Normal thymus cells were also harvested from control zebrafish lck mCherry.,,pubmed:35504924,,IRF4 overexpression with p53 mutation RNA seq #2,GSM4134351,,tissue:lck IRF4;p53+/ |genotype/variation:IRF4 overexpression and p53 mutation,IRF4 overexpression with p53 mutation RNA seq #2,RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/  were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4  with the intersection strict mode  was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts  differentially expressed genes,lck IRF4;p53+/ ,No treatment,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end  100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,genotype/variation:IRF4 overexpression and p53 mutation,GSM4134351,GSM4134351: IRF4 overexpression with p53 mutation RNA seq #2; Danio rerio; RNA Seq,GSM4134351,,1,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end  100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM4134351,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP226571,,,IRF4xp53_3_1.fastq.gz IRF4xp53_3_2.fastq.gz,fastq fastq,8647695276.0,86535602.0,GSM4134351 r1,0:99.93 1:99.93,A:2336303355;C:1960332457;G:1974896588;T:2376162876;N:0,99,99,,,2336303355,1960332457,1974896588,2376162876,0,SRX7032952,SRS5553012,SRA982884,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94146,,0.26739,,0.77739,,0.49821,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2019-10-22,Undetermined,Undetermined,Multi-tissue,Multi-system
55374,SRR10322140,SRX7032951,SRS5553011,SRP226571,PRJNA578840,RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4,GSE139226,Transcriptome Analysis,RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter.  Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation.   Normal thymus cells were also harvested from control zebrafish lck mCherry.,,pubmed:35504924,,IRF4 overexpression with p53 mutation RNA seq #1,GSM4134350,,tissue:lck IRF4;p53+/ |genotype/variation:IRF4 overexpression and p53 mutation,IRF4 overexpression with p53 mutation RNA seq #1,RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/  were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4  with the intersection strict mode  was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts  differentially expressed genes,lck IRF4;p53+/ ,No treatment,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end  100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,genotype/variation:IRF4 overexpression and p53 mutation,GSM4134350,GSM4134350: IRF4 overexpression with p53 mutation RNA seq #1; Danio rerio; RNA Seq,GSM4134350,,1,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end  100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM4134350,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP226571,,,IRF4xp53_1_1.fastq.gz IRF4xp53_1_2.fastq.gz,fastq fastq,8579468052.0,85855086.0,GSM4134350 r1,0:99.93 1:99.93,A:2293476693;C:1963039176;G:1985578185;T:2337373998;N:0,99,99,,,2293476693,1963039176,1985578185,2337373998,0,SRX7032951,SRS5553011,SRA982884,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94576,,0.27683,,0.77589,,0.47851,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2019-10-22,Undetermined,Undetermined,Multi-tissue,Multi-system
55375,SRR10322139,SRX7032950,SRS5553010,SRP226571,PRJNA578840,RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4,GSE139226,Transcriptome Analysis,RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter.  Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation.   Normal thymus cells were also harvested from control zebrafish lck mCherry.,,pubmed:35504924,,IRF4 overexpression RNA seq #2,GSM4134349,,tissue:lck IRF4|genotype/variation:IRF4 overexpression,IRF4 overexpression RNA seq #2,RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/  were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4  with the intersection strict mode  was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts  differentially expressed genes,lck IRF4,No treatment,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end  100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,genotype/variation:IRF4 overexpression,GSM4134349,GSM4134349: IRF4 overexpression RNA seq #2; Danio rerio; RNA Seq,GSM4134349,,1,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end  100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM4134349,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP226571,,,IRF4_2_1.fastq.gz IRF4_2_2.fastq.gz,fastq fastq,8625409426.0,86311782.0,GSM4134349 r1,0:99.93 1:99.93,A:2345513123;C:1941948054;G:1962855201;T:2375093048;N:0,99,99,,,2345513123,1941948054,1962855201,2375093048,0,SRX7032950,SRS5553010,SRA982884,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94815,,0.35561,,0.79117,,0.50866,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2019-10-22,Undetermined,Undetermined,Multi-tissue,Multi-system
55376,SRR10322138,SRX7032949,SRS5553009,SRP226571,PRJNA578840,RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4,GSE139226,Transcriptome Analysis,RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter.  Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation.   Normal thymus cells were also harvested from control zebrafish lck mCherry.,,pubmed:35504924,,IRF4 overexpression RNA seq #1,GSM4134348,,tissue:lck IRF4|genotype/variation:IRF4 overexpression,IRF4 overexpression RNA seq #1,RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/  were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4  with the intersection strict mode  was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts  differentially expressed genes,lck IRF4,No treatment,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end  100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,genotype/variation:IRF4 overexpression,GSM4134348,GSM4134348: IRF4 overexpression RNA seq #1; Danio rerio; RNA Seq,GSM4134348,,1,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end  100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM4134348,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP226571,,,IRF4_1_1.fastq.gz IRF4_1_2.fastq.gz,fastq fastq,8560288616.0,85661544.0,GSM4134348 r1,0:99.93 1:99.93,A:2300488079;C:1940898245;G:1978951452;T:2339950840;N:0,99,99,,,2300488079,1940898245,1978951452,2339950840,0,SRX7032949,SRS5553009,SRA982884,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94019,,0.24387,,0.75789,,0.49007,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2019-10-22,Undetermined,Undetermined,Multi-tissue,Multi-system
