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
11148,ERR10034072,ERX9574476,ERS12562187,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Metamorphic tissue without xxx from Danio rerio,Drerio metamorphic 5,SAMEA110464159,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464159|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE25|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE25|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19178,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr25.1.fastq.gz S879Nr25.2.fastq.gz,fastq fastq,10120435126.0,50403985.0,ena RUN TAB 05 08 2022 14:25:08:835 19179,0:100.39 1:100.39,A:2679131890;C:2420708190;G:2483153503;T:2537307238;N:134305,100,100,,,2679131890,2420708190,2483153503,2537307238,134305,ERX9574476,ERS12562187,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.96973,0.97106,0.04979,0.04949,0.71252,0.71654,0.4806,0.49338,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Undetermined,Undetermined,Trunk,Surface Structure
11149,ERR10034071,ERX9574475,ERS12562186,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Metamorphic tissue without xxx from Danio rerio,Drerio metamorphic 4,SAMEA110464158,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464158|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE24|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE24|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19176,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr24.1.fastq.gz S879Nr24.2.fastq.gz,fastq fastq,7845661906.0,39121993.0,ena RUN TAB 05 08 2022 14:25:08:835 19177,0:100.27 1:100.27,A:2096079479;C:1862247618;G:1929220494;T:1958006859;N:107456,100,100,,,2096079479,1862247618,1929220494,1958006859,107456,ERX9574475,ERS12562186,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.96989,0.96986,0.04901,0.04902,0.71599,0.72301,0.48965,0.48827,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Undetermined,Undetermined,Trunk,Surface Structure
11150,ERR10034070,ERX9574474,ERS12562185,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Metamorphic tissue without xxx from Danio rerio,Drerio metamorphic 3,SAMEA110464157,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464157|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE23|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE23|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19174,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr23.1.fastq.gz S879Nr23.2.fastq.gz,fastq fastq,8270390422.0,41338131.0,ena RUN TAB 05 08 2022 14:25:08:835 19175,0:100.03 1:100.03,A:2156060704;C:1998612686;G:2055201244;T:2060404840;N:110948,100,100,,,2156060704,1998612686,2055201244,2060404840,110948,ERX9574474,ERS12562185,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.97085,0.97083,0.04232,0.04236,0.7219,0.72671,0.47325,0.4807,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Undetermined,Undetermined,Trunk,Surface Structure
11151,ERR10034069,ERX9574473,ERS12562184,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Metamorphic tissue without xxx from Danio rerio,Drerio metamorphic 2,SAMEA110464156,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464156|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE22|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE22|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:834 19172,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr22.1.fastq.gz S879Nr22.2.fastq.gz,fastq fastq,10977356920.0,54380062.0,ena RUN TAB 05 08 2022 14:25:08:834 19173,0:100.93 1:100.93,A:2852856166;C:2671616791;G:2798184312;T:2654546853;N:152798,100,100,,,2852856166,2671616791,2798184312,2654546853,152798,ERX9574473,ERS12562184,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.9765,0.97629,0.03531,0.03529,0.72025,0.72705,0.47808,0.46326,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Undetermined,Undetermined,Trunk,Surface Structure
