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
8057,ERR022488,ERX008921,ERS012706,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,E MTAB 308:Zebrafish embryo 3 dpf 2,SAMEA898404,Wellcome Sanger Institute,Age:3 days|Alias:E MTAB 308:Zebrafish embryo 3 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012706|Sample Name:ERS012706|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 3 dpf,RNA from Zebrafish embryo 3 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.,Experimental Factor: AGE:3 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,5141_6.srf,srf,3787933176.0,24920613.0,E MTAB 434:5141 6.srf,0:76 1:76,A:1051092006;C:842721213;G:838644314;T:1048667825;N:6807818,76,76,,,1051092006,842721213,838644314,1048667825,6807818,ERX008921,ERS012706,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.95952,0.95914,0.16277,0.16553,0.66352,0.6661,0.46603,0.46879,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Larval,Larval,Whole Organism,All anatomical structures
8061,ERR022482,ERX008919,ERS000084,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,5 dpf sample1,SAMEA708828,Wellcome Sanger Institute,Alias:5 dpf sample1|Description:RNA extracted from zebrafish embryo at 5 dpf|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000084|Sample Name:ERS000084|Sex:mixed|Strain:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 5 dpf,RNA from Zebrafish embryo 5 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.,Experimental Factor: AGE:5 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,2719_7.srf,srf,1764668160.0,16339520.0,E MTAB 434:2719 7.srf,0:54 1:54,A:470580161;C:399075336;G:417290042;T:474450367;N:3272254,54,54,,,470580161,399075336,417290042,474450367,3272254,ERX008919,ERS000084,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.9454,0.94288,0.20211,0.2029,0.66856,0.67207,0.4856,0.48119,54,54,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-02-26,Larval,Larval,Whole Organism,All anatomical structures
8062,ERR022483,ERX008919,ERS000084,ERP000400,PRJEB2333,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E-MTAB-434,Other,,,,,5 dpf sample1,SAMEA708828,Wellcome Sanger Institute,Alias:5 dpf sample1|Description:RNA extracted from zebrafish embryo at 5 dpf|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000084|Sample Name:ERS000084|Sex:mixed|Strain:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,E MTAB 434:sequencing of Zebrafish embryo 5 dpf,RNA from Zebrafish embryo 5 dpf,Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.,Experimental Factor: AGE:5 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism,FL-cDNA,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000400,Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer,ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16,2719_8.srf,srf,1678321188.0,15540011.0,E MTAB 434:2719 8.srf,0:54 1:54,A:446988405;C:380486018;G:396533911;T:451117596;N:3195258,54,54,,,446988405,380486018,396533911,451117596,3195258,ERX008919,ERS000084,ERA015179,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.94565,0.94277,0.19929,0.19877,0.66584,0.67014,0.47973,0.46826,54,54,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2010-02-26,Larval,Larval,Whole Organism,All anatomical structures
39687,SRR2051113,SRX1048368,SRS952733,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P39,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 4,P39,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P39_EL4517_GATCAG_L001_R1_001.fastq.gz P39_EL4517_GATCAG_L002_R1_001.fastq.gz P39_EL4517_GATCAG_L007_R1_001.fastq.gz P39_EL4517_GATCAG_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4090297192.0,40497992.0,P39,0:101,A:1016157993;C:993771683;G:965986507;T:1113686588;N:694421,101,,,,1016157993,993771683,965986507,1113686588,694421,SRX1048368,SRS952733,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9417,,0.14428,,0.68937,,0.5438,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39688,SRR2051110,SRX1048367,SRS952731,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P37,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 3,P37,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P37_EL4516_ACTTGA_L008_R1_001.fastq.gz P37_EL4516_ACTTGA_L007_R1_001.fastq.gz P37_EL4516_ACTTGA_L002_R1_001.fastq.gz P37_EL4516_ACTTGA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4647442886.0,46014286.0,P37,0:101,A:1149955739;C:1129088798;G:1093234722;T:1274375148;N:788479,101,,,,1149955739,1129088798,1093234722,1274375148,788479,SRX1048367,SRS952731,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94585,,0.12571,,0.68633,,0.52597,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39689,SRR2051112,SRX1048366,SRS952732,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P36,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 2,P36,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P36_EL4527_CCGTCC_L008_R1_001.fastq.gz P36_EL4527_CCGTCC_L007_R1_001.fastq.gz P36_EL4527_CCGTCC_L002_R1_001.fastq.gz P36_EL4527_CCGTCC_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4296894611.0,42543511.0,P36,0:101,A:1050039699;C:1061123166;G:1022913715;T:1162094624;N:723407,101,,,,1050039699,1061123166,1022913715,1162094624,723407,SRX1048366,SRS952732,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94977,,0.13188,,0.70976,,0.52728,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39690,SRR2051109,SRX1048365,SRS952730,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P35,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 1,P35,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P35_EL4526_ATGTCA_L008_R1_001.fastq.gz P35_EL4526_ATGTCA_L007_R1_001.fastq.gz P35_EL4526_ATGTCA_L002_R1_001.fastq.gz P35_EL4526_ATGTCA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4094752706.0,40542106.0,P35,0:101,A:1009779802;C:1004374749;G:969241794;T:1110655194;N:701167,101,,,,1009779802,1004374749,969241794,1110655194,701167,SRX1048365,SRS952730,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94442,,0.13203,,0.70023,,0.53953,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39691,SRR2051102,SRX1048364,SRS952729,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P29,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 4,P29,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P29_EL4510_CTTGTA_L008_R1_001.fastq.gz P29_EL4510_CTTGTA_L007_R1_001.fastq.gz P29_EL4510_CTTGTA_L002_R1_001.fastq.gz P29_EL4510_CTTGTA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4983571896.0,49342296.0,P29,0:101,A:1247122516;C:1202173111;G:1173654831;T:1359775597;N:845841,101,,,,1247122516,1202173111,1173654831,1359775597,845841,SRX1048364,SRS952729,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94329,,0.13234,,0.68286,,0.51586,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39692,SRR2051100,SRX1048363,SRS952727,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P28,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 3,P28,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P28_EL4509_CAGATC_L008_R1_001.fastq.gz P28_EL4509_CAGATC_L007_R1_001.fastq.gz P28_EL4509_CAGATC_L002_R1_001.fastq.gz P28_EL4509_CAGATC_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4032678914.0,39927514.0,P28,0:101,A:1015356577;C:970369004;G:937306142;T:1108957703;N:689488,101,,,,1015356577,970369004,937306142,1108957703,689488,SRX1048363,SRS952727,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.93887,,0.13869,,0.69079,,0.52237,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39693,SRR2051101,SRX1048362,SRS952728,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P26,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 2,P26,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P26_EL4508_GCCAAT_L001_R1_001.fastq.gz P26_EL4508_GCCAAT_L007_R1_001.fastq.gz P26_EL4508_GCCAAT_L008_R1_001.fastq.gz P26_EL4508_GCCAAT_L002_R1_001.fastq.gz,fastq fastq fastq fastq,6526758875.0,64621375.0,P26,0:101,A:1635664768;C:1568967965;G:1518148006;T:1802863908;N:1114228,101,,,,1635664768,1568967965,1518148006,1802863908,1114228,SRX1048362,SRS952728,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.93822,,0.15203,,0.68609,,0.53171,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39694,SRR2051096,SRX1048361,SRS952726,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P25,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 1,P25,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P25_EL4511_ATCACG_L001_R1_001.fastq.gz P25_EL4511_ATCACG_L002_R1_001.fastq.gz P25_EL4511_ATCACG_L007_R1_001.fastq.gz