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
48009,SRR6910782,SRX3858788,SRS3106147,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury  whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart yap sham 3,GSM3070341,,tissue:7 xxx post injury  sham  yap mutant zebrafish heart  replicate 3|injury type:Sham Injured|genotype:yap  / ,zebrafish heart yap sham 3,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2 was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury  sham  yap mutant zebrafish heart  replicate 3,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Sham Injured|genotype:yap  / ,GSM3070341,GSM3070341: zebrafish heart yap sham 3; Danio rerio; RNA Seq,GSM3070341,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070341,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAFRACPEI-39_1.fq.gz,fastq,951999850.0,19039997.0,GSM3070341 r1,0:50,A:264195948;C:210535284;G:216206679;T:260149711;N:912228,50,,,,264195948,210535284,216206679,260149711,912228,SRX3858788,SRS3106147,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.94079,,0.07209,,0.77506,,0.57202,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System
48010,SRR6910781,SRX3858787,SRS3106141,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury  whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart yap sham 2,GSM3070340,,tissue:7 xxx post injury  sham  yap mutant zebrafish heart  replicate 2|injury type:Sham Injured|genotype:yap  / ,zebrafish heart yap sham 2,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2 was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury  sham  yap mutant zebrafish heart  replicate 2,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Sham Injured|genotype:yap  / ,GSM3070340,GSM3070340: zebrafish heart yap sham 2; Danio rerio; RNA Seq,GSM3070340,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070340,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAERABPEI-38_1.fq.gz,fastq,1422243650.0,28444873.0,GSM3070340 r1,0:50,A:396912878;C:311739320;G:316711298;T:395335784;N:1544370,50,,,,396912878,311739320,316711298,395335784,1544370,SRX3858787,SRS3106141,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.92453,,0.08919,,0.75402,,0.56482,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System
48011,SRR6910780,SRX3858786,SRS3106146,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury  whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart yap sham 1,GSM3070339,,tissue:7 xxx post injury  sham  yap mutant zebrafish heart  replicate 1|injury type:Sham Injured|genotype:yap  / ,zebrafish heart yap sham 1,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2 was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury  sham  yap mutant zebrafish heart  replicate 1,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Sham Injured|genotype:yap  / ,GSM3070339,GSM3070339: zebrafish heart yap sham 1; Danio rerio; RNA Seq,GSM3070339,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070339,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAADRABPEI-35_1.fq.gz,fastq,1414732800.0,28294656.0,GSM3070339 r1,0:50,A:382546700;C:323161121;G:333740729;T:373569891;N:1714359,50,,,,382546700,323161121,333740729,373569891,1714359,SRX3858786,SRS3106146,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93663,,0.06374,,0.78476,,0.50181,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System
48012,SRR6910779,SRX3858785,SRS3106140,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury  whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart yap cryo 3,GSM3070338,,tissue:7 xxx post injury  cryoinjury  yap mutant zebrafish heart  replicate 3|injury type:Cryoinjured|genotype:yap  / ,zebrafish heart yap cryo 3,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2 was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury  cryoinjury  yap mutant zebrafish heart  replicate 3,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Cryoinjured|genotype:yap  / ,GSM3070338,GSM3070338: zebrafish heart yap cryo 3; Danio rerio; RNA Seq,GSM3070338,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070338,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAALRABPEI-45_1.fq.gz,fastq,1417604550.0,28352091.0,GSM3070338 r1,0:50,A:396320928;C:310857539;G:315507312;T:393521845;N:1396926,50,,,,396320928,310857539,315507312,393521845,1396926,SRX3858785,SRS3106140,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93466,,0.08509,,0.76339,,0.55298,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System
48013,SRR6910778,SRX3858784,SRS3106139,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury  whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart yap cryo 2,GSM3070337,,tissue:7 xxx post injury  cryoinjury  yap mutant zebrafish heart  replicate 2|injury type:Cryoinjured|genotype:yap  / ,zebrafish heart yap cryo 2,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2 was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury  cryoinjury  yap mutant zebrafish heart  replicate 2,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Cryoinjured|genotype:yap  / ,GSM3070337,GSM3070337: zebrafish heart yap cryo 2; Danio rerio; RNA Seq,GSM3070337,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070337,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAKRABPEI-44_1.fq.gz,fastq,1411684000.0,28233680.0,GSM3070337 r1,0:50,A:380723872;C:320871596;G:326847305;T:381926882;N:1314345,50,,,,380723872,320871596,326847305,381926882,1314345,SRX3858784,SRS3106139,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93583,,0.07153,,0.76209,,0.53446,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System