11152,ERR10034068,ERX9574472,ERS12562183,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Metamorphic tissue without xxx from Danio rerio,Drerio metamorphic 1,SAMEA110464155,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464155|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE21|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE21|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:834 19170,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr21.1.fastq.gz S879Nr21.2.fastq.gz,fastq fastq,11346084502.0,56210802.0,ena RUN TAB 05 08 2022 14:25:08:834 19171,0:100.92 1:100.92,A:2950787998;C:2755514202;G:2902131288;T:2737495846;N:155168,100,100,,,2950787998,2755514202,2902131288,2737495846,155168,ERX9574472,ERS12562183,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.9732,0.97208,0.02959,0.02983,0.72322,0.73135,0.47796,0.47326,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Undetermined,Undetermined,Trunk,Surface Structure
24906,SRR25532497,SRX21261798,SRS18515093,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,control1,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.42 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S10,S10,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,CK1_1.fq.gz CK1_2.fq.gz,fastq fastq,6650697900.0,22168993.0,CK1 1.fq.gz,0:150 1:150,A:1918460669;C:1420936092;G:1412569553;T:1898656995;N:74591,150,150,,,1918460669,1420936092,1412569553,1898656995,74591,SRX21261798,SRS18515093,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.91765,0.91694,0.15569,0.15461,0.70185,0.7027,0.47761,0.47369,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24907,SRR25532498,SRX21261797,SRS18515092,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTH3,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.41 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S9,S9,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTH3_2.fq.gz MBTH3_1.fq.gz,fastq fastq,6333332100.0,21111107.0,MBTH3 1.fq.gz,0:150 1:150,A:1755718187;C:1429192980;G:1420776066;T:1727550080;N:94787,150,150,,,1755718187,1429192980,1420776066,1727550080,94787,SRX21261797,SRS18515092,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.93518,0.93355,0.11668,0.11602,0.67799,0.67817,0.47705,0.47875,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24908,SRR25532499,SRX21261796,SRS18515091,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTH2,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.40 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S8,S8,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTH2_1.fq.gz MBTH2_2.fq.gz,fastq fastq,6373733400.0,21245778.0,MBTH2 1.fq.gz,0:150 1:150,A:1775132718;C:1430955007;G:1424605018;T:1742942742;N:97915,150,150,,,1775132718,1430955007,1424605018,1742942742,97915,SRX21261796,SRS18515091,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.93081,0.93016,0.12061,0.11947,0.68215,0.68172,0.47956,0.48186,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24909,SRR25532500,SRX21261795,SRS18515090,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTH1,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.39 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S7,S7,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTH1_1.fq.gz MBTH1_2.fq.gz,fastq fastq,6224052600.0,20746842.0,MBTH1 1.fq.gz,0:150 1:150,A:1753175301;C:1379045823;G:1371537072;T:1720226102;N:68302,150,150,,,1753175301,1379045823,1371537072,1720226102,68302,SRX21261795,SRS18515090,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.9276,0.92379,0.13642,0.13482,0.68416,0.68479,0.47638,0.47581,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24910,SRR25532501,SRX21261794,SRS18515089,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTM3,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.38 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S6,S6,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTM3_2.fq.gz MBTM3_1.fq.gz,fastq fastq,6885667800.0,22952226.0,MBTM3 1.fq.gz,0:150 1:150,A:1936367424;C:1526831248;G:1520656271;T:1901736749;N:76108,150,150,,,1936367424,1526831248,1520656271,1901736749,76108,SRX21261794,SRS18515089,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92736,0.92516,0.12801,0.12693,0.68982,0.69063,0.47163,0.4612,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24911,SRR25532502,SRX21261793,SRS18515088,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTM2,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.37 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S5,S5,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTM2_1.fq.gz MBTM2_2.fq.gz,fastq fastq,6529427400.0,21764758.0,MBTM2 