55377,SRR10322137,SRX7032948,SRS5553008,SRP226571,PRJNA578840,RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4,GSE139226,Transcriptome Analysis,RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter.  Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation.   Normal thymus cells were also harvested from control zebrafish lck mCherry.,,pubmed:35504924,,mCherry control RNA seq #2,GSM4134347,,tissue:lck mCherry|genotype/variation:control,mCherry control RNA seq #2,RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/  were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4  with the intersection strict mode  was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts  differentially expressed genes,lck mCherry,No treatment,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end  100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,genotype/variation:control,GSM4134347,GSM4134347: mCherry control RNA seq #2; Danio rerio; RNA Seq,GSM4134347,,1,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end  100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM4134347,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP226571,,,Lck_mch_2_1.fastq.gz Lck_mch_2_2.fastq.gz,fastq fastq,8556568306.0,85629202.0,GSM4134347 r1,0:99.93 1:99.93,A:2299427498;C:1945648999;G:1981590842;T:2329900967;N:0,99,99,,,2299427498,1945648999,1981590842,2329900967,0,SRX7032948,SRS5553008,SRA982884,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94792,,0.25274,,0.80085,,0.51772,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2019-10-22,Undetermined,Undetermined,Multi-tissue,Multi-system
55378,SRR10322136,SRX7032947,SRS5553007,SRP226571,PRJNA578840,RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4,GSE139226,Transcriptome Analysis,RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter.  Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation.   Normal thymus cells were also harvested from control zebrafish lck mCherry.,,pubmed:35504924,,mCherry control RNA seq #1,GSM4134346,,tissue:lck mCherry|genotype/variation:control,mCherry control RNA seq #1,RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/  were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4  with the intersection strict mode  was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts  differentially expressed genes,lck mCherry,No treatment,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end  100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,genotype/variation:control,GSM4134346,GSM4134346: mCherry control RNA seq #1; Danio rerio; RNA Seq,GSM4134346,,1,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end  100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM4134346,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP226571,,,Lck_mch_1_1.fastq.gz Lck_mch_1_2.fastq.gz,fastq fastq,8544218824.0,85502654.0,GSM4134346 r1,0:99.93 1:99.93,A:2294044731;C:1942271608;G:1967598065;T:2340304420;N:0,99,99,,,2294044731,1942271608,1967598065,2340304420,0,SRX7032947,SRS5553007,SRA982884,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94337,,0.28212,,0.79239,,0.47106,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2019-10-22,Undetermined,Undetermined,Multi-tissue,Multi-system
58579,SRR11425295,SRX8003661,SRS6377641,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus  by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin  we could sort osteoblasts into separate Erk+ and Erk  populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically  dusp2  dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal  which anti correlates with Erk activity.,,pubmed:33408418,,high Erk activity; rep1,GSM4433141,,tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,high Erk activity; rep1,Reads were trimmed by Trim Galore 0.4.1  with  q 15   paired and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,high Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially  events were gated using Forward versus Side Scatter Areas 488 nm laser. Then  single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally  H2A mCherry+ Venus hGeminin  and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales  in three rows  from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp  all regenerating scales were plucked  and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade   Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min  500 µl of supernatant was removed  quenched with 65µl sheep serum Sigma S2263 on ice  and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,GSM4433141,GSM4433141: high Erk activity; rep1; Danio rerio; RNA Seq,GSM4433141,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433141,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,3G_plus_1.fq.gz 3G_plus_2.fq.gz,fastq fastq,4698595200.0,46985952.0,GSM4433141 r1,0:100 1:100,A:1261622105;C:1085007643;G:1066886112;T:1285079340;N:0,100,100,,,1261622105,1085007643,1066886112,1285079340,0,SRX8003661,SRS6377641,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.86576,,0.11767,,0.81262,,0.52377,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
58580,SRR11425294,SRX8003660,SRS6377640,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus  by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin  we could sort osteoblasts into separate Erk+ and Erk  populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically  dusp2  dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal  which anti correlates with Erk activity.,,pubmed:33408418,,low Erk activity; rep3,GSM4433140,,tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,low Erk activity; rep3,Reads were trimmed by Trim Galore 0.4.1  with  q 15   paired and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,low Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially  events were gated using Forward versus Side Scatter Areas 488 nm laser. Then  single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally  H2A mCherry+ Venus hGeminin  and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales  in three rows  from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp  all regenerating scales were plucked  and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade   Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min  500 µl of supernatant was removed  quenched with 65µl sheep serum Sigma S2263 on ice  and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,GSM4433140,GSM4433140: low Erk activity; rep3; Danio rerio; RNA Seq,GSM4433140,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433140,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,6B_minus_1.fq.gz 6B_minus_2.fq.gz,fastq fastq,4707217000.0,47072170.0,GSM4433140 r1,0:100 1:100,A:1268188059;C:1086056259;G:1067448053;T:1285524629;N:0,100,100,,,1268188059,1086056259,1067448053,1285524629,0,SRX8003660,SRS6377640,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.88883,,0.05585,,0.82071,,0.47905,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