48014,SRR6910777,SRX3858783,SRS3106138,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury  whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart yap cryo 1,GSM3070336,,tissue:7 xxx post injury  cryoinjury  yap mutant zebrafish heart  replicate 1|injury type:Cryoinjured|genotype:yap  / ,zebrafish heart yap cryo 1,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2 was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury  cryoinjury  yap mutant zebrafish heart  replicate 1,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Cryoinjured|genotype:yap  / ,GSM3070336,GSM3070336: zebrafish heart yap cryo 1; Danio rerio; RNA Seq,GSM3070336,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070336,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170901_I13_CL100030164_L2_HK500ZEBljgRAAARAAPEI-2_1.fq.gz,fastq,983464900.0,19669298.0,GSM3070336 r1,0:50,A:281927620;C:213905948;G:225993312;T:260949314;N:688706,50,,,,281927620,213905948,225993312,260949314,688706,SRX3858783,SRS3106138,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93596,,0.08164,,0.75753,,0.5319,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System
48015,SRR6910776,SRX3858782,SRS3106137,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury  whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart wt sham 3,GSM3070335,,tissue:7 xxx post injury  sham  wildtype zebrafish heart  replicate 3|injury type:Sham Injured|genotype:yap +/+,zebrafish heart wt sham 3,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2 was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury  sham  wildtype zebrafish heart  replicate 3,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Sham Injured|genotype:yap +/+,GSM3070335,GSM3070335: zebrafish heart wt sham 3; Danio rerio; RNA Seq,GSM3070335,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070335,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAACRABPEI-34_1.fq.gz,fastq,1422074600.0,28441492.0,GSM3070335 r1,0:50,A:391714900;C:316763778;G:323715902;T:388371260;N:1508760,50,,,,391714900,316763778,323715902,388371260,1508760,SRX3858782,SRS3106137,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93511,,0.06875,,0.78374,,0.5442,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System
48016,SRR6910775,SRX3858781,SRS3106142,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury  whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart wt sham 2,GSM3070334,,tissue:7 xxx post injury  sham  wildtype zebrafish heart  replicate 2|injury type:Sham Injured|genotype:yap +/+,zebrafish heart wt sham 2,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2 was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury  sham  wildtype zebrafish heart  replicate 2,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Sham Injured|genotype:yap +/+,GSM3070334,GSM3070334: zebrafish heart wt sham 2; Danio rerio; RNA Seq,GSM3070334,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070334,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAABRABPEI-32_1.fq.gz,fastq,1422698650.0,28453973.0,GSM3070334 r1,0:50,A:393538224;C:315070062;G:319739652;T:393085965;N:1264747,50,,,,393538224,315070062,319739652,393085965,1264747,SRX3858781,SRS3106142,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93436,,0.08499,,0.76599,,0.51331,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System
48017,SRR6910774,SRX3858780,SRS3106135,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury  whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart wt sham 1,GSM3070333,,tissue:7 xxx post injury  sham  wildtype zebrafish heart  replicate 1|injury type:Sham Injured|genotype:yap +/+,zebrafish heart wt sham 1,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2 was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury  sham  wildtype zebrafish heart  replicate 1,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Sham Injured|genotype:yap +/+,GSM3070333,GSM3070333: zebrafish heart wt sham 1; Danio rerio; RNA Seq,GSM3070333,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070333,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAARAAPEI-30_1.fq.gz,fastq,1421323500.0,28426470.0,GSM3070333 r1,0:50,A:398883510;C:309497967;G:316648847;T:394532024;N:1761152,50,,,,398883510,309497967,316648847,394532024,1761152,SRX3858780,SRS3106135,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93565,,0.0827,,0.77749,,0.54321,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System
48018,SRR6910773,SRX3858779,SRS3106136,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury  whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart wt cryo 3,GSM3070332,,tissue:7 xxx post injury  cryoinjury  wildtype zebrafish heart  replicate 3|injury type:Cryoinjured|genotype:yap +/+,zebrafish heart wt cryo 3,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2 was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury  cryoinjury  wildtype zebrafish heart  replicate 3,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Cryoinjured|genotype:yap +/+,GSM3070332,GSM3070332: zebrafish heart wt cryo 3; Danio rerio; RNA Seq,GSM3070332,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070332,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAIRABPEI-42_1.fq.gz,fastq,1420446700.0,28408934.0,GSM3070332 r1,0:50,A:390252025;C:317481829;G:322013373;T:389237056;N:1462417,50,,,,390252025,317481829,322013373,389237056,1462417,SRX3858779,SRS3106136,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.92817,,0.08055,,0.75304,,0.54626,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System