P25_EL4511_ATCACG_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4185957322.0,41445122.0,P25,0:101,A:1081936223;C:978799105;G:956795307;T:1167714259;N:712428,101,,,,1081936223,978799105,956795307,1167714259,712428,SRX1048361,SRS952726,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9288,,0.17032,,0.6801,,0.51298,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39695,SRR2051095,SRX1048360,SRS952725,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P19,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 4,P19,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P19_EL4521_GGCTAC_L008_R1_001.fastq.gz P19_EL4521_GGCTAC_L007_R1_001.fastq.gz P19_EL4521_GGCTAC_L002_R1_001.fastq.gz P19_EL4521_GGCTAC_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4293546461.0,42510361.0,P19,0:101,A:1062707728;C:1045602693;G:1011860446;T:1172670772;N:704822,101,,,,1062707728,1045602693,1011860446,1172670772,704822,SRX1048360,SRS952725,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94381,,0.13697,,0.69051,,0.51415,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39696,SRR2051094,SRX1048359,SRS952724,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P18,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 3,P18,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P18_EL4520_TAGCTT_L008_R1_001.fastq.gz P18_EL4520_TAGCTT_L007_R1_001.fastq.gz P18_EL4520_TAGCTT_L002_R1_001.fastq.gz P18_EL4520_TAGCTT_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4257944163.0,42157863.0,P18,0:101,A:1044532409;C:1049992329;G:1010166097;T:1152524203;N:729125,101,,,,1044532409,1049992329,1010166097,1152524203,729125,SRX1048359,SRS952724,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94262,,0.14592,,0.69014,,0.52498,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39697,SRR2051093,SRX1048358,SRS952723,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P17,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 2,P17,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P17_EL4522_AGTCAA_L007_R1_001.fastq.gz P17_EL4522_AGTCAA_L008_R1_001.fastq.gz P17_EL4522_AGTCAA_L002_R1_001.fastq.gz P17_EL4522_AGTCAA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4278385553.0,42360253.0,P17,0:101,A:1040955882;C:1060023973;G:1019487833;T:1157186726;N:731139,101,,,,1040955882,1060023973,1019487833,1157186726,731139,SRX1048358,SRS952723,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94697,,0.14458,,0.69643,,0.53451,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39698,SRR2051092,SRX1048357,SRS952722,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,P15,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 1,P15,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,P15_EL4523_AGTTCC_L001_R1_001.fastq.gz P15_EL4523_AGTTCC_L002_R1_001.fastq.gz P15_EL4523_AGTTCC_L007_R1_001.fastq.gz P15_EL4523_AGTTCC_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4341747499.0,42987599.0,P15,0:101,A:1052621077;C:1088380866;G:1041958433;T:1158051746;N:735377,101,,,,1052621077,1088380866,1041958433,1158051746,735377,SRX1048357,SRS952722,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94563,,0.153,,0.69822,,0.54133,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-06-04,Larval,Larval,Whole Organism,All anatomical structures
39699,SRR2051091,SRX1048356,SRS952721,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN9,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 4,CN9,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,CN9_EL4515_TTAGGC_L001_R1_001.fastq.gz CN9_EL4515_TTAGGC_L002_R1_001.fastq.gz CN9_EL4515_TTAGGC_L007_R1_001.fastq.gz CN9_EL4515_TTAGGC_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4220387212.0,41786012.0,CN9,0:101,A:1031722430;C:1044497851;G:1005706674;T:1137783022;N:677235,101,,,,1031722430,1044497851,1005706674,1137783022,677235,SRX1048356,SRS952721,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.95231,,0.14084,,0.69682,,0.52966,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39700,SRR2051090,SRX1048354,SRS952719,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN8,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 3,CN8,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,CN8_EL4505_CGATGT_L008_R1_001.fastq.gz CN8_EL4505_CGATGT_L007_R1_001.fastq.gz CN8_EL4505_CGATGT_L002_R1_001.fastq.gz CN8_EL4505_CGATGT_L001_R1_001.fastq.gz,fastq fastq fastq fastq,5835502553.0,57777253.0,CN8,0:101,A:1424369529;C:1441755207;G:1391851806;T:1576540272;N:985739,101,,,,1424369529,1441755207,1391851806,1576540272,985739,SRX1048354,SRS952719,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94643,,0.12925,,0.70725,,0.52949,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39701,SRR2050894,SRX1048353,SRS952718,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN7,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 2,CN7,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,CN7_EL4507_ACAGTG_L008_R1_001.fastq.gz CN7_EL4507_ACAGTG_L007_R1_001.fastq.gz CN7_EL4507_ACAGTG_L002_R1_001.fastq.gz CN7_EL4507_ACAGTG_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4789094477.0,47416777.0,CN7,0:101,A:1160528098;C:1197558725;G:1155573375;T:1274638263;N:796016,101,,,,1160528098,1197558725,1155573375,1274638263,796016,SRX1048353,SRS952718,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9501,,0.14828,,0.69966,,0.52764,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39702,SRR2050892,SRX1048352,SRS952717,SRP059060,PRJNA285816,Danio rerio Raw sequence reads,PRJNA285816,Whole Genome Sequencing,Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.,,,,,CN5,,breed:wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 1,CN5,CN5 EL4506 TGACCA,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP059060,,,CN5_EL4506_TGACCA_L001_R1_001.fastq.gz CN5_EL4506_TGACCA_L002_R1_001.fastq.gz CN5_EL4506_TGACCA_L007_R1_001.fastq.gz CN5_EL4506_TGACCA_L008_R1_001.fastq.gz,fastq fastq fastq fastq,4526144512.0,44813312.0,CN5,0:101,A:1109966549;C:1116619353;G:1075422479;T:1223366972;N:769159,101,,,,1109966549,1116619353,1075422479,1223366972,769159,SRX1048352,SRS952717,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94604,,0.14084,,0.69004,,0.53407,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
52829,SRR9277355,SRX6047142,SRS4950160,SRP201168,PRJNA548449,Dyskerin impairment in zebrafish,PRJNA548449,Other,One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.,,,sample04,,dkc1 elu1 mut1,,isolate:biological replicate 1|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:mutant|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf,MUT1,MUT1,Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,MUT-1_R1.fastq.gz,fastq,2425739178.0,32540543.0,MUT 1 R1.fastq.gz,0:74.55 1:0,A:562954867;C:599474858;G:575980257;T:687194946;N:134250,74,0,,,562954867,599474858,575980257,687194946,134250,SRX6047142,SRS4950160,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.96592,,0.05193,,0.69181,,0.46287,,75,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,Hungary,2019-06-12,Larval,Larval,Whole Organism,All anatomical structures
52830,SRR9277356,SRX6047141,SRS4950159,SRP201168,PRJNA548449,Dyskerin impairment in zebrafish,PRJNA548449,Other,One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.,,,sample03,,dkc1 elu1 sib3,,isolate:biological replicate 3|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:wild|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf,SIB3,SIB3,Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,SIB-3_R1.fastq.gz,fastq,2525161946.0,33921476.0,SIB 3 R1.fastq.gz,0:74.44 1:0,A:617606365;C:576906982;G:574368411;T:756144418;N:135770,74,0,,,617606365,576906982,574368411,756144418,135770,SRX6047141,SRS4950159,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.95481,,0.09246,,0.70187,,0.48651,,74,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,Hungary,2019-06-12,Larval,Larval,Whole Organism,All anatomical structures
52831,SRR9277357,SRX6047140,SRS4950158,SRP201168,PRJNA548449,Dyskerin impairment in zebrafish,PRJNA548449,Other,One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.,,,sample02,,dkc1 elu1 sib2,,isolate:biological replicate 2|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:wild|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf,SIB2,SIB2,Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,SIB-2_R1.fastq.gz,fastq,2500753589.0,33594139.0,SIB 2 R1.fastq.gz,0:74.44 1:0,A:594107753;C:588927623;G:585955773;T:731305179;N:457261,74,0,,,594107753,588927623,585955773,731305179,457261,SRX6047140,SRS4950158,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.95785,,0.07623,,0.70512,,0.49187,,75,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,Hungary,2019-06-12,Larval,Larval,Whole Organism,All anatomical structures