58581,SRR11425293,SRX8003659,SRS6377639,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus  by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin  we could sort osteoblasts into separate Erk+ and Erk  populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically  dusp2  dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal  which anti correlates with Erk activity.,,pubmed:33408418,,low Erk activity; rep2,GSM4433139,,tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,low Erk activity; rep2,Reads were trimmed by Trim Galore 0.4.1  with  q 15   paired and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,low Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially  events were gated using Forward versus Side Scatter Areas 488 nm laser. Then  single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally  H2A mCherry+ Venus hGeminin  and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales  in three rows  from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp  all regenerating scales were plucked  and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade   Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min  500 µl of supernatant was removed  quenched with 65µl sheep serum Sigma S2263 on ice  and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,GSM4433139,GSM4433139: low Erk activity; rep2; Danio rerio; RNA Seq,GSM4433139,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,5G_minus_1.fq.gz 5G_minus_2.fq.gz,fastq fastq,4705295600.0,47052956.0,GSM4433139 r1,0:100 1:100,A:1240779500;C:1112511484;G:1096653049;T:1255351567;N:0,100,100,,,1240779500,1112511484,1096653049,1255351567,0,SRX8003659,SRS6377639,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.89254,,0.04065,,0.81197,,0.46307,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
58582,SRR11425292,SRX8003658,SRS6377638,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus  by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin  we could sort osteoblasts into separate Erk+ and Erk  populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically  dusp2  dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal  which anti correlates with Erk activity.,,pubmed:33408418,,low Erk activity; rep1,GSM4433138,,tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,low Erk activity; rep1,Reads were trimmed by Trim Galore 0.4.1  with  q 15   paired and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,low Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially  events were gated using Forward versus Side Scatter Areas 488 nm laser. Then  single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally  H2A mCherry+ Venus hGeminin  and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales  in three rows  from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp  all regenerating scales were plucked  and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade   Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min  500 µl of supernatant was removed  quenched with 65µl sheep serum Sigma S2263 on ice  and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,GSM4433138,GSM4433138: low Erk activity; rep1; Danio rerio; RNA Seq,GSM4433138,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433138,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,3G_minus_1.fq.gz 3G_minus_2.fq.gz,fastq fastq,4707783400.0,47077834.0,GSM4433138 r1,0:100 1:100,A:1275040914;C:1077730597;G:1059242617;T:1295769272;N:0,100,100,,,1275040914,1077730597,1059242617,1295769272,0,SRX8003658,SRS6377638,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.8629,,0.13994,,0.7838,,0.50568,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
58583,SRR11425297,SRX8003657,SRS6377637,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus  by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin  we could sort osteoblasts into separate Erk+ and Erk  populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically  dusp2  dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal  which anti correlates with Erk activity.,,pubmed:33408418,,high Erk activity; rep3,GSM4433143,,tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,high Erk activity; rep3,Reads were trimmed by Trim Galore 0.4.1  with  q 15   paired and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,high Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially  events were gated using Forward versus Side Scatter Areas 488 nm laser. Then  single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally  H2A mCherry+ Venus hGeminin  and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales  in three rows  from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp  all regenerating scales were plucked  and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade   Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min  500 µl of supernatant was removed  quenched with 65µl sheep serum Sigma S2263 on ice  and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,GSM4433143,GSM4433143: high Erk activity; rep3; Danio rerio; RNA Seq,GSM4433143,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433143,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,6B_plus_1.fq.gz 6B_plus_2.fq.gz,fastq fastq,4703728000.0,47037280.0,GSM4433143 r1,0:100 1:100,A:1231849303;C:1116643672;G:1102072724;T:1253162301;N:0,100,100,,,1231849303,1116643672,1102072724,1253162301,0,SRX8003657,SRS6377637,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.89702,,0.07131,,0.82978,,0.49499,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