48019,SRR6910772,SRX3858778,SRS3106133,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury  whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart wt cryo 2,GSM3070331,,tissue:7 xxx post injury  cryoinjury  wildtype zebrafish heart  replicate 2|injury type:Cryoinjured|genotype:yap +/+,zebrafish heart wt cryo 2,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2 was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury  cryoinjury  wildtype zebrafish heart  replicate 2,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Cryoinjured|genotype:yap +/+,GSM3070331,GSM3070331: zebrafish heart wt cryo 2; Danio rerio; RNA Seq,GSM3070331,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070331,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAHRABPEI-41_1.fq.gz,fastq,1422338300.0,28446766.0,GSM3070331 r1,0:50,A:393674065;C:315125662;G:322045666;T:389932855;N:1560052,50,,,,393674065,315125662,322045666,389932855,1560052,SRX3858778,SRS3106133,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.9294,,0.08412,,0.75749,,0.52514,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System
48020,SRR6910771,SRX3858777,SRS3106134,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury  whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart wt cryo 1,GSM3070330,,tissue:7 xxx post injury  cryoinjury  wildtype zebrafish heart  replicate 1|injury type:Cryoinjured|genotype:yap +/+,zebrafish heart wt cryo 1,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2 was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury  cryoinjury  wildtype zebrafish heart  replicate 1,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Cryoinjured|genotype:yap +/+,GSM3070330,GSM3070330: zebrafish heart wt cryo 1; Danio rerio; RNA Seq,GSM3070330,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070330,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAGRABPEI-40_1.fq.gz,fastq,1419380450.0,28387609.0,GSM3070330 r1,0:50,A:393618390;C:313492075;G:321642338;T:389289283;N:1338364,50,,,,393618390,313492075,321642338,389289283,1338364,SRX3858777,SRS3106134,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93599,,0.08586,,0.75381,,0.52578,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System
48812,SRR7341816,SRX4215318,SRS3417596,SRP150521,PRJNA476105,Transcriptome analysis of wildtype and sox3 /  zebrafish adult ovary,GSE115806,Transcriptome Analysis,The goals of this study are to compare the differentially expressed genes between wildtype and sox3 /  zebrafish ovaries based on RNA seq data and some of these genes were validated by qRT–PCR. Further  the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Ovary mRNA profiles of adult wildtype and sox3 /  zebrafish were generated by deep sequencing.,,pubmed:30588557,,KO mix,GSM3190267,,source name:Ovary|strain:AB|tissue:Ovary|age:Adult,KO mix,Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz10 whole genome using HISAT  mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Genome build: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample.,Ovary,,Ovaries were isolated  frozen on dry ice  and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.,,strain:AB|tissue:Ovary|age:Adult,GSM3190267,GSM3190267: KO mix; Danio rerio; RNA Seq,GSM3190267,,1,Ovaries were isolated  frozen on dry ice  and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.,GEO Accession:GSM3190267,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP150521,,,KO-ovary.fq.gz,fastq,1173123100.0,23462462.0,GSM3190267 r1,0:50 1:0,A:308426188;C:271468505;G:292019086;T:300532126;N:677195,50,0,,,308426188,271468505,292019086,300532126,677195,SRX4215318,SRS3417596,SRA721702,GEO,Wuhan university,1,0.93261,,0.02261,,0.76132,,0.4585,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2018-06-14,Adult,Adult,Gonad,Reproductive System
48813,SRR7341815,SRX4215317,SRS3417595,SRP150521,PRJNA476105,Transcriptome analysis of wildtype and sox3 /  zebrafish adult ovary,GSE115806,Transcriptome Analysis,The goals of this study are to compare the differentially expressed genes between wildtype and sox3 /  zebrafish ovaries based on RNA seq data and some of these genes were validated by qRT–PCR. Further  the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Ovary mRNA profiles of adult wildtype and sox3 /  zebrafish were generated by deep sequencing.,,pubmed:30588557,,WT mix,GSM3190266,,source name:Ovary|strain:AB|tissue:Ovary|age:Adult,WT mix,Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz10 whole genome using HISAT  mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Genome build: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample.,Ovary,,Ovaries were isolated  frozen on dry ice  and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.,,strain:AB|tissue:Ovary|age:Adult,GSM3190266,GSM3190266: WT mix; Danio rerio; RNA Seq,GSM3190266,,1,Ovaries were isolated  frozen on dry ice  and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.,GEO Accession:GSM3190266,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP150521,,,WT-ovary.fq.gz,fastq,1176463600.0,23529272.0,GSM3190266 r1,0:50 1:0,A:311869864;C:270650722;G:289863261;T:303489229;N:590524,50,0,,,311869864,270650722,289863261,303489229,590524,SRX4215317,SRS3417595,SRA721702,GEO,Wuhan university,1,0.93489,,0.02765,,0.75627,,0.46875,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2018-06-14,Adult,Adult,Gonad,Reproductive System