52832,SRR9277358,SRX6047139,SRS4950157,SRP201168,PRJNA548449,Dyskerin impairment in zebrafish,PRJNA548449,Other,One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.,,,sample01,,dkc1 elu1 sib1,,isolate:biological replicate 1|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:wild|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf,SIB1,SIB1,Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,SIB-1_R1.fastq.gz,fastq,2611643150.0,35032800.0,SIB 1 R1.fastq.gz,0:74.55 1:0,A:594796815;C:658132193;G:620365621;T:738201586;N:146935,74,0,,,594796815,658132193,620365621,738201586,146935,SRX6047139,SRS4950157,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.97084,,0.05106,,0.69858,,0.46901,,73,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,Hungary,2019-06-12,Larval,Larval,Whole Organism,All anatomical structures
52833,SRR9277359,SRX6047138,SRS4950156,SRP201168,PRJNA548449,Dyskerin impairment in zebrafish,PRJNA548449,Other,One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.,,,sample06,,dkc1 elu1 mut3,,isolate:biological replicate 3|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:mutant|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf,MUT3,MUT3,Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,MUT-3_R1.fastq.gz,fastq,2503783299.0,33623629.0,MUT 3 R1.fastq.gz,0:74.46 1:0,A:603400760;C:568138093;G:589455352;T:742564020;N:225074,74,0,,,603400760,568138093,589455352,742564020,225074,SRX6047138,SRS4950156,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.95328,,0.08246,,0.69581,,0.48805,,74,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,Hungary,2019-06-12,Larval,Larval,Whole Organism,All anatomical structures
52834,SRR9277360,SRX6047137,SRS4950155,SRP201168,PRJNA548449,Dyskerin impairment in zebrafish,PRJNA548449,Other,One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.,,,sample05,,dkc1 elu1 mut2,,isolate:biological replicate 2|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:mutant|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf,MUT2,MUT2,Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,MUT-2_R1.fastq.gz,fastq,2437701211.0,32733070.0,MUT 2 R1.fastq.gz,0:74.47 1:0,A:590961375;C:565727869;G:562583560;T:718173630;N:254777,74,0,,,590961375,565727869,562583560,718173630,254777,SRX6047137,SRS4950155,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.95589,,0.07601,,0.70317,,0.49704,,75,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,Hungary,2019-06-12,Larval,Larval,Whole Organism,All anatomical structures
54188,SRR10095964,SRX6828145,SRS5370320,SRP221273,PRJNA564810,A Single Cell Transcriptome Atlas for Zebrafish Development,PRJNA564810,Other,The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge  we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap  we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore  we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes  including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis  to launch an effort to define the diversity of cell types during zebrafish organogenesis  and to examine the transcriptional profiles that produce each cell type over developmental time.,,,,,5b,,strain:Tgolig2:GFPvu12|age:5 dpf|sex:unknown|tissue:whole embryo|Replicate name:5b|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,5b,5b,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,loader:latf load,olig2gfp120hb_S5_L001_R1_001.fastq olig2gfp120hb_S5_L001_R2_001.fastq olig2gfp120hb_S5_L002_R1_001.fastq olig2gfp120hb_S5_L002_R2_001.fastq olig2gfp120hb_S5_L003_R1_001.fastq olig2gfp120hb_S5_L003_R2_001.fastq olig2gfp120hb_S5_L004_R1_001.fastq olig2gfp120hb_S5_L004_R2_001.fastq olig2gfp120hb_S5_L005_R1_001.fastq olig2gfp120hb_S5_L005_R2_001.fastq olig2gfp120hb_S5_L006_R1_001.fastq olig2gfp120hb_S5_L006_R2_001.fastq olig2gfp120hb_S5_L007_R1_001.fastq olig2gfp120hb_S5_L007_R2_001.fastq olig2gfp120hb_S5_L008_R1_001.fastq olig2gfp120hb_S5_L008_R2_001.fastq,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,90080193105.0,566542095.0,5b.gz,0:26 1:133,A:25143336916;C:20071432223;G:20537826191;T:24313961041;N:13636734,26,133,,,25143336916,20071432223,20537826191,24313961041,13636734,SRX6828145,SRS5370320,SRA960102,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.00976,0.95301,0.00215,0.10077,0.97926,0.77851,0.44407,0.5221,26,133,T,B,sc-like readlen,illumina,hiseq_era,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United States,2019-12-10,Larval,Larval,Whole Organism,All anatomical structures
54189,SRR10095965,SRX6828144,SRS5370319,SRP221273,PRJNA564810,A Single Cell Transcriptome Atlas for Zebrafish Development,PRJNA564810,Other,The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge  we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap  we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore  we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes  including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis  to launch an effort to define the diversity of cell types during zebrafish organogenesis  and to examine the transcriptional profiles that produce each cell type over developmental time.,,,,,5a,,strain:Tgolig2:GFPvu12|age:5 dpf|sex:unknown|tissue:whole embryo|Replicate name:5a|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,5a,5a,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,loader:latf load,olig2gfp120ha_S4_L001_R1_001.fastq olig2gfp120ha_S4_L001_R2_001.fastq olig2gfp120ha_S4_L002_R1_001.fastq olig2gfp120ha_S4_L002_R2_001.fastq olig2gfp120ha_S4_L003_R1_001.fastq olig2gfp120ha_S4_L003_R2_001.fastq olig2gfp120ha_S4_L004_R1_001.fastq olig2gfp120ha_S4_L004_R2_001.fastq olig2gfp120ha_S4_L005_R1_001.fastq olig2gfp120ha_S4_L005_R2_001.fastq olig2gfp120ha_S4_L006_R1_001.fastq olig2gfp120ha_S4_L006_R2_001.fastq olig2gfp120ha_S4_L007_R1_001.fastq olig2gfp120ha_S4_L007_R2_001.fastq olig2gfp120ha_S4_L008_R1_001.fastq olig2gfp120ha_S4_L008_R2_001.fastq,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,106640540616.0,670695224.0,5a.gz,0:26 1:133,A:29532468637;C:23968826821;G:24791831474;T:28331248539;N:16165145,26,133,,,29532468637,23968826821,24791831474,28331248539,16165145,SRX6828144,SRS5370319,SRA960102,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.01014,0.95016,0.00222,0.09527,0.97855,0.78212,0.41929,0.50263,26,133,T,B,sc-like readlen,illumina,hiseq_era,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United States,2019-12-10,Larval,Larval,Whole Organism,All anatomical structures
64122,SRR14272168,SRX10633820,SRS8730202,SRP315319,PRJNA722925,Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation,PRJNA722925,Other,Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Pancreas islet 6dpf B2,Pancreas islets   Islet 6d B2 AGN000787,,strain:TU/AB|age:not applicable|dev stage:Day 6|sex:pooled male and female|tissue:pancreas|molecule:mRNA|selection:pA|sample ref:AGS000684|replicate ref:AGN000787|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Pancreas islet 6dpf B2,AGR001074,AGR001074,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001074_R1.fastq.gz,fastq,467368080.0,6149580.0,AGR001074 R1.fastq.gz,0:76 1:0,A:144866246;C:90980862;G:90828673;T:140671264;N:21035,76,0,,,144866246,90980862,90828673,140671264,21035,SRX10633820,SRS8730202,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.86223,,0.47625,,0.68556,,0.52132,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Pancreas,Endocrine System
64123,SRR14272169,SRX10633819,SRS8730201,SRP315319,PRJNA722925,Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation,PRJNA722925,Other,Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Pancreas islet 6dpf B1,Pancreas islets   Islet 6d B1 AGN000786,,strain:TU/AB|age:not applicable|dev stage:Day 6|sex:pooled male and female|tissue:pancreas|molecule:mRNA|selection:pA|sample ref:AGS000684|replicate ref:AGN000786|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Pancreas islet 6dpf B1,AGR001073,AGR001073,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001073_R1.fastq.gz,fastq,592506792.0,7796142.0,AGR001073 R1.fastq.gz,0:76 1:0,A:179281934;C:120318002;G:119990438;T:172891644;N:24774,76,0,,,179281934,120318002,119990438,172891644,24774,SRX10633819,SRS8730201,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.84252,,0.35277,,0.69219,,0.54723,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Pancreas,Endocrine System