1.fq.gz,0:150 1:150,A:1808908277;C:1472638598;G:1467975655;T:1779801002;N:103868,150,150,,,1808908277,1472638598,1467975655,1779801002,103868,SRX21261793,SRS18515088,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.9296,0.93217,0.11772,0.11735,0.68262,0.68331,0.4724,0.4721,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24912,SRR25532503,SRX21261792,SRS18515087,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTM1,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.36 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S4,S4,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTM1_2.fq.gz MBTM1_1.fq.gz,fastq fastq,6733924800.0,22446416.0,MBTM1 1.fq.gz,0:150 1:150,A:1847490053;C:1535661831;G:1528806965;T:1821868439;N:97512,150,150,,,1847490053,1535661831,1528806965,1821868439,97512,SRX21261792,SRS18515087,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.93177,0.93448,0.11165,0.11192,0.67722,0.67823,0.47325,0.46912,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24913,SRR25532504,SRX21261791,SRS18515086,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTL3,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.35 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S3,S3,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTL3_1.fq.gz MBTL3_2.fq.gz,fastq fastq,9066238500.0,30220795.0,MBTL3 1.fq.gz,0:150 1:150,A:2629692873;C:1932648084;G:1927694770;T:2576111685;N:91088,150,150,,,2629692873,1932648084,1927694770,2576111685,91088,SRX21261791,SRS18515086,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.93079,0.91809,0.1476,0.14446,0.69201,0.69258,0.47663,0.47687,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24914,SRR25532505,SRX21261790,SRS18515085,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,control3,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.44 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S12,S12,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,CK3_1.fq.gz CK3_2.fq.gz,fastq fastq,6596041200.0,21986804.0,CK3 1.fq.gz,0:150 1:150,A:1886076947;C:1431757712;G:1423068767;T:1855067482;N:70292,150,150,,,1886076947,1431757712,1423068767,1855067482,70292,SRX21261790,SRS18515085,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92168,0.92147,0.14797,0.14768,0.68962,0.68935,0.47874,0.48307,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24915,SRR25532506,SRX21261789,SRS18515084,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,control2,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.43 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S11,S11,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,CK2_1.fq.gz CK2_2.fq.gz,fastq fastq,6749651400.0,22498838.0,CK2 1.fq.gz,0:150 1:150,A:1934306700;C:1451979582;G:1445551014;T:1917740723;N:73381,150,150,,,1934306700,1451979582,1445551014,1917740723,73381,SRX21261789,SRS18515084,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92261,0.92062,0.15096,0.14969,0.69783,0.69702,0.48303,0.49016,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24916,SRR25532507,SRX21261788,SRS18515083,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTL2,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.34 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S2,S2,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTL2_1.fq.gz MBTL2_2.fq.gz,fastq fastq,6868354800.0,22894516.0,MBTL2 1.fq.gz,0:150 1:150,A:1956017484;C:1493585329;G:1486220640;T:1932456728;N:74619,150,150,,,1956017484,1493585329,1486220640,1932456728,74619,SRX21261788,SRS18515083,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92126,0.91908,0.14701,0.14525,0.69394,0.69363,0.47281,0.47636,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24917,SRR25532508,SRX21261787,SRS18515082,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTL1,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.33 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S1,S1,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTL1_1.fq.gz MBTL1_2.fq.gz,fastq fastq,6305127900.0,21017093.0,MBTL1 1.fq.gz,0:150 1:150,A:1797030982;C:1364002775;G:1357954929;T:1786051425;N:87789,150,150,,,1797030982,1364002775,1357954929,1786051425,87789,SRX21261787,SRS18515082,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92195,0.92138,0.14404,0.1433,0.69656,0.69623,0.47185,0.46936,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