58584,SRR11425296,SRX8003656,SRS6377636,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus  by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin  we could sort osteoblasts into separate Erk+ and Erk  populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically  dusp2  dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal  which anti correlates with Erk activity.,,pubmed:33408418,,high Erk activity; rep2,GSM4433142,,tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,high Erk activity; rep2,Reads were trimmed by Trim Galore 0.4.1  with  q 15   paired and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,high Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially  events were gated using Forward versus Side Scatter Areas 488 nm laser. Then  single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally  H2A mCherry+ Venus hGeminin  and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales  in three rows  from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp  all regenerating scales were plucked  and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade   Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min  500 µl of supernatant was removed  quenched with 65µl sheep serum Sigma S2263 on ice  and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,GSM4433142,GSM4433142: high Erk activity; rep2; Danio rerio; RNA Seq,GSM4433142,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433142,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,5G_plus_1.fq.gz 5G_plus_2.fq.gz,fastq fastq,4708623600.0,47086236.0,GSM4433142 r1,0:100 1:100,A:1200601624;C:1150903127;G:1136628277;T:1220490572;N:0,100,100,,,1200601624,1150903127,1136628277,1220490572,0,SRX8003656,SRS6377636,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.90729,,0.03751,,0.84433,,0.50342,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
59480,SRR11922874,SRX8468588,SRS6769276,SRP265910,PRJNA637219,Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes,GSE151770,Transcriptome Analysis,Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf,,pubmed:32980661,,zebrafish embryo Aldh3a1 KO rep6,GSM4590772,,source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf,zebrafish embryo Aldh3a1 KO rep6,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,zebrafish embryo,Not applicable,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation,genotype:aldh3a1 KO|tissue:embryo|age:48 hpf,GSM4590772,GSM4590772: zebrafish embryo Aldh3a1 KO rep6; Danio rerio; RNA Seq,GSM4590772,,1,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM4590772,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP265910,,,12_aldh3a1----homo-48hpf-6_1.fq.gz 12_aldh3a1----homo-48hpf-6_2.fq.gz,fastq fastq,4660603600.0,46606036.0,GSM4590772 r1,0:100 1:100,A:1396899993;C:924291840;G:902974172;T:1436437595;N:0,100,100,,,1396899993,924291840,902974172,1436437595,0,SRX8468588,SRS6769276,SRA1083013,GEO,"ZMF, University Heidelberg",1,0.90281,,0.2525,,0.75943,,0.62165,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2020-06-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
59481,SRR11922873,SRX8468587,SRS6769275,SRP265910,PRJNA637219,Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes,GSE151770,Transcriptome Analysis,Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf,,pubmed:32980661,,zebrafish embryo Aldh3a1 KO rep5,GSM4590771,,source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf,zebrafish embryo Aldh3a1 KO rep5,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,zebrafish embryo,Not applicable,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation,genotype:aldh3a1 KO|tissue:embryo|age:48 hpf,GSM4590771,GSM4590771: zebrafish embryo Aldh3a1 KO rep5; Danio rerio; RNA Seq,GSM4590771,,1,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM4590771,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP265910,,,11_aldh3a1----homo-48hpf-5_1.fq.gz 11_aldh3a1----homo-48hpf-5_2.fq.gz,fastq fastq,3919649800.0,39196498.0,GSM4590771 r1,0:100 1:100,A:1203194756;C:742776682;G:744133378;T:1229544984;N:0,100,100,,,1203194756,742776682,744133378,1229544984,0,SRX8468587,SRS6769275,SRA1083013,GEO,"ZMF, University Heidelberg",1,0.86745,,0.31349,,0.76702,,0.63864,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2020-06-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
59482,SRR11922872,SRX8468586,SRS6769274,SRP265910,PRJNA637219,Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes,GSE151770,Transcriptome Analysis,Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf,,pubmed:32980661,,zebrafish embryo Aldh3a1 KO rep4,GSM4590770,,source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf,zebrafish embryo Aldh3a1 KO rep4,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,zebrafish embryo,Not applicable,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation,genotype:aldh3a1 KO|tissue:embryo|age:48 hpf,GSM4590770,GSM4590770: zebrafish embryo Aldh3a1 KO rep4; Danio rerio; RNA Seq,GSM4590770,,1,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM4590770,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP265910,,,10_aldh3a1----homo-48hpf-4_2.fq.gz 10_aldh3a1----homo-48hpf-4_1.fq.gz,fastq fastq,4549625000.0,45496250.0,GSM4590770 r1,0:100 1:100,A:1345145181;C:925949636;G:905779914;T:1372750269;N:0,100,100,,,1345145181,925949636,905779914,1372750269,0,SRX8468586,SRS6769274,SRA1083013,GEO,"ZMF, University Heidelberg",1,0.9117,,0.23055,,0.72545,,0.50968,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2020-06-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
59483,SRR11922871,SRX8468585,SRS6769273,SRP265910,PRJNA637219,Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes,GSE151770,Transcriptome Analysis,Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf,,pubmed:32980661,,zebrafish embryo Aldh3a1 KO rep3,GSM4590769,,source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf,zebrafish embryo Aldh3a1 KO rep3,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,zebrafish embryo,Not applicable,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation,genotype:aldh3a1 KO|tissue:embryo|age:48 hpf,GSM4590769,GSM4590769: zebrafish embryo Aldh3a1 KO rep3; Danio rerio; RNA Seq,GSM4590769,,1,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM4590769,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP265910,,,9_aldh3a1----homo-48hpf-3_1.fq.gz 9_aldh3a1----homo-48hpf-3_2.fq.gz,fastq fastq,4194991600.0,41949916.0,GSM4590769 r1,0:100 1:100,A:1258296885;C:833884600;G:816600639;T:1286209476;N:0,100,100,,,1258296885,833884600,816600639,1286209476,0,SRX8468585,SRS6769273,SRA1083013,GEO,"ZMF, University Heidelberg",1,0.89574,,0.28139,,0.73397,,0.56688,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2020-06-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