64124,SRR14272170,SRX10633818,SRS8730200,SRP315319,PRJNA722925,Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation,PRJNA722925,Other,Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Embryo 4dpf B2,Pancreas islets   Emb 4d B2 AGN000908,,strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000683|replicate ref:AGN000908|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Embryo 4dpf B2,AGR001079,AGR001079,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001079_R1.fastq.gz,fastq,964097696.0,12685496.0,AGR001079 R1.fastq.gz,0:76 1:0,A:283521084;C:189406746;G:187691764;T:303421304;N:56798,76,0,,,283521084,189406746,187691764,303421304,56798,SRX10633818,SRS8730200,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.90888,,0.23944,,0.71198,,0.48798,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Embryo Imprecise,All anatomical structures
64125,SRR14272171,SRX10633817,SRS8730199,SRP315319,PRJNA722925,Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation,PRJNA722925,Other,Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Embryo 4dpf B1,Pancreas islets   Emb 4d B1 AGN000784,,strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000683|replicate ref:AGN000784|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Embryo 4dpf B1,AGR001072,AGR001072,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001072_R1.fastq.gz,fastq,361950000.0,4762500.0,AGR001072 R1.fastq.gz,0:76 1:0,A:105125535;C:73506847;G:72633174;T:110668542;N:15902,76,0,,,105125535,73506847,72633174,110668542,15902,SRX10633817,SRS8730199,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.86314,,0.22928,,0.71522,,0.48757,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Embryo Imprecise,All anatomical structures
64126,SRR14272172,SRX10633816,SRS8730198,SRP315319,PRJNA722925,Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation,PRJNA722925,Other,Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Embryo 4dpf beta cell ablation B2,Pancreas islets   Emb b cell abt 4d B2 AGN000783,,strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:embryo|treatment:metronidazole|molecule:mRNA|selection:pA|sample ref:AGS000682|replicate ref:AGN000783|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Embryo 4dpf beta cell ablation B2,AGR001071,AGR001071,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001071_R1.fastq.gz,fastq,322597884.0,4244709.0,AGR001071 R1.fastq.gz,0:76 1:0,A:99462715;C:64593856;G:62943431;T:95583878;N:14004,76,0,,,99462715,64593856,62943431,95583878,14004,SRX10633816,SRS8730198,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.80734,,0.28119,,0.74126,,0.50382,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Embryo Imprecise,All anatomical structures
64127,SRR14272173,SRX10633815,SRS8730197,SRP315319,PRJNA722925,Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation,PRJNA722925,Other,Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Embryo 4dpf beta cell ablation B1,Pancreas islets   Emb b cell abt 4d B1 AGN000907,,strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:embryo|treatment:metronidazole|molecule:mRNA|selection:pA|sample ref:AGS000682|replicate ref:AGN000907|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Embryo 4dpf beta cell ablation B1,AGR001078,AGR001078,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001078_R1.fastq.gz,fastq,686122452.0,9027927.0,AGR001078 R1.fastq.gz,0:76 1:0,A:196244052;C:132201159;G:130878329;T:226758661;N:40251,76,0,,,196244052,132201159,130878329,226758661,40251,SRX10633815,SRS8730197,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.89799,,0.26844,,0.7236,,0.49736,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Embryo Imprecise,All anatomical structures
64128,SRR14272174,SRX10633814,SRS8730196,SRP315319,PRJNA722925,Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation,PRJNA722925,Other,Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B2,Pancreas islets   Islet SST b cell abt 4d B2 AGN000782,,strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:pancreas|treatment:metronidazole|molecule:mRNA|selection:pA|sample ref:AGS000680|replicate ref:AGN000782|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B2,AGR001070,AGR001070,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001070_R1.fastq.gz,fastq,481320616.0,6333166.0,AGR001070 R1.fastq.gz,0:76 1:0,A:151409804;C:91026556;G:90673968;T:148189727;N:20561,76,0,,,151409804,91026556,90673968,148189727,20561,SRX10633814,SRS8730196,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.82954,,0.59765,,0.75538,,0.53049,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Pancreas,Endocrine System
64129,SRR14272175,SRX10633813,SRS8730195,SRP315319,PRJNA722925,Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation,PRJNA722925,Other,Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B1,Pancreas islets   Islet SST b cell abt 4d B1 AGN000781,,strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:pancreas|treatment:metronidazole|molecule:mRNA|selection:pA|sample ref:AGS000680|replicate ref:AGN000781|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B1,AGR001069,AGR001069,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001069_R1.fastq.gz,fastq,379230956.0,4989881.0,AGR001069 R1.fastq.gz,0:76 1:0,A:116227158;C:75587948;G:75371178;T:112027929;N:16743,76,0,,,116227158,75587948,75371178,112027929,16743,SRX10633813,SRS8730195,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.87385,,0.38949,,0.69242,,0.47061,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Pancreas,Endocrine System
64130,SRR14272176,SRX10633812,SRS8730194,SRP315319,PRJNA722925,Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation,PRJNA722925,Other,Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Embryo 6dpf B2,Pancreas islets   Emb 6d B2 AGN000906,,strain:TU/AB|age:not applicable|dev stage:Day 6|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000686|replicate ref:AGN000906|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Embryo 6dpf B2,AGR001077,AGR001077,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001077_R1.fastq.gz,fastq,2384214848.0,31371248.0,AGR001077 R1.fastq.gz,0:76 1:0,A:714742449;C:464163353;G:470448118;T:734706441;N:154487,76,0,,,714742449,464163353,470448118,734706441,154487,SRX10633812,SRS8730194,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.88871,,0.28853,,0.71409,,0.54974,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Embryo Imprecise,All anatomical structures
64131,SRR14272177,SRX10633811,SRS8730193,SRP315319,PRJNA722925,Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation,PRJNA722925,Other,Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Embryo 6dpf B1,Pancreas islets   Emb 6d B1 AGN000905,,strain:TU/AB|age:not applicable|dev stage:Day 6|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000686|replicate ref:AGN000905|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Embryo 6dpf B1,AGR001075,AGR001075,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001075_R1.fastq.gz,fastq,969784016.0,12760316.0,AGR001075 R1.fastq.gz,0:76 1:0,A:281305895;C:200784367;G:201647944;T:285982138;N:63672,76,0,,,281305895,200784367,201647944,285982138,63672,SRX10633811,SRS8730193,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.90503,,0.22448,,0.69976,,0.50012,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Embryo Imprecise,All anatomical structures
64132,SRR14272178,SRX10633810,SRS8730193,SRP315319,PRJNA722925,Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation,PRJNA722925,Other,Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Embryo 6dpf B1,Pancreas islets   Emb 6d B1 AGN000905,,strain:TU/AB|age:not applicable|dev stage:Day 6|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000686|replicate ref:AGN000905|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Embryo 6dpf B1,AGR001076,AGR001076,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001076_R1.fastq.gz,fastq,4355542368.0,57309768.0,AGR001076 R1.fastq.gz,0:76 1:0,A:1257915324;C:889208248;G:890382954;T:1317821338;N:214504,76,0,,,1257915324,889208248,890382954,1317821338,214504,SRX10633810,SRS8730193,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.90632,,0.23035,,0.70019,,0.49617,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Embryo Imprecise,All anatomical structures