30702,SRR28328136,SRX23936571,SRS20740255,SRP494948,PRJNA1086823,Danio rerio Raw sequence reads,PRJNA1086823,Whole Genome Sequencing,Study the effects on the body when this gene is lost,,,Study the effects on the body when this gene is lost,Model organism or animal sample from Danio rerio,tu ,,strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:missing|BioSampleModel:Model organism or animal,,,,,,,,,SampleF,6,6,control,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,HiSeq X Ten,,SRP494948,,,tu_3.R1.raw.fastq.gz tu_3.R2.raw.fastq.gz,fastq fastq,6836795894.0,22638397.0,tu 3.R1.raw.fastq.gz,0:151 1:151,A:1911756035;C:1496221872;G:1563235044;T:1865509810;N:73133,151,151,,,1911756035,1496221872,1563235044,1865509810,73133,SRX23936571,SRS20740255,SRA1823374,Hunan Normal University|Hunan Normal University,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-13,Undetermined,Undetermined,Trunk,Surface Structure
30703,SRR28328137,SRX23936570,SRS20740255,SRP494948,PRJNA1086823,Danio rerio Raw sequence reads,PRJNA1086823,Whole Genome Sequencing,Study the effects on the body when this gene is lost,,,Study the effects on the body when this gene is lost,Model organism or animal sample from Danio rerio,tu ,,strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:missing|BioSampleModel:Model organism or animal,,,,,,,,,SampleE,5,5,control,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,HiSeq X Ten,,SRP494948,,,tu_2.R1.raw.fastq.gz tu_2.R2.raw.fastq.gz,fastq fastq,6933313282.0,22957991.0,tu 2.R1.raw.fastq.gz,0:151 1:151,A:1895897966;C:1562896362;G:1633152399;T:1841286721;N:79834,151,151,,,1895897966,1562896362,1633152399,1841286721,79834,SRX23936570,SRS20740255,SRA1823374,Hunan Normal University|Hunan Normal University,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-13,Undetermined,Undetermined,Trunk,Surface Structure
30704,SRR28328138,SRX23936569,SRS20740255,SRP494948,PRJNA1086823,Danio rerio Raw sequence reads,PRJNA1086823,Whole Genome Sequencing,Study the effects on the body when this gene is lost,,,Study the effects on the body when this gene is lost,Model organism or animal sample from Danio rerio,tu ,,strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:missing|BioSampleModel:Model organism or animal,,,,,,,,,SampleD,4,4,control,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,HiSeq X Ten,,SRP494948,,,tu_1.R1.raw.fastq.gz tu_1.R2.raw.fastq.gz,fastq fastq,6953463930.0,23024715.0,tu 1.R1.raw.fastq.gz,0:151 1:151,A:1914281996;C:1558685345;G:1630355775;T:1850061551;N:79263,151,151,,,1914281996,1558685345,1630355775,1850061551,79263,SRX23936569,SRS20740255,SRA1823374,Hunan Normal University|Hunan Normal University,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-13,Undetermined,Undetermined,Trunk,Surface Structure
30705,SRR28328139,SRX23936568,SRS20740254,SRP494948,PRJNA1086823,Danio rerio Raw sequence reads,PRJNA1086823,Whole Genome Sequencing,Study the effects on the body when this gene is lost,,,Study the effects on the body when this gene is lost,Model organism or animal sample from Danio rerio,myo7aa,,strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,SampleC,3,3,treatment,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,HiSeq X Ten,,SRP494948,,,myo7aa_3.R1.raw.fastq.gz myo7aa_3.R2.raw.fastq.gz,fastq fastq,6793366180.0,22494590.0,myo7aa 3.R1.raw.fastq.gz,0:151 1:151,A:1786353133;C:1602317410;G:1674855786;T:1729822151;N:17700,151,151,,,1786353133,1602317410,1674855786,1729822151,17700,SRX23936568,SRS20740254,SRA1823374,Hunan Normal University|Hunan Normal University,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-13,Undetermined,Undetermined,Trunk,Surface Structure
30706,SRR28328140,SRX23936567,SRS20740254,SRP494948,PRJNA1086823,Danio rerio Raw sequence reads,PRJNA1086823,Whole Genome Sequencing,Study the effects on the body when this gene is lost,,,Study the effects on the body when this gene is lost,Model organism or animal sample from Danio rerio,myo7aa,,strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,SampleB,2,2,treatment,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,HiSeq X Ten,,SRP494948,,,myo7aa_2.R1.raw.fastq.gz myo7aa_2.R2.raw.fastq.gz,fastq fastq,6762797438.0,22393369.0,myo7aa 2.R1.raw.fastq.gz,0:151 1:151,A:1816704062;C:1557768239;G:1627373716;T:1760926609;N:24812,151,151,,,1816704062,1557768239,1627373716,1760926609,24812,SRX23936567,SRS20740254,SRA1823374,Hunan Normal University|Hunan Normal University,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-13,Undetermined,Undetermined,Trunk,Surface Structure