50717,SRR8257205,SRX5074433,SRS4088243,SRP171045,PRJNA507426,Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq],GSE123058,Transcriptome Analysis,The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants,parent bioproject:PRJNA507423,pubmed:31296872,,RNAseq in zebrafish wild type embryos at 36hpf replicate 3,GSM3494529,,tissue:whole embryo|developmental stage:36hpf|genotype:WT,RNAseq in zebrafish wild type embryos at 36hpf replicate 3,Reads were aligned against reference genome using STAR software  and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were cultivated at 28°C in E3 medium until desired developmental stage,developmental stage:36hpf|genotype:WT,GSM3494529,GSM3494529: RNAseq in zebrafish wild type embryos at 36hpf replicate 3; Danio rerio; RNA Seq,GSM3494529,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM3494529,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP171045,,,RNAseq_zebra_WT_36hpf_rep3.fq.gz,fastq,2560587500.0,51211750.0,GSM3494529 r1,0:50,A:719232941;C:550474431;G:576590260;T:714289868;N:0,50,,,,719232941,550474431,576590260,714289868,0,SRX5074433,SRS4088243,SRA815839,GEO,CABD/CSIC,1,0.93981,,0.10951,,0.71388,,0.48297,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2018-11-28,Pharyngula,Embryo,Whole Organism,All anatomical structures
50718,SRR8257204,SRX5074432,SRS4088242,SRP171045,PRJNA507426,Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq],GSE123058,Transcriptome Analysis,The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants,parent bioproject:PRJNA507423,pubmed:31296872,,RNAseq in zebrafish wild type embryos at 36hpf replicate 2,GSM3494528,,tissue:whole embryo|developmental stage:36hpf|genotype:WT,RNAseq in zebrafish wild type embryos at 36hpf replicate 2,Reads were aligned against reference genome using STAR software  and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were cultivated at 28°C in E3 medium until desired developmental stage,developmental stage:36hpf|genotype:WT,GSM3494528,GSM3494528: RNAseq in zebrafish wild type embryos at 36hpf replicate 2; Danio rerio; RNA Seq,GSM3494528,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM3494528,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP171045,,,RNAseq_zebra_WT_36hpf_rep2.fq.gz,fastq,2775840750.0,55516815.0,GSM3494528 r1,0:50,A:783053027;C:587947172;G:603351259;T:801489292;N:0,50,,,,783053027,587947172,603351259,801489292,0,SRX5074432,SRS4088242,SRA815839,GEO,CABD/CSIC,1,0.93386,,0.11853,,0.7007,,0.48856,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2018-11-28,Pharyngula,Embryo,Whole Organism,All anatomical structures
50719,SRR8257203,SRX5074431,SRS4088241,SRP171045,PRJNA507426,Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq],GSE123058,Transcriptome Analysis,The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants,parent bioproject:PRJNA507423,pubmed:31296872,,RNAseq in zebrafish wild type embryos at 36hpf replicate 1,GSM3494527,,tissue:whole embryo|developmental stage:36hpf|genotype:WT,RNAseq in zebrafish wild type embryos at 36hpf replicate 1,Reads were aligned against reference genome using STAR software  and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were cultivated at 28°C in E3 medium until desired developmental stage,developmental stage:36hpf|genotype:WT,GSM3494527,GSM3494527: RNAseq in zebrafish wild type embryos at 36hpf replicate 1; Danio rerio; RNA Seq,GSM3494527,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM3494527,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP171045,,,RNAseq_zebra_WT_36hpf_rep1.fq.gz,fastq,2638769750.0,52775395.0,GSM3494527 r1,0:50,A:749627286;C:556213831;G:574654547;T:758274086;N:0,50,,,,749627286,556213831,574654547,758274086,0,SRX5074431,SRS4088241,SRA815839,GEO,CABD/CSIC,1,0.92992,,0.12022,,0.72174,,0.49097,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2018-11-28,Pharyngula,Embryo,Whole Organism,All anatomical structures
50720,SRR8257202,SRX5074430,SRS4088240,SRP171045,PRJNA507426,Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq],GSE123058,Transcriptome Analysis,The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants,parent bioproject:PRJNA507423,pubmed:31296872,,RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3,GSM3494526,,tissue:whole embryo|developmental stage:36hpf|genotype:tp63  / ,RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3,Reads were aligned against reference genome using STAR software  and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were cultivated at 28°C in E3 medium until desired developmental stage,developmental stage:36hpf|genotype:tp63  / ,GSM3494526,GSM3494526: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3; Danio rerio; RNA Seq,GSM3494526,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM3494526,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP171045,,,RNAseq_zebra_p63mut_36hpf_rep3.fq.gz,fastq,2651169450.0,53023389.0,GSM3494526 r1,0:50,A:752539060;C:560162268;G:581624300;T:756843822;N:0,50,,,,752539060,560162268,581624300,756843822,0,SRX5074430,SRS4088240,SRA815839,GEO,CABD/CSIC,1,0.94022,,0.12949,,0.70019,,0.50336,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2018-11-28,Pharyngula,Embryo,Whole Organism,All anatomical structures