64133,SRR14272179,SRX10633809,SRS8730192,SRP315319,PRJNA722925,Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation,PRJNA722925,Other,Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP B2,Pancreas islets   Islet SST 4d B2 AGN000780,,strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:pancreas|molecule:mRNA|selection:pA|sample ref:AGS000678|replicate ref:AGN000780|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP B2,AGR001068,AGR001068,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001068_R1.fastq.gz,fastq,1025641204.0,13495279.0,AGR001068 R1.fastq.gz,0:76 1:0,A:313399325;C:201992871;G:202026959;T:308179140;N:42909,76,0,,,313399325,201992871,202026959,308179140,42909,SRX10633809,SRS8730192,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.8692,,0.47406,,0.68081,,0.54006,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Pancreas,Endocrine System
64134,SRR14272180,SRX10633808,SRS8730191,SRP315319,PRJNA722925,Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation,PRJNA722925,Other,Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP B1,Pancreas islets   Islet SST 4d B1 AGN000779,,strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:pancreas|molecule:mRNA|selection:pA|sample ref:AGS000678|replicate ref:AGN000779|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP B1,AGR001067,AGR001067,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001067_R1.fastq.gz,fastq,645391392.0,8491992.0,AGR001067 R1.fastq.gz,0:76 1:0,A:198297729;C:127050955;G:126777924;T:193238145;N:26639,76,0,,,198297729,127050955,126777924,193238145,26639,SRX10633808,SRS8730191,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.85746,,0.50636,,0.68286,,0.48271,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Pancreas,Endocrine System
67683,SRR17235493,SRX13414611,SRS11316492,SRP350846,PRJNA789116,RNAseq of Bbs1 KO Zebrafish larval eyes,PRJNA789116,Other,Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.,,,,,BBS1 MUT 10dpf S1,,strain:Bbs1ka742|age:10dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype: / |Paired group:D|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larval bbs1 mutant eye,BBS1 MUT 10dpf S1,BBS1 MUT 10dpf S1,TruSeq Stranded Total RNA Library Prep Gold,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP350846,,fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4,BBS1_MUT_10dpf_S4_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa,bam bam,3635985845.0,36892654.0,BBS1 MUT 10dpf S4 merged.bam,0:98.56,A:951181543;C:805662797;G:846180468;T:1032919946;N:41091,98,,,,951181543,805662797,846180468,1032919946,41091,SRX13414611,SRS11316492,SRA1343787,University of Zurich (UZH)|Molecular Life Science,University of Zurich (UZH),1,0.93818,,0.32197,,0.69451,,0.47394,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,trueseq,bulk,bulk,bulk,,Switzerland,2021-12-15,Larval,Larval,Eye,Sensory System
67684,SRR17235494,SRX13414610,SRS11316490,SRP350846,PRJNA789116,RNAseq of Bbs1 KO Zebrafish larval eyes,PRJNA789116,Other,Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.,,,,,BBS1 CTRL 10dpf S3,,strain:Bbs1ka742|age:10dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype:+/ |Paired group:F|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larval bbs1 mutant eye,BBS1 CTRL 10dpf S3,BBS1 CTRL 10dpf S3,TruSeq Stranded Total RNA Library Prep Gold,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP350846,,fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4,BBS1_CTRL_10dpf_S6_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa,bam bam,3130875298.0,31620050.0,BBS1 CTRL 10dpf S6 merged.bam,0:99.02,A:814143728;C:694726254;G:728135378;T:893834285;N:35653,99,,,,814143728,694726254,728135378,893834285,35653,SRX13414610,SRS11316490,SRA1343787,University of Zurich (UZH)|Molecular Life Science,University of Zurich (UZH),1,0.94014,,0.33329,,0.69735,,0.47408,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,trueseq,bulk,bulk,bulk,,Switzerland,2021-12-15,Larval,Larval,Eye,Sensory System
67685,SRR17235495,SRX13414609,SRS11316491,SRP350846,PRJNA789116,RNAseq of Bbs1 KO Zebrafish larval eyes,PRJNA789116,Other,Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.,,,,,BBS1 CTRL 10dpf S2,,strain:Bbs1ka742|age:10dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype:+/ |Paired group:E|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larval bbs1 mutant eye,BBS1 CTRL 10dpf S2,BBS1 CTRL 10dpf S2,TruSeq Stranded Total RNA Library Prep Gold,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP350846,,fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4,BBS1_CTRL_10dpf_S5_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa,bam bam,3062763746.0,31000736.0,BBS1 CTRL 10dpf S5 merged.bam,0:98.80,A:786649223;C:679725108;G:723425238;T:872929361;N:34816,98,,,,786649223,679725108,723425238,872929361,34816,SRX13414609,SRS11316491,SRA1343787,University of Zurich (UZH)|Molecular Life Science,University of Zurich (UZH),1,0.94626,,0.26532,,0.68793,,0.46861,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,trueseq,bulk,bulk,bulk,,Switzerland,2021-12-15,Larval,Larval,Eye,Sensory System
67686,SRR17235496,SRX13414608,SRS11316489,SRP350846,PRJNA789116,RNAseq of Bbs1 KO Zebrafish larval eyes,PRJNA789116,Other,Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.,,,,,BBS1 Ctrl 10dpf S1,,strain:Bbs1ka742|age:10dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype:+/ |Paired group:D|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larval bbs1 mutant eye,BBS1 Ctrl 10dpf S1,BBS1 Ctrl 10dpf S1,TruSeq Stranded Total RNA Library Prep Gold,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP350846,,fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4,BBS1_CTRL_10dpf_S4_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa,bam bam,4388386557.0,44385344.0,BBS1 CTRL 10dpf S4 merged.bam,0:98.87,A:1141948730;C:979155774;G:1019331809;T:1247901031;N:49213,98,,,,1141948730,979155774,1019331809,1247901031,49213,SRX13414608,SRS11316489,SRA1343787,University of Zurich (UZH)|Molecular Life Science,University of Zurich (UZH),1,0.94326,,0.28573,,0.69296,,0.47244,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,trueseq,bulk,bulk,bulk,,Switzerland,2021-12-15,Larval,Larval,Eye,Sensory System
67687,SRR17235497,SRX13414607,SRS11316488,SRP350846,PRJNA789116,RNAseq of Bbs1 KO Zebrafish larval eyes,PRJNA789116,Other,Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.,,,,,BBS1 MUT 5dpf S3,,strain:Bbs1ka742|age:5dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype: / |Paired group:C|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larval bbs1 mutant eye,BBS1 MUT 5dpf S3,BBS1 MUT 5dpf S3,TruSeq Stranded Total RNA Library Prep Gold,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP350846,,fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4,BBS1_MUT_5dpf_S3_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa,bam bam,3030482374.0,30617366.0,BBS1 MUT 5dpf S3 merged.bam,0:98.98,A:813926164;C:646079228;G:694857531;T:875585698;N:33753,98,,,,813926164,646079228,694857531,875585698,33753,SRX13414607,SRS11316488,SRA1343787,University of Zurich (UZH)|Molecular Life Science,University of Zurich (UZH),1,0.92861,,0.41464,,0.69051,,0.49332,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,trueseq,bulk,bulk,bulk,,Switzerland,2021-12-15,Larval,Larval,Eye,Sensory System
67688,SRR17235498,SRX13414606,SRS11316487,SRP350846,PRJNA789116,RNAseq of Bbs1 KO Zebrafish larval eyes,PRJNA789116,Other,Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.,,,,,BBS1 MUT 5dpf S2,,strain:Bbs1ka742|age:5dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype: / |Paired group:B|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larval bbs1 mutant eye,BBS1 MUT 5dpf S2,BBS1 MUT 5dpf S2,TruSeq Stranded Total RNA Library Prep Gold,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP350846,,fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4,BBS1_MUT_5dpf_S2_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa,bam bam,3714404169.0,37505417.0,BBS1 MUT 5dpf S2 merged.bam,0:99.04,A:968857332;C:821571707;G:867307403;T:1056625911;N:41816,99,,,,968857332,821571707,867307403,1056625911,41816,SRX13414606,SRS11316487,SRA1343787,University of Zurich (UZH)|Molecular Life Science,University of Zurich (UZH),1,0.93912,,0.32694,,0.68781,,0.48549,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,trueseq,bulk,bulk,bulk,,Switzerland,2021-12-15,Larval,Larval,Eye,Sensory System