59484,SRR11922870,SRX8468584,SRS6769272,SRP265910,PRJNA637219,Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes,GSE151770,Transcriptome Analysis,Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf,,pubmed:32980661,,zebrafish embryo Aldh3a1 KO rep2,GSM4590768,,source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf,zebrafish embryo Aldh3a1 KO rep2,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,zebrafish embryo,Not applicable,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation,genotype:aldh3a1 KO|tissue:embryo|age:48 hpf,GSM4590768,GSM4590768: zebrafish embryo Aldh3a1 KO rep2; Danio rerio; RNA Seq,GSM4590768,,1,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM4590768,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP265910,,,8_aldh3a1----homo-48hpf-2_1.fq.gz 8_aldh3a1----homo-48hpf-2_2.fq.gz,fastq fastq,5097901600.0,50979016.0,GSM4590768 r1,0:100 1:100,A:1487281075;C:1055394796;G:1035616985;T:1519608744;N:0,100,100,,,1487281075,1055394796,1035616985,1519608744,0,SRX8468584,SRS6769272,SRA1083013,GEO,"ZMF, University Heidelberg",1,0.92556,,0.18622,,0.73026,,0.5187,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2020-06-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
59485,SRR11922869,SRX8468583,SRS6769271,SRP265910,PRJNA637219,Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes,GSE151770,Transcriptome Analysis,Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf,,pubmed:32980661,,zebrafish embryo Aldh3a1 KO rep1,GSM4590767,,source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf,zebrafish embryo Aldh3a1 KO rep1,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,zebrafish embryo,Not applicable,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation,genotype:aldh3a1 KO|tissue:embryo|age:48 hpf,GSM4590767,GSM4590767: zebrafish embryo Aldh3a1 KO rep1; Danio rerio; RNA Seq,GSM4590767,,1,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM4590767,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP265910,,,7_aldh3a1----homo-48hpf-1_1.fq.gz 7_aldh3a1----homo-48hpf-1_2.fq.gz,fastq fastq,5075421000.0,50754210.0,GSM4590767 r1,0:100 1:100,A:1523744143;C:1008915874;G:985443760;T:1557317223;N:0,100,100,,,1523744143,1008915874,985443760,1557317223,0,SRX8468583,SRS6769271,SRA1083013,GEO,"ZMF, University Heidelberg",1,0.90167,,0.27915,,0.75879,,0.6673,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2020-06-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
59486,SRR11922868,SRX8468582,SRS6769270,SRP265910,PRJNA637219,Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes,GSE151770,Transcriptome Analysis,Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf,,pubmed:32980661,,zebrafish embryo wildtype rep5,GSM4590766,,source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf,zebrafish embryo wildtype rep5,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,zebrafish embryo,Not applicable,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation,genotype:WT|tissue:embryo|age:48 hpf,GSM4590766,GSM4590766: zebrafish embryo wildtype rep5; Danio rerio; RNA Seq,GSM4590766,,1,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM4590766,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP265910,,,6_aldh3a1+-+-wt-48hpf-R_1.fq.gz 6_aldh3a1+-+-wt-48hpf-R_2.fq.gz,fastq fastq,5097636600.0,50976366.0,GSM4590766 r1,0:100 1:100,A:1402424015;C:1146863463;G:1121174200;T:1427174922;N:0,100,100,,,1402424015,1146863463,1121174200,1427174922,0,SRX8468582,SRS6769270,SRA1083013,GEO,"ZMF, University Heidelberg",1,0.95115,,0.09816,,0.69781,,0.46194,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2020-06-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
59487,SRR11922867,SRX8468581,SRS6769269,SRP265910,PRJNA637219,Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes,GSE151770,Transcriptome Analysis,Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf,,pubmed:32980661,,zebrafish embryo wildtype rep4,GSM4590765,,source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf,zebrafish embryo wildtype rep4,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,zebrafish embryo,Not applicable,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation,genotype:WT|tissue:embryo|age:48 hpf,GSM4590765,GSM4590765: zebrafish embryo wildtype rep4; Danio rerio; RNA Seq,GSM4590765,,1,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM4590765,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP265910,,,4_aldh3a1+-+-wt-48hpf-4_1.fq.gz 4_aldh3a1+-+-wt-48hpf-4_2.fq.gz,fastq fastq,4847250800.0,48472508.0,GSM4590765 r1,0:100 1:100,A:1351516729;C:1070410976;G:1050113082;T:1375210013;N:0,100,100,,,1351516729,1070410976,1050113082,1375210013,0,SRX8468581,SRS6769269,SRA1083013,GEO,"ZMF, University Heidelberg",1,0.94418,,0.12404,,0.69374,,0.49948,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2020-06-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
59488,SRR11922866,SRX8468580,SRS6769268,SRP265910,PRJNA637219,Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes,GSE151770,Transcriptome Analysis,Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf,,pubmed:32980661,,zebrafish embryo wildtype rep3,GSM4590764,,source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf,zebrafish embryo wildtype rep3,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,zebrafish embryo,Not applicable,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation,genotype:WT|tissue:embryo|age:48 hpf,GSM4590764,GSM4590764: zebrafish embryo wildtype rep3; Danio rerio; RNA Seq,GSM4590764,,1,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM4590764,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP265910,,,3_aldh3a1+-+-wt-48hpf-3_1.fq.gz 3_aldh3a1+-+-wt-48hpf-3_2.fq.gz,fastq fastq,5083417400.0,50834174.0,GSM4590764 r1,0:100 1:100,A:1375006484;C:1168556107;G:1139277849;T:1400576960;N:0,100,100,,,1375006484,1168556107,1139277849,1400576960,0,SRX8468580,SRS6769268,SRA1083013,GEO,"ZMF, University Heidelberg",1,0.95419,,0.09201,,0.69209,,0.48244,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2020-06-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
59489,SRR11922865,SRX8468579,SRS6769267,SRP265910,PRJNA637219,Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes,GSE151770,Transcriptome Analysis,Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf,,pubmed:32980661,,zebrafish embryo wildtype rep2,GSM4590763,,source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf,zebrafish embryo wildtype rep2,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,zebrafish embryo,Not applicable,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation,genotype:WT|tissue:embryo|age:48 hpf,GSM4590763,GSM4590763: zebrafish embryo wildtype rep2; Danio rerio; RNA Seq,GSM4590763,,1,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM4590763,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP265910,,,2_aldh3a1+-+-wt-48hpf-2_1.fq.gz 2_aldh3a1+-+-wt-48hpf-2_2.fq.gz,fastq fastq,5089646400.0,50896464.0,GSM4590763 r1,0:100 1:100,A:1384714450;C:1161015785;G:1138313445;T:1405602720;N:0,100,100,,,1384714450,1161015785,1138313445,1405602720,0,SRX8468579,SRS6769267,SRA1083013,GEO,"ZMF, University Heidelberg",1,0.95309,,0.09301,,0.69798,,0.48524,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2020-06-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