50721,SRR8257201,SRX5074429,SRS4088239,SRP171045,PRJNA507426,Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq],GSE123058,Transcriptome Analysis,The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants,parent bioproject:PRJNA507423,pubmed:31296872,,RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2,GSM3494525,,tissue:whole embryo|developmental stage:36hpf|genotype:tp63  / ,RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2,Reads were aligned against reference genome using STAR software  and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were cultivated at 28°C in E3 medium until desired developmental stage,developmental stage:36hpf|genotype:tp63  / ,GSM3494525,GSM3494525: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2; Danio rerio; RNA Seq,GSM3494525,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM3494525,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP171045,,,RNAseq_zebra_p63mut_36hpf_rep2.fq.gz,fastq,2821501700.0,56430034.0,GSM3494525 r1,0:50,A:795357588;C:599294949;G:620563224;T:806285939;N:0,50,,,,795357588,599294949,620563224,806285939,0,SRX5074429,SRS4088239,SRA815839,GEO,CABD/CSIC,1,0.93671,,0.12314,,0.6957,,0.48362,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2018-11-28,Pharyngula,Embryo,Whole Organism,All anatomical structures
50722,SRR8257200,SRX5074428,SRS4088238,SRP171045,PRJNA507426,Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq],GSE123058,Transcriptome Analysis,The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants,parent bioproject:PRJNA507423,pubmed:31296872,,RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1,GSM3494524,,tissue:whole embryo|developmental stage:36hpf|genotype:tp63  / ,RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1,Reads were aligned against reference genome using STAR software  and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were cultivated at 28°C in E3 medium until desired developmental stage,developmental stage:36hpf|genotype:tp63  / ,GSM3494524,GSM3494524: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1; Danio rerio; RNA Seq,GSM3494524,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM3494524,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP171045,,,RNAseq_zebra_p63mut_36hpf_rep1.fq.gz,fastq,2592494100.0,51849882.0,GSM3494524 r1,0:50,A:730978948;C:550803197;G:572081489;T:738630466;N:0,50,,,,730978948,550803197,572081489,738630466,0,SRX5074428,SRS4088238,SRA815839,GEO,CABD/CSIC,1,0.94035,,0.11571,,0.70796,,0.49468,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2018-11-28,Pharyngula,Embryo,Whole Organism,All anatomical structures
52944,SRR9609439,SRX6372833,SRS5033898,SRP212216,PRJNA551488,TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,PBCAB Replicate 3,GSM3909672,,tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB,PBCAB Replicate 3,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean  0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:PBCAB,GSM3909672,GSM3909672: PBCAB Replicate 3; Danio rerio; RNA Seq,GSM3909672,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909672,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,PBCAB_12hpf_zebrafish_biological_replicate3.fq.gz,fastq,1283013300.0,25660266.0,GSM3909672 r1,0:50,A:339417002;C:304649204;G:297783450;T:341163644;N:0,50,,,,339417002,304649204,297783450,341163644,0,SRX6372833,SRS5033898,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94342,,0.10559,,0.72401,,0.47431,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures
52945,SRR9609438,SRX6372832,SRS5033897,SRP212216,PRJNA551488,TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,PBCAB Replicate 2,GSM3909671,,tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB,PBCAB Replicate 2,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean  0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:PBCAB,GSM3909671,GSM3909671: PBCAB Replicate 2; Danio rerio; RNA Seq,GSM3909671,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909671,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,PBCAB_12hpf_zebrafish_biological_replicate2.fq.gz,fastq,1282475700.0,25649514.0,GSM3909671 r1,0:50,A:339635626;C:302447093;G:295507893;T:344885088;N:0,50,,,,339635626,302447093,295507893,344885088,0,SRX6372832,SRS5033897,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94396,,0.10502,,0.71465,,0.47566,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures
52946,SRR9609437,SRX6372831,SRS5033896,SRP212216,PRJNA551488,TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,PBCAB Replicate 1,GSM3909670,,tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB,PBCAB Replicate 1,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean  0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:PBCAB,GSM3909670,GSM3909670: PBCAB Replicate 1; Danio rerio; RNA Seq,GSM3909670,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909670,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,PBCAB_12hpf_zebrafish_biological_replicate1.fq.gz,fastq,1147572700.0,22951454.0,GSM3909670 r1,0:50,A:300633532;C:273711082;G:268229512;T:304998574;N:0,50,,,,300633532,273711082,268229512,304998574,0,SRX6372831,SRS5033896,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94418,,0.09965,,0.72746,,0.47644,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures
52947,SRR9609436,SRX6372830,SRS5033895,SRP212216,PRJNA551488,TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,NF YA DN Replicate 3,GSM3909669,,tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN,NF YA DN Replicate 3,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean  0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:NF YA DN,GSM3909669,GSM3909669: NF YA DN Replicate 3; Danio rerio; RNA Seq,GSM3909669,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909669,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,NFYADN_12hpf_zebrafish_biological_replicate3.fq.gz,fastq,1282414400.0,25648288.0,GSM3909669 r1,0:50,A:334687310;C:307161534;G:302070174;T:338495382;N:0,50,,,,334687310,307161534,302070174,338495382,0,SRX6372830,SRS5033895,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94359,,0.09476,,0.72529,,0.47117,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures
52948,SRR9609435,SRX6372829,SRS5033894,SRP212216,PRJNA551488,TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,NF YA DN Replicate 2,GSM3909668,,tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN,NF YA DN Replicate 2,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean  0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:NF YA DN,GSM3909668,GSM3909668: NF YA DN Replicate 2; Danio rerio; RNA Seq,GSM3909668,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909668,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,NFYADN_12hpf_zebrafish_biological_replicate2.fq.gz,fastq,1281370000.0,25627400.0,GSM3909668 r1,0:50,A:335735118;C:306450529;G:298815464;T:340368889;N:0,50,,,,335735118,306450529,298815464,340368889,0,SRX6372829,SRS5033894,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94338,,0.09412,,0.7204,,0.48662,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures
52949,SRR9609434,SRX6372828,SRS5033893,SRP212216,PRJNA551488,TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,NF YA DN Replicate 1,GSM3909667,,tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN,NF YA DN Replicate 1,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean  0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:NF YA DN,GSM3909667,GSM3909667: NF YA DN Replicate 1; Danio rerio; RNA Seq,GSM3909667,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909667,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,NFYADN_12hpf_zebrafish_biological_replicate1.fq.gz,fastq,1278504750.0,25570095.0,GSM3909667 r1,0:50,A:334370606;C:306252389;G:299065406;T:338816349;N:0,50,,,,334370606,306252389,299065406,338816349,0,SRX6372828,SRS5033893,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94373,,0.09279,,0.7191,,0.48836,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures
52950,SRR9609433,SRX6372827,SRS5033892,SRP212216,PRJNA551488,TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,GFP Replicate 3,GSM3909666,,tissue:Whole Embryo|Stage:12 hpf|treatment:GFP,GFP Replicate 3,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean  0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:GFP,GSM3909666,GSM3909666: GFP Replicate 3; Danio rerio; RNA Seq,GSM3909666,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909666,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,GFP_12hpf_zebrafish_biological_replicate3.fq.gz,fastq,1284828600.0,25696572.0,GSM3909666 r1,0:50,A:340467505;C:302914392;G:291984238;T:349462465;N:0,50,,,,340467505,302914392,291984238,349462465,0,SRX6372827,SRS5033892,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94288,,0.0963,,0.71713,,0.4793,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures
52951,SRR9609432,SRX6372826,SRS5033891,SRP212216,PRJNA551488,TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,GFP Replicate 2,GSM3909665,,tissue:Whole Embryo|Stage:12 hpf|treatment:GFP,GFP Replicate 2,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean  0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:GFP,GSM3909665,GSM3909665: GFP Replicate 2; Danio rerio; RNA Seq,GSM3909665,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909665,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,GFP_12hpf_zebrafish_biological_replicate2.fq.gz,fastq,1274433150.0,25488663.0,GSM3909665 r1,0:50,A:336050330;C:303141446;G:297353928;T:337887446;N:0,50,,,,336050330,303141446,297353928,337887446,0,SRX6372826,SRS5033891,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94266,,0.0966,,0.72476,,0.47615,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures
52952,SRR9609431,SRX6372825,SRS5033890,SRP212216,PRJNA551488,TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,GFP Replicate 1,GSM3909664,,tissue:Whole Embryo|Stage:12 hpf|treatment:GFP,GFP Replicate 1,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean  0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:GFP,GSM3909664,GSM3909664: GFP Replicate 1; Danio rerio; RNA Seq,GSM3909664,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909664,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,GFP_12hpf_zebrafish_biological_replicate1.fq.gz,fastq,1278273350.0,25565467.0,GSM3909664 r1,0:50,A:336762127;C:304299745;G:297929933;T:339281545;N:0,50,,,,336762127,304299745,297929933,339281545,0,SRX6372825,SRS5033890,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94207,,0.09472,,0.72642,,0.47988,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,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