67689,SRR17235499,SRX13414605,SRS11316486,SRP350846,PRJNA789116,RNAseq of Bbs1 KO Zebrafish larval eyes,PRJNA789116,Other,Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.,,,,,BBS1 MUT 5dpf S1,,strain:Bbs1ka742|age:5dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype: / |Paired group:A|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larval bbs1 mutant eye,BBS1 MUT 5dpf S1,BBS1 MUT 5dpf S1,TruSeq Stranded Total RNA Library Prep Gold,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP350846,,fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4,BBS1_MUT_5dpf_S1_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa,bam bam,3699896449.0,37382583.0,BBS1 MUT 5dpf S1 merged.bam,0:98.97,A:977907912;C:830475992;G:855441672;T:1036029492;N:41381,98,,,,977907912,830475992,855441672,1036029492,41381,SRX13414605,SRS11316486,SRA1343787,University of Zurich (UZH)|Molecular Life Science,University of Zurich (UZH),1,0.93133,,0.40806,,0.69562,,0.5114,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,trueseq,bulk,bulk,bulk,,Switzerland,2021-12-15,Larval,Larval,Eye,Sensory System
67690,SRR17235500,SRX13414604,SRS11316485,SRP350846,PRJNA789116,RNAseq of Bbs1 KO Zebrafish larval eyes,PRJNA789116,Other,Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.,,,,,BBS1 CTRL 5dpf S3,,strain:Bbs1ka742|age:5dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype:+/ |Paired group:C|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larval bbs1 mutant eye,BBS1 CTRL 5dpf S3,BBS1 CTRL 5dpf S3,TruSeq Stranded Total RNA Library Prep Gold,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP350846,,fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4,BBS1_CTRL_5dpf_S3_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa,bam bam,3505192259.0,35384389.0,BBS1 CTRL 5dpf S3 merged.bam,0:99.06,A:910433958;C:775887812;G:822289434;T:996540997;N:40058,99,,,,910433958,775887812,822289434,996540997,40058,SRX13414604,SRS11316485,SRA1343787,University of Zurich (UZH)|Molecular Life Science,University of Zurich (UZH),1,0.94274,,0.28843,,0.68678,,0.47383,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,trueseq,bulk,bulk,bulk,,Switzerland,2021-12-15,Larval,Larval,Eye,Sensory System
67691,SRR17235501,SRX13414603,SRS11316483,SRP350846,PRJNA789116,RNAseq of Bbs1 KO Zebrafish larval eyes,PRJNA789116,Other,Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.,,,,,BBS1 MUT 10dpf S3,,strain:Bbs1ka742|age:10dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype: / |Paired group:F|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larval bbs1 mutant eye,BBS1 MUT 10dpf S3,BBS1 MUT 10dpf S3,TruSeq Stranded Total RNA Library Prep Gold,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP350846,,fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4,BBS1_MUT_10dpf_S6_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa,bam bam,3821277753.0,38662066.0,BBS1 MUT 10dpf S6 merged.bam,0:98.84,A:1019329287;C:820362185;G:870436357;T:1111106893;N:43031,98,,,,1019329287,820362185,870436357,1111106893,43031,SRX13414603,SRS11316483,SRA1343787,University of Zurich (UZH)|Molecular Life Science,University of Zurich (UZH),1,0.93021,,0.40772,,0.70019,,0.47824,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,trueseq,bulk,bulk,bulk,,Switzerland,2021-12-15,Larval,Larval,Eye,Sensory System
67692,SRR17235502,SRX13414602,SRS11316484,SRP350846,PRJNA789116,RNAseq of Bbs1 KO Zebrafish larval eyes,PRJNA789116,Other,Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.,,,,,BBS1 MUT 10dpf S2,,strain:Bbs1ka742|age:10dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype: / |Paired group:E|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larval bbs1 mutant eye,BBS1 MUT 10dpf S2,BBS1 MUT 10dpf S2,TruSeq Stranded Total RNA Library Prep Gold,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP350846,,fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4,BBS1_MUT_10dpf_S5_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa,bam bam,2747848263.0,27781273.0,BBS1 MUT 10dpf S5 merged.bam,0:98.91,A:726140802;C:605265574;G:628347573;T:788063451;N:30863,98,,,,726140802,605265574,628347573,788063451,30863,SRX13414602,SRS11316484,SRA1343787,University of Zurich (UZH)|Molecular Life Science,University of Zurich (UZH),1,0.93216,,0.39301,,0.70009,,0.50624,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,trueseq,bulk,bulk,bulk,,Switzerland,2021-12-15,Larval,Larval,Eye,Sensory System
67693,SRR17235503,SRX13414601,SRS11316482,SRP350846,PRJNA789116,RNAseq of Bbs1 KO Zebrafish larval eyes,PRJNA789116,Other,Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.,,,,,BBS1 CTRL 5dpf S2,,strain:Bbs1ka742|age:5dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype:+/ |Paired group:B|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larval bbs1 mutant eye,BBS1 CTRL 5dpf S2,BBS1 CTRL 5dpf S2,TruSeq Stranded Total RNA Library Prep Gold,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP350846,,fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4,BBS1_CTRL_5dpf_S2_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa,bam bam,3371457502.0,33990750.0,BBS1 CTRL 5dpf S2 merged.bam,0:99.19,A:865249225;C:752466820;G:799272800;T:954431124;N:37533,99,,,,865249225,752466820,799272800,954431124,37533,SRX13414601,SRS11316482,SRA1343787,University of Zurich (UZH)|Molecular Life Science,University of Zurich (UZH),1,0.94297,,0.30382,,0.68523,,0.49502,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,trueseq,bulk,bulk,bulk,,Switzerland,2021-12-15,Larval,Larval,Eye,Sensory System
67694,SRR17235504,SRX13414600,SRS11316481,SRP350846,PRJNA789116,RNAseq of Bbs1 KO Zebrafish larval eyes,PRJNA789116,Other,Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy  intellectual disability  polydactyly  obesity and renal anomalies. In photoreceptors PR  light sensation occurs in outer segments OSs  which are specialized primary cilia. BBS1  the major BBS gene  is part of a protein complex called BBSome  which is involved in intracellular protein transport. However  the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.,,,,,BBS1 CTRL 5dpf S1,,strain:Bbs1ka742|age:5dpf|dev stage:Larvae|sex:not applicable|tissue:Eye|genotype:+/ |Paired group:A|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larval bbs1 mutant eye,BBS1 CTRL 5dpf S1,BBS1 CTRL 5dpf S1,TruSeq Stranded Total RNA Library Prep Gold,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP350846,,fasta file:Danio rerio.GRCz11.dna.primary assembly.fa|assembly:GCA 000002035.4,BBS1_CTRL_5dpf_S1_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa,bam bam,3243942424.0,32951170.0,BBS1 CTRL 5dpf S1 merged.bam,0:98.45,A:886651528;C:694664952;G:729637645;T:932951711;N:36588,98,,,,886651528,694664952,729637645,932951711,36588,SRX13414600,SRS11316481,SRA1343787,University of Zurich (UZH)|Molecular Life Science,University of Zurich (UZH),1,0.92662,,0.42838,,0.69404,,0.48808,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,trueseq,bulk,bulk,bulk,,Switzerland,2021-12-15,Larval,Larval,Eye,Sensory System
74579,SRR23974542,SRX19779002,SRS17142416,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed parents,D1,,isolate:10|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Gly parental larvae,10,10,larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TP1F.fq.gz,fastq,2956240050.0,19708267.0,TP1F.fq.gz,0:150 1:0,A:785689496;C:695356949;G:702558232;T:772610474;N:24899,150,0,,,785689496,695356949,702558232,772610474,24899,SRX19779002,SRS17142416,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.93915,,0.07675,,0.68534,,0.4891,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74580,SRR23974543,SRX19779001,SRS17142414,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,C3,,isolate:9|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae parental,9,9,control larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CP3F.fq.gz,fastq,3243688800.0,21624592.0,CP3F.fq.gz,0:150 1:0,A:866441929;C:744536766;G:783433493;T:849247758;N:28854,150,0,,,866441929,744536766,783433493,849247758,28854,SRX19779001,SRS17142414,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.91011,,0.086,,0.68972,,0.48291,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74581,SRR23974544,SRX19779000,SRS17142415,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,C2,,isolate:8|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae parental,8,8,control larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CP2F.fq.gz,fastq,3455536800.0,23036912.0,CP2F.fq.gz,0:150 1:0,A:955162327;C:765147222;G:797594182;T:937601078;N:31991,150,0,,,955162327,765147222,797594182,937601078,31991,SRX19779000,SRS17142415,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.90361,,0.13207,,0.69345,,0.48842,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74582,SRR23974545,SRX19778999,SRS17142412,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,C1,,isolate:7|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae parental,7,7,control larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CP1F.fq.gz,fastq,3394157850.0,22627719.0,CP1F.fq.gz,0:150 1:0,A:918865518;C:780289302;G:793602009;T:901371269;N:29752,150,0,,,918865518,780289302,793602009,901371269,29752,SRX19778999,SRS17142412,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.93417,,0.08314,,0.68006,,0.48695,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74583,SRR23974546,SRX19778998,SRS17142413,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed larvae,B3,,isolate:6|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Gly larvae exposed,6,6,larvae exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TE3F.fq.gz,fastq,3021012750.0,20140085.0,TE3F.fq.gz,0:150 1:0,A:802754479;C:697084034;G:736507600;T:784641365;N:25272,150,0,,,802754479,697084034,736507600,784641365,25272,SRX19778998,SRS17142413,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.9039,,0.08388,,0.6997,,0.49603,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74584,SRR23974547,SRX19778997,SRS17142411,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed larvae,B2,,isolate:5|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Gly larvae exposed,5,5,larvae exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TE2F.fq.gz,fastq,3037657950.0,20251053.0,TE2F.fq.gz,0:150 1:0,A:806162990;C:709397050;G:731668622;T:790403768;N:25520,150,0,,,806162990,709397050,731668622,790403768,25520,SRX19778997,SRS17142411,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.92641,,0.07865,,0.69798,,0.46929,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74585,SRR23974548,SRX19778996,SRS17142410,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed larvae,B1,,isolate:4|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Gly larvae exposed,4,4,larvae exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TE1F.fq.gz,fastq,3459122100.0,23060814.0,TE1F.fq.gz,0:150 1:0,A:957107791;C:768667835;G:795319703;T:937996052;N:30719,150,0,,,957107791,768667835,795319703,937996052,30719,SRX19778996,SRS17142410,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.90435,,0.12237,,0.70128,,0.47725,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74586,SRR23974549,SRX19778995,SRS17142409,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,A3,,isolate:3|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae,3,3,larvae control,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CE3F.fq.gz,fastq,3496645950.0,23310973.0,CE3F.fq.gz,0:150 1:0,A:927418130;C:820945235;G:834908249;T:913344868;N:29468,150,0,,,927418130,820945235,834908249,913344868,29468,SRX19778995,SRS17142409,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.93227,,0.08275,,0.69339,,0.49066,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74587,SRR23974550,SRX19778994,SRS17142408,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed parents,D3,,isolate:12|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Gly parental larvae,12,12,larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TP3F.fq.gz,fastq,3317790150.0,22118601.0,TP3F.fq.gz,0:150 1:0,A:883540292;C:768555339;G:796741351;T:868924072;N:29096,150,0,,,883540292,768555339,796741351,868924072,29096,SRX19778994,SRS17142408,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74588,SRR23974551,SRX19778993,SRS17142407,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed parents,D2,,isolate:11|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Gly parental larvae,11,11,larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TP2F.fq.gz,fastq,2948738400.0,19658256.0,TP2F.fq.gz,0:150 1:0,A:777218056;C:697066948;G:709846212;T:764582431;N:24753,150,0,,,777218056,697066948,709846212,764582431,24753,SRX19778993,SRS17142407,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74589,SRR23974552,SRX19778992,SRS17142405,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,A2,,isolate:2|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae,2,2,larvae control,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CE2F.fq.gz,fastq,3760293450.0,25068623.0,CE2F.fq.gz,0:150 1:0,A:1000790271;C:868241486;G:905025923;T:986203921;N:31849,150,0,,,1000790271,868241486,905025923,986203921,31849,SRX19778992,SRS17142405,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74590,SRR23974553,SRX19778991,SRS17142406,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,A1,,isolate:1|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae,1,1,larvae control,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CE1F.fq.gz,fastq,3446794950.0,22978633.0,CE1F.fq.gz,0:150 1:0,A:916043654;C:787898255;G:842788936;T:900033406;N:30699,150,0,,,916043654,787898255,842788936,900033406,30699,SRX19778991,SRS17142406,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.89022,,0.09813,,0.69954,,0.49171,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74615,SRR24037111,SRX19839674,SRS17198396,SRP427499,PRJNA945049,linc mipep and linc wrb encode micropeptides that regulate chromatin accessibility in vertebrate specific neural cells,PRJNA945049,Other,Thousands of long intergenic non coding RNAs lincRNAs are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However  systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep  also called lnc rps25  and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein  Hmgn1  and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically  we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes   evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions  with implications for neurodevelopmental disorders and disease.,,,,linc mipep scMultiome 6d brains   Wild type linc mipep siblings scRNA seq [10x BAM],linc mipep scMultiome 6d brains   WT scRNA AGN002631 [10x BAM],,strain:TU/AB|age:144|dev stage:Day 6|sex:pooled male and female|tissue:brain|genotype:+/+|strain maternal:linc mipep WT|strain paternal:linc mipep WT|molecule:RNA|sample ref:AGS002041|replicate ref:AGN002631|replicate order:1|project label long:linc mipep homozygous mutant vs WT siblings sc Multiome 6dpf brains|project label short:linc mipep scMultiome 6d brains|sample label short:WT RNA|replicate label short:WT scRNA|filetype:bam|BioSampleModel:Model organism or animal,,,,,,,,,linc mipep scMultiome 6d brains   Wild type linc mipep siblings scRNA seq [10x BAM],AGR003365 AGR003384,AGR003365 AGR003384,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP427499,,assembly:GRCz11,linc_mipep_scMultiome_6d_brains_WT_AGN002631_gex_possorted_bam.bam,10X Genomics bam file,17819875800.0,197998620.0,linc mipep scMultiome 6d brains WT AGN002631 gex possorted bam.bam,0:90,A:5656585750;C:3315807167;G:3546967171;T:5300024689;N:491023,90,,,,5656585750,3315807167,3546967171,5300024689,491023,SRX19839674,SRS17198396,SRA1614141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.87958,,0.45053,,0.7709,,0.50096,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United States,2023-03-31,Larval,Larval,Brain,Nervous System
74616,SRR24037113,SRX19839672,SRS17198394,SRP427499,PRJNA945049,linc mipep and linc wrb encode micropeptides that regulate chromatin accessibility in vertebrate specific neural cells,PRJNA945049,Other,Thousands of long intergenic non coding RNAs lincRNAs are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However  systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep  also called lnc rps25  and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein  Hmgn1  and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically  we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes   evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions  with implications for neurodevelopmental disorders and disease.,,,,linc mipep scMultiome 6d brains   linc mipep mutant scRNA seq [10x BAM],linc mipep scMultiome 6d brains   linc mipepMut scRNA AGN002629 [10x BAM],,strain:TU/AB|age:144|dev stage:Day 6|sex:pooled male and female|tissue:brain|genotype: / |strain maternal:linc mipep MUT|strain paternal:linc mipep MUT|molecule:RNA|sample ref:AGS002016|replicate ref:AGN002629|replicate order:1|project label long:linc mipep homozygous mutant vs WT siblings sc Multiome 6dpf brains|project label short:linc mipep scMultiome 6d brains|sample label short:Mut RNA|replicate label short:linc mipepMut scRNA|filetype:bam|BioSampleModel:Model organism or animal,,,,,,,,,linc mipep scMultiome 6d brains   linc mipep mutant scRNA seq [10x BAM],AGR003363 AGR003382,AGR003363 AGR003382,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP427499,,assembly:GRCz11,linc_mipep_scMultiome_6d_brains_Mut_AGN002629_gex_possorted_bam.bam,10X Genomics bam file,18530138610.0,205890429.0,linc mipep scMultiome 6d brains Mut AGN002629 gex possorted bam.bam,0:90,A:5801406623;C:3514275581;G:3726649190;T:5487294607;N:512609,90,,,,5801406623,3514275581,3726649190,5487294607,512609,SRX19839672,SRS17198394,SRA1614141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.89012,,0.4464,,0.76867,,0.52212,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United States,2023-03-31,Larval,Larval,Brain,Nervous System