59490,SRR11922864,SRX8468578,SRS6769266,SRP265910,PRJNA637219,Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 /  Zebrafish Embryo Transcriptomes,GSE151770,Transcriptome Analysis,Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level  we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 /  larvae at 48 hpf.An overview of RNA Seq  including quality control  principal component analysis PCA  volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score   1.72; p=0.0006. Interestingly  endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together  these results further suggest Aldh3a1 as an important regulator in the development  morphology and insulin secretion function of primary pancreas. Furthermore  we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 /  zebrafish embryo at 48 hpf,,pubmed:32980661,,zebrafish embryo wildtype rep1,GSM4590762,,source name:zebrafish embryo|genotype:WT|tissue:embryo|age:48 hpf,zebrafish embryo wildtype rep1,trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,zebrafish embryo,Not applicable,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,Zebrafish were raised and staged  under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation,genotype:WT|tissue:embryo|age:48 hpf,GSM4590762,GSM4590762: zebrafish embryo wildtype rep1; Danio rerio; RNA Seq,GSM4590762,,1,Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM4590762,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP265910,,,1_aldh3a1+-+-wt-48hpf-1_1.fq.gz 1_aldh3a1+-+-wt-48hpf-1_2.fq.gz,fastq fastq,5098267400.0,50982674.0,GSM4590762 r1,0:100 1:100,A:1406329756;C:1147290302;G:1118206731;T:1426440611;N:0,100,100,,,1406329756,1147290302,1118206731,1426440611,0,SRX8468578,SRS6769266,SRA1083013,GEO,"ZMF, University Heidelberg",1,0.95039,,0.10482,,0.69641,,0.47979,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2020-06-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
60203,SRR12173066,SRX8687829,SRS6966493,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,100B,GSM4661929,,source name:SCA12|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:male,100B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,SCA12,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:M,GSM4661929,GSM4661929: 100B; Danio rerio; RNA Seq,GSM4661929,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661929,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,100B_2.fq 100B_1.fq,fastq fastq,4300755000.0,43007550.0,GSM4661929 r1,0:100 1:100,A:1195013481;C:933832983;G:962461499;T:1209447037;N:0,100,100,,,1195013481,933832983,962461499,1209447037,0,SRX8687829,SRS6966493,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.91912,,0.15522,,0.71829,,0.50865,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60204,SRR12173065,SRX8687828,SRS6966492,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,99B,GSM4661928,,source name:SCA10|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:male,99B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,SCA10,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:M,GSM4661928,GSM4661928: 99B; Danio rerio; RNA Seq,GSM4661928,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661928,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,99B_2.fq 99B_1.fq,fastq fastq,4953251000.0,49532510.0,GSM4661928 r1,0:100 1:100,A:1415039103;C:1040525484;G:1060332314;T:1437354099;N:0,100,100,,,1415039103,1040525484,1060332314,1437354099,0,SRX8687828,SRS6966492,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.91619,,0.16544,,0.71922,,0.51996,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60205,SRR12173064,SRX8687827,SRS6966491,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,121B,GSM4661927,,source name:SCA14|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:male,121B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,SCA14,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:M,GSM4661927,GSM4661927: 121B; Danio rerio; RNA Seq,GSM4661927,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661927,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,121B_1.fq 121B_2.fq,fastq fastq,4482694600.0,44826946.0,GSM4661927 r1,0:100 1:100,A:1292365837;C:920169200;G:950296696;T:1319862867;N:0,100,100,,,1292365837,920169200,950296696,1319862867,0,SRX8687827,SRS6966491,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.90277,,0.17799,,0.72295,,0.51987,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60206,SRR12173063,SRX8687826,SRS6966490,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,97B,GSM4661926,,source name:SCA5|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:male,97B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,SCA5,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:M,GSM4661926,GSM4661926: 97B; Danio rerio; RNA Seq,GSM4661926,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661926,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,97B_1.fq 97B_2.fq,fastq fastq,5178357000.0,51783570.0,GSM4661926 r1,0:100 1:100,A:1442148425;C:1119935128;G:1149243236;T:1467030211;N:0,100,100,,,1442148425,1119935128,1149243236,1467030211,0,SRX8687826,SRS6966490,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.91869,,0.1619,,0.71047,,0.50907,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60207,SRR12173062,SRX8687825,SRS6966489,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,80B,GSM4661925,,source name:SCA8|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:female,80B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,SCA8,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:F,GSM4661925,GSM4661925: 80B; Danio rerio; RNA Seq,GSM4661925,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661925,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,80B_1.fq 80B_2.fq,fastq fastq,4927736800.0,49277368.0,GSM4661925 r1,0:100 1:100,A:1384189069;C:1048151377;G:1079300714;T:1416095640;N:0,100,100,,,1384189069,1048151377,1079300714,1416095640,0,SRX8687825,SRS6966489,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.9104,,0.17333,,0.71102,,0.50853,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60208,SRR12173061,SRX8687824,SRS6966488,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,79B,GSM4661924,,source