57168,SRR11237928,SRX7849591,SRS6259054,SRP251591,PRJNA610302,Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development,GSE146394,Transcriptome Analysis,To study the function of zebrafish nuclear pores during early embryogenesis  we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology,,,,MZ 7hpf Dome,GSM4379949,,source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:7 hpf nup85 / ;nup133 / ,MZ 7hpf Dome,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,strain:AB|tissue:whole mount embryo|developmental stage:7 hpf nup85 / ;nup133 / ,GSM4379949,GSM4379949: MZ 7hpf Dome; Danio rerio; RNA Seq,GSM4379949,,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,GEO Accession:GSM4379949,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP251591,,,MZ_7h_Dome_1.fq.gz,fastq,1065702100.0,21314042.0,GSM4379949 r1,0:50 1:0,A:283324952;C:247492025;G:242059243;T:291819466;N:1006414,50,0,,,283324952,247492025,242059243,291819466,1006414,SRX7849591,SRS6259054,SRA1051151,GEO,"School of life science, Tsinghua University",1,0.9445,,0.07752,,0.72565,,0.4828,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2020-03-04,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
57169,SRR11237927,SRX7849590,SRS6259053,SRP251591,PRJNA610302,Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development,GSE146394,Transcriptome Analysis,To study the function of zebrafish nuclear pores during early embryogenesis  we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology,,,,MZ 4.3hpf 1k,GSM4379948,,source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf nup85 / ;nup133 / ,MZ 4.3hpf 1k,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf nup85 / ;nup133 / ,GSM4379948,GSM4379948: MZ 4.3hpf 1k; Danio rerio; RNA Seq,GSM4379948,,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,GEO Accession:GSM4379948,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP251591,,,MZ_4.3h_1k_1.fq.gz,fastq,1059959500.0,21199190.0,GSM4379948 r1,0:50 1:0,A:278456455;C:249622199;G:244991579;T:285847713;N:1041554,50,0,,,278456455,249622199,244991579,285847713,1041554,SRX7849590,SRS6259053,SRA1051151,GEO,"School of life science, Tsinghua University",1,0.94882,,0.03659,,0.74361,,0.48435,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2020-03-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures
57170,SRR11237926,SRX7849589,SRS6259052,SRP251591,PRJNA610302,Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development,GSE146394,Transcriptome Analysis,To study the function of zebrafish nuclear pores during early embryogenesis  we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology,,,,WT 4.3hpf Dome,GSM4379947,,source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf type,WT 4.3hpf Dome,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf type,GSM4379947,GSM4379947: WT 4.3hpf Dome; Danio rerio; RNA Seq,GSM4379947,,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,GEO Accession:GSM4379947,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP251591,,,WT_4.3h_Dome_1.fq.gz,fastq,1058158950.0,21163179.0,GSM4379947 r1,0:50 1:0,A:279307143;C:247873321;G:244308380;T:285580565;N:1089541,50,0,,,279307143,247873321,244308380,285580565,1089541,SRX7849589,SRS6259052,SRA1051151,GEO,"School of life science, Tsinghua University",1,0.94374,,0.05294,,0.74164,,0.48705,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2020-03-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures
57259,SRR11294128,SRX7899687,SRS6307737,SRP252540,PRJNA612190,Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration,GSE146859,Transcriptome Analysis,Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.,,pubmed:32877671,,Ventricles  uninj p53 pos.rep3,GSM4407932,,source name:Ventricles of uninjured TgtpWT zebrafish|genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles,Ventricles  uninj p53 pos.rep3,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count 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,Ventricles of uninjured TgtpWT zebrafish,Fish were treated  17 hours  with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated.,Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol  genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing  with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis.,Fish were grown at 28 degrees.  Male and female animals between 6 month and 12 month and of 2 cm in length were used.,genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles,GSM4407932,GSM4407932: Ventricles  uninj p53 pos.rep3; Danio rerio; RNA Seq,GSM4407932,,1,Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol  genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing  with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis.,GEO Accession:GSM4407932,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP252540,,,CL100137114_L1_HK500ZEBortRAADRAAPEI-512_1.fq.gz,fastq,1835058950.0,36701179.0,GSM4407932 r1,0:50,A:502113193;C:411542245;G:409297699;T:512105813;N:0,50,,,,502113193,411542245,409297699,512105813,0,SRX7899687,SRS6307737,SRA1054226,GEO,"Poss, Cell Biology, Duke University",1,0.93734,,0.0825,,0.77094,,0.54336,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-12,Adult,Adult,Heart,Cardiovascular System