74617,SRR24010013,SRX19812857,SRS17053325,SRP427499,PRJNA945049,linc mipep and linc wrb encode micropeptides that regulate chromatin accessibility in vertebrate specific neural cells,PRJNA945049,Other,Thousands of long intergenic non coding RNAs lincRNAs are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However  systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep  also called lnc rps25  and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein  Hmgn1  and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically  we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes   evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions  with implications for neurodevelopmental disorders and disease.,,,,linc mipep scMultiome 6d brains   Wild type linc mipep siblings scRNA seq,linc mipep scMultiome 6d brains   WT scRNA AGN002631,,strain:TU/AB|age:144|dev stage:Day 6|sex:pooled male and female|tissue:brain|genotype:+/+|strain maternal:linc mipep WT|strain paternal:linc mipep WT|molecule:RNA|sample ref:AGS002041|replicate ref:AGN002631|replicate order:1|project label long:linc mipep homozygous mutant vs WT siblings sc Multiome 6dpf brains|project label short:linc mipep scMultiome 6d brains|sample label short:WT RNA|replicate label short:WT scRNA|BioSampleModel:Model organism or animal,,,,,,,,,linc mipep scMultiome 6d brains   Wild type linc mipep siblings scRNA seq,AGR003384,AGR003384,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP427499,,,AGR003384_I1.fastq.gz AGR003384_R1.fastq.gz AGR003384_R2.fastq.gz AGR003384_R3.fastq.gz,fastq fastq fastq fastq,27323809560.0,197998620.0,AGR003384 I1.fastq.gz,0:10 1:28 2:10 3:90,A:5656585750;C:3315807167;G:3546967171;T:5300024689;N:491023,10,28,10,90,5656585750,3315807167,3546967171,5300024689,491023,SRX19812857,SRS17053325,SRA1612740,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.87892,,0.45104,,0.76976,,0.49827,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-29,Larval,Larval,Brain,Nervous System
74618,SRR24010014,SRX19812856,SRS17053325,SRP427499,PRJNA945049,linc mipep and linc wrb encode micropeptides that regulate chromatin accessibility in vertebrate specific neural cells,PRJNA945049,Other,Thousands of long intergenic non coding RNAs lincRNAs are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However  systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep  also called lnc rps25  and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein  Hmgn1  and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically  we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes   evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions  with implications for neurodevelopmental disorders and disease.,,,,linc mipep scMultiome 6d brains   Wild type linc mipep siblings scRNA seq,linc mipep scMultiome 6d brains   WT scRNA AGN002631,,strain:TU/AB|age:144|dev stage:Day 6|sex:pooled male and female|tissue:brain|genotype:+/+|strain maternal:linc mipep WT|strain paternal:linc mipep WT|molecule:RNA|sample ref:AGS002041|replicate ref:AGN002631|replicate order:1|project label long:linc mipep homozygous mutant vs WT siblings sc Multiome 6dpf brains|project label short:linc mipep scMultiome 6d brains|sample label short:WT RNA|replicate label short:WT scRNA|BioSampleModel:Model organism or animal,,,,,,,,,linc mipep scMultiome 6d brains   Wild type linc mipep siblings scRNA seq,AGR003365,AGR003365,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP427499,,,AGR003365_I1.fastq.gz AGR003365_R1.fastq.gz AGR003365_R2.fastq.gz AGR003365_R3.fastq.gz,fastq fastq fastq fastq,1086745584.0,7874968.0,AGR003365 I1.fastq.gz,0:10 1:28 2:10 3:90,A:224554980;C:132053090;G:141496532;T:210627089;N:15429,10,28,10,90,224554980,132053090,141496532,210627089,15429,SRX19812856,SRS17053325,SRA1612740,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.87972,,0.45315,,0.77011,,0.49128,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-29,Larval,Larval,Brain,Nervous System
74619,SRR24010017,SRX19812853,SRS17053323,SRP427499,PRJNA945049,linc mipep and linc wrb encode micropeptides that regulate chromatin accessibility in vertebrate specific neural cells,PRJNA945049,Other,Thousands of long intergenic non coding RNAs lincRNAs are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However  systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep  also called lnc rps25  and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein  Hmgn1  and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically  we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes   evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions  with implications for neurodevelopmental disorders and disease.,,,,linc mipep scMultiome 6d brains   linc mipep mutant scRNA seq,linc mipep scMultiome 6d brains   linc mipepMut scRNA AGN002629,,strain:TU/AB|age:144|dev stage:Day 6|sex:pooled male and female|tissue:brain|genotype: / |strain maternal:linc mipep MUT|strain paternal:linc mipep MUT|molecule:RNA|sample ref:AGS002016|replicate ref:AGN002629|replicate order:1|project label long:linc mipep homozygous mutant vs WT siblings sc Multiome 6dpf brains|project label short:linc mipep scMultiome 6d brains|sample label short:Mut RNA|replicate label short:linc mipepMut scRNA|BioSampleModel:Model organism or animal,,,,,,,,,linc mipep scMultiome 6d brains   linc mipep mutant scRNA seq,AGR003382,AGR003382,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP427499,,,AGR003382_I1.fastq.gz AGR003382_R1.fastq.gz AGR003382_R2.fastq.gz AGR003382_R3.fastq.gz,fastq fastq fastq fastq,28412879202.0,205890429.0,AGR003382 I1.fastq.gz,0:10 1:28 2:10 3:90,A:5801406623;C:3514275581;G:3726649190;T:5487294607;N:512609,10,28,10,90,5801406623,3514275581,3726649190,5487294607,512609,SRX19812853,SRS17053323,SRA1612740,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.89026,,0.44521,,0.76905,,0.51993,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-29,Larval,Larval,Brain,Nervous System
74620,SRR24010018,SRX19812852,SRS17053323,SRP427499,PRJNA945049,linc mipep and linc wrb encode micropeptides that regulate chromatin accessibility in vertebrate specific neural cells,PRJNA945049,Other,Thousands of long intergenic non coding RNAs lincRNAs are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However  systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep  also called lnc rps25  and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein  Hmgn1  and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically  we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes   evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions  with implications for neurodevelopmental disorders and disease.,,,,linc mipep scMultiome 6d brains   linc mipep mutant scRNA seq,linc mipep scMultiome 6d brains   linc mipepMut scRNA AGN002629,,strain:TU/AB|age:144|dev stage:Day 6|sex:pooled male and female|tissue:brain|genotype: / |strain maternal:linc mipep MUT|strain paternal:linc mipep MUT|molecule:RNA|sample ref:AGS002016|replicate ref:AGN002629|replicate order:1|project label long:linc mipep homozygous mutant vs WT siblings sc Multiome 6dpf brains|project label short:linc mipep scMultiome 6d brains|sample label short:Mut RNA|replicate label short:linc mipepMut scRNA|BioSampleModel:Model organism or animal,,,,,,,,,linc mipep scMultiome 6d brains   linc mipep mutant scRNA seq,AGR003363,AGR003363,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP427499,,,AGR003363_I1.fastq.gz AGR003363_R1.fastq.gz AGR003363_R2.fastq.gz AGR003363_R3.fastq.gz,fastq fastq fastq fastq,1373742804.0,9954658.0,AGR003363 I1.fastq.gz,0:10 1:28 2:10 3:90,A:279788766;C:170196269;G:180765631;T:265150486;N:18068,10,28,10,90,279788766,170196269,180765631,265150486,18068,SRX19812852,SRS17053323,SRA1612740,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.88902,,0.44548,,0.76879,,0.52005,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,unknown,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-29,Larval,Larval,Brain,Nervous System