name:SCA7|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:female,79B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,SCA7,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:F,GSM4661924,GSM4661924: 79B; Danio rerio; RNA Seq,GSM4661924,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661924,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,79B_1.fq 79B_2.fq,fastq fastq,5158717400.0,51587174.0,GSM4661924 r1,0:100 1:100,A:1423369091;C:1127803059;G:1156903341;T:1450641909;N:0,100,100,,,1423369091,1127803059,1156903341,1450641909,0,SRX8687824,SRS6966488,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.91578,,0.15498,,0.70841,,0.50875,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60209,SRR12173060,SRX8687823,SRS6966487,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,78B,GSM4661923,,source name:SCA6|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:female,78B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,SCA6,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:F,GSM4661923,GSM4661923: 78B; Danio rerio; RNA Seq,GSM4661923,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661923,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,78B_2.fq 78B_1.fq,fastq fastq,4080284000.0,40802840.0,GSM4661923 r1,0:100 1:100,A:1146760011;C:872005355;G:893480498;T:1168038136;N:0,100,100,,,1146760011,872005355,893480498,1168038136,0,SRX8687823,SRS6966487,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.89506,,0.16061,,0.7147,,0.51109,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60210,SRR12173059,SRX8687822,SRS6966486,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,77B,GSM4661922,,source name:SCA4|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:female,77B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,SCA4,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:F,GSM4661922,GSM4661922: 77B; Danio rerio; RNA Seq,GSM4661922,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661922,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,77B_1.fq 77B_2.fq,fastq fastq,5053965200.0,50539652.0,GSM4661922 r1,0:100 1:100,A:1432899891;C:1065155546;G:1092749323;T:1463160440;N:0,100,100,,,1432899891,1065155546,1092749323,1463160440,0,SRX8687822,SRS6966486,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.90965,,0.17028,,0.71259,,0.51804,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60211,SRR12173058,SRX8687821,SRS6966485,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,95B,GSM4661921,,source name:PH8|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:male,95B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,PH8,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:M,GSM4661921,GSM4661921: 95B; Danio rerio; RNA Seq,GSM4661921,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661921,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,95B_2.fq 95B_1.fq,fastq fastq,4984910800.0,49849108.0,GSM4661921 r1,0:100 1:100,A:1404088729;C:1063272664;G:1094657988;T:1422891419;N:0,100,100,,,1404088729,1063272664,1094657988,1422891419,0,SRX8687821,SRS6966485,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.91574,,0.16729,,0.71776,,0.51526,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60212,SRR12173057,SRX8687820,SRS6966484,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,94B,GSM4661920,,source name:PH7|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:male,94B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,PH7,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:M,GSM4661920,GSM4661920: 94B; Danio rerio; RNA Seq,GSM4661920,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661920,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,94B_2.fq 94B_1.fq,fastq fastq,4973104000.0,49731040.0,GSM4661920 r1,0:100 1:100,A:1403074698;C:1055981307;G:1089110444;T:1424937551;N:0,100,100,,,1403074698,1055981307,1089110444,1424937551,0,SRX8687820,SRS6966484,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.91432,,0.16183,,0.72001,,0.51323,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60213,SRR12173056,SRX8687819,SRS6966483,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,93B,GSM4661919,,source name:PH6|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:male,93B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,PH6,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:M,GSM4661919,GSM4661919: 93B; Danio rerio; RNA Seq,GSM4661919,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661919,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,93B_2.fq 93B_1.fq,fastq fastq,4896774400.0,48967744.0,GSM4661919 r1,0:100 1:100,A:1403923710;C:1011507726;G:1048273729;T:1433069235;N:0,100,100,,,1403923710,1011507726,1048273729,1433069235,0,SRX8687819,SRS6966483,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.91124,,0.1598,,0.72247,,0.54532,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60214,SRR12173055,SRX8687818,SRS6966482,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,92B,GSM4661918,,source name:PH4|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:male,92B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,PH4,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:M,GSM4661918,GSM4661918: 92B; Danio rerio; RNA Seq,GSM4661918,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661918,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,92B_1.fq 92B_2.fq,fastq fastq,5153962600.0,51539626.0,GSM4661918 r1,0:100 1:100,A:1429538166;C:1118723084;G:1151444792;T:1454256558;N:0,100,100,,,1429538166,1118723084,1151444792,1454256558,0,SRX8687818,SRS6966482,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.91817,,0.15904,,0.71088,,0.51009,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60215,SRR12173054,SRX8687817,SRS6966481,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,75B,GSM4661917,,source name:PH10|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:female,75B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,PH10,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:F,GSM4661917,GSM4661917: 75B; Danio rerio; RNA Seq,GSM4661917,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661917,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,75B_1.fq 75B_2.fq,fastq fastq,4868261600.0,48682616.0,GSM4661917 r1,0:100 1:100,A:1376009816;C:1028298503;G:1057930129;T:1406023152;N:0,100,100,,,1376009816,1028298503,1057930129,1406023152,0,SRX8687817,SRS6966481,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.9126,,0.1697,,0.71638,,0.50591,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60216,SRR12173053,SRX8687816,SRS6966480,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,74B,GSM4661916,,source