57260,SRR11294127,SRX7899686,SRS6307736,SRP252540,PRJNA612190,Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration,GSE146859,Transcriptome Analysis,Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.,,pubmed:32877671,,Ventricles  uninj p53 pos.rep2,GSM4407931,,source name:Ventricles of uninjured TgtpWT zebrafish|genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles,Ventricles  uninj p53 pos.rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count 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,Ventricles of uninjured TgtpWT zebrafish,Fish were treated  17 hours  with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated.,Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol  genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing  with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis.,Fish were grown at 28 degrees.  Male and female animals between 6 month and 12 month and of 2 cm in length were used.,genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles,GSM4407931,GSM4407931: Ventricles  uninj p53 pos.rep2; Danio rerio; RNA Seq,GSM4407931,,1,Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol  genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing  with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis.,GEO Accession:GSM4407931,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP252540,,,CL100137114_L1_HK500ZEBortRAACRAAPEI-511_1.fq.gz,fastq,1834865450.0,36697309.0,GSM4407931 r1,0:50,A:505143598;C:405191113;G:410587735;T:513943004;N:0,50,,,,505143598,405191113,410587735,513943004,0,SRX7899686,SRS6307736,SRA1054226,GEO,"Poss, Cell Biology, Duke University",1,0.93631,,0.08049,,0.76481,,0.50179,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-12,Adult,Adult,Heart,Cardiovascular System
57261,SRR11294126,SRX7899685,SRS6307735,SRP252540,PRJNA612190,Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration,GSE146859,Transcriptome Analysis,Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.,,pubmed:32877671,,Ventricles  uninj p53 pos.rep1,GSM4407930,,source name:Ventricles of uninjured TgtpWT zebrafish|genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles,Ventricles  uninj p53 pos.rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count 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,Ventricles of uninjured TgtpWT zebrafish,Fish were treated  17 hours  with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated.,Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol  genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing  with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis.,Fish were grown at 28 degrees.  Male and female animals between 6 month and 12 month and of 2 cm in length were used.,genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles,GSM4407930,GSM4407930: Ventricles  uninj p53 pos.rep1; Danio rerio; RNA Seq,GSM4407930,,1,Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol  genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing  with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis.,GEO Accession:GSM4407930,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP252540,,,CL100137114_L1_HK500ZEBortRAABRAAPEI-510_1.fq.gz,fastq,1834689950.0,36693799.0,GSM4407930 r1,0:50,A:504160420;C:403583740;G:412496526;T:514449264;N:0,50,,,,504160420,403583740,412496526,514449264,0,SRX7899685,SRS6307735,SRA1054226,GEO,"Poss, Cell Biology, Duke University",1,0.93629,,0.08291,,0.77356,,0.49244,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-12,Adult,Adult,Heart,Cardiovascular System
57262,SRR11294125,SRX7899684,SRS6307734,SRP252540,PRJNA612190,Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration,GSE146859,Transcriptome Analysis,Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.,,pubmed:32877671,,Ventricles  uninj p53 neg.rep3,GSM4407929,,source name:Ventricles of uninjured Tgtp53M214K zebrafish|genotype:Tgtp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles,Ventricles  uninj p53 neg.rep3,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count 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,Ventricles of uninjured Tgtp53M214K zebrafish,Fish were treated  17 hours  with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated.,Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol  genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing  with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis.,Fish were grown at 28 degrees.  Male and female animals between 6 month and 12 month and of 2 cm in length were used.,genotype:Tgtp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles,GSM4407929,GSM4407929: Ventricles  uninj p53 neg.rep3; Danio rerio; RNA Seq,GSM4407929,,1,Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol  genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing  with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis.,GEO Accession:GSM4407929,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP252540,,,CL100137114_L1_HK500ZEBortRAAIRAAPEI-521_1.fq.gz,fastq,1834395600.0,36687912.0,GSM4407929 r1,0:50,A:499900882;C:409384440;G:414252017;T:510858261;N:0,50,,,,499900882,409384440,414252017,510858261,0,SRX7899684,SRS6307734,SRA1054226,GEO,"Poss, Cell Biology, Duke University",1,0.93583,,0.07847,,0.76974,,0.54357,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-12,Adult,Adult,Heart,Cardiovascular System