name:PH9|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:female,74B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,PH9,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:F,GSM4661916,GSM4661916: 74B; Danio rerio; RNA Seq,GSM4661916,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661916,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,74B_1.fq 74B_2.fq,fastq fastq,5179173200.0,51791732.0,GSM4661916 r1,0:100 1:100,A:1449133916;C:1117631254;G:1139937410;T:1472470620;N:0,100,100,,,1449133916,1117631254,1139937410,1472470620,0,SRX8687816,SRS6966480,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.91222,,0.16046,,0.71029,,0.50076,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60217,SRR12173052,SRX8687815,SRS6966479,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,72B,GSM4661915,,source name:PH2|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:female,72B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,PH2,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:F,GSM4661915,GSM4661915: 72B; Danio rerio; RNA Seq,GSM4661915,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661915,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,72B_1.fq 72B_2.fq,fastq fastq,5878512600.0,58785126.0,GSM4661915 r1,0:100 1:100,A:1639773073;C:1271766251;G:1298391071;T:1668582205;N:0,100,100,,,1639773073,1271766251,1298391071,1668582205,0,SRX8687815,SRS6966479,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.91084,,0.16615,,0.70713,,0.5033,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60218,SRR12173051,SRX8687814,SRS6966478,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,71B,GSM4661914,,source name:PH1|tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:female,71B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,PH1,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F1|Sex:F,GSM4661914,GSM4661914: 71B; Danio rerio; RNA Seq,GSM4661914,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661914,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,71B_1.fq 71B_2.fq,fastq fastq,2921419400.0,29214194.0,GSM4661914 r1,0:100 1:100,A:838032642;C:606973028;G:618918524;T:857495206;N:0,100,100,,,838032642,606973028,618918524,857495206,0,SRX8687814,SRS6966478,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.90765,,0.17712,,0.71015,,0.48691,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60219,SRR12173050,SRX8687813,SRS6966477,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,173B,GSM4661913,,source name:SCA10|tissue:whole brain|age:adult|strain:AB line|generation:F2|Sex:male,173B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,SCA10,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F2|Sex:M,GSM4661913,GSM4661913: 173B; Danio rerio; RNA Seq,GSM4661913,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661913,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,V300016697_L3_DKRT190808OligoTB44-68_1.fq.gz V300016697_L3_DKRT190808OligoTB44-68_2.fq.gz,fastq fastq,4933950400.0,49339504.0,GSM4661913 r1,0:100 1:100,A:1477278267;C:971417805;G:982397108;T:1502857220;N:0,100,100,,,1477278267,971417805,982397108,1502857220,0,SRX8687813,SRS6966477,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.90094,,0.26419,,0.73066,,0.51886,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60220,SRR12173049,SRX8687812,SRS6966476,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,172B,GSM4661912,,source name:SCA7|tissue:whole brain|age:adult|strain:AB line|generation:F2|Sex:male,172B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,SCA7,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F2|Sex:M,GSM4661912,GSM4661912: 172B; Danio rerio; RNA Seq,GSM4661912,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661912,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,V300016697_L3_DKRT190808OligoTB43-67_1.fq.gz V300016697_L3_DKRT190808OligoTB43-67_2.fq.gz,fastq fastq,4916317800.0,49163178.0,GSM4661912 r1,0:100 1:100,A:1456100891;C:983643530;G:996293468;T:1480279911;N:0,100,100,,,1456100891,983643530,996293468,1480279911,0,SRX8687812,SRS6966476,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.90484,,0.24497,,0.72563,,0.51605,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System
60221,SRR12173048,SRX8687811,SRS6966475,SRP270926,PRJNA644883,Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154020,Transcriptome Analysis,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. Thus  we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0  genes and pathways related to glutamatergic synapse activity Gene Ontology and Reactome databases were significantly enriched and may explain the behavioral effects. In F1 and F2 generations  mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation. Overall design: RNA sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation,,pubmed:33752003,,171B,GSM4661911,,source name:SCA5|tissue:whole brain|age:adult|strain:AB line|generation:F2|Sex:male,171B,Base calling and prefiltering adaptor removal was performed by BGI STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters Counts of reads per gene were obtained with HTSeq v0.11.2 gtf annotation file GRCz11.97 Use of DESeq2 v1.24.0 for differential gene expression analysis Genome build: DanRer11 Supplementary files format and content: csv file including raw counts obtained from htseq unnormalized.,SCA5,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,,tissue:whole brain|age:adult|strain:AB line|generation:F2|Sex:M,GSM4661911,GSM4661911: 171B; Danio rerio; RNA Seq,GSM4661911,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and RNA was extracted using TriPrep extraction kit Macherey Nagel. One microg of total RNA was sent to BGI Europe A/S for pair ended transcriptome sequencing on BGI Seq500 according to BGI standard protocol,GEO Accession:GSM4661911,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP270926,,,V300016697_L3_DKRT190808OligoTB42-66_1.fq.gz V300016697_L3_DKRT190808OligoTB42-66_2.fq.gz,fastq fastq,4935261800.0,49352618.0,GSM4661911 r1,0:100 1:100,A:1445056643;C:1003559733;G:1015728708;T:1470916716;N:0,100,100,,,1445056643,1003559733,1015728708,1470916716,0,SRX8687811,SRS6966475,SRA1096323,GEO,"UMR MARBEC, INRAE",1,0.90817,,0.23047,,0.72086,,0.5134,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,France,2020-07-08,Adult,Adult,Brain,Nervous System