30707,SRR28328141,SRX23936566,SRS20740254,SRP494948,PRJNA1086823,Danio rerio Raw sequence reads,PRJNA1086823,Whole Genome Sequencing,Study the effects on the body when this gene is lost,,,Study the effects on the body when this gene is lost,Model organism or animal sample from Danio rerio,myo7aa,,strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,SampleA,1,1,treatment,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,HiSeq X Ten,,SRP494948,,,myo7aa_1.R1.raw.fastq.gz myo7aa_1.R2.raw.fastq.gz,fastq fastq,6605710628.0,21873214.0,myo7aa 1.R1.raw.fastq.gz,0:151 1:151,A:1728796843;C:1565920605;G:1629477870;T:1681497978;N:17332,151,151,,,1728796843,1565920605,1629477870,1681497978,17332,SRX23936566,SRS20740254,SRA1823374,Hunan Normal University|Hunan Normal University,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-13,Undetermined,Undetermined,Trunk,Surface Structure
34053,SRR31034578,SRX26420033,SRS22939666,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,eif5a1/2 morpholino 3,GSM8579963,,source name:whole body|tissue:whole body|treatment:eif5a1/2 morpholino|geo loc name:missing|collection date:missing,eif5a1/2 morpholino 3,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:eif5a1/2 morpholino,GSM8579963,GSM8579963: eif5a1/2 morpholino 3; Danio rerio; RNA Seq,GSM8579963 r1,GSM8579963,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,eIF5AMO3_1.fq.gz eIF5AMO3_2.fq.gz,fastq fastq,6591810600.0,21972702.0,GSM8579963 r1,0:150 1:150,A:1735827111;C:1561621052;G:1576813159;T:1717549278;N:0,150,150,,,1735827111,1561621052,1576813159,1717549278,0,SRX26420033,SRS22939666,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34054,SRR31034579,SRX26420032,SRS22939665,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,eif5a1/2 morpholino 2,GSM8579962,,source name:whole body|tissue:whole body|treatment:eif5a1/2 morpholino|geo loc name:missing|collection date:missing,eif5a1/2 morpholino 2,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:eif5a1/2 morpholino,GSM8579962,GSM8579962: eif5a1/2 morpholino 2; Danio rerio; RNA Seq,GSM8579962 r1,GSM8579962,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,eIF5AMO2_1.fq.gz eIF5AMO2_2.fq.gz,fastq fastq,6615856500.0,22052855.0,GSM8579962 r1,0:150 1:150,A:1712890711;C:1594159797;G:1606364019;T:1702441973;N:0,150,150,,,1712890711,1594159797,1606364019,1702441973,0,SRX26420032,SRS22939665,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34055,SRR31034580,SRX26420031,SRS22939663,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,eif5a1/2 morpholino 1,GSM8579961,,source name:whole body|tissue:whole body|treatment:eif5a1/2 morpholino|geo loc name:missing|collection date:missing,eif5a1/2 morpholino 1,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:eif5a1/2 morpholino,GSM8579961,GSM8579961: eif5a1/2 morpholino 1; Danio rerio; RNA Seq,GSM8579961 r1,GSM8579961,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,eIF5AMO1_1.fq.gz eIF5AMO1_2.fq.gz,fastq fastq,6172597200.0,20575324.0,GSM8579961 r1,0:150 1:150,A:1612632964;C:1473173555;G:1490511736;T:1596278945;N:0,150,150,,,1612632964,1473173555,1490511736,1596278945,0,SRX26420031,SRS22939663,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34056,SRR31034581,SRX26420030,SRS22939664,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,dhps morpholino 3,GSM8579960,,source name:whole body|tissue:whole body|treatment:dhps morpholino|geo loc name:missing|collection date:missing,dhps morpholino 3,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:dhps morpholino,GSM8579960,GSM8579960: dhps morpholino 3; Danio rerio; RNA Seq,GSM8579960 r1,GSM8579960,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,DHPSMO3_1.fq.gz DHPSMO3_2.fq.gz,fastq fastq,6620802600.0,22069342.0,GSM8579960 r1,0:150 1:150,A:1736599369;C:1572800715;G:1587922794;T:1723479722;N:0,150,150,,,1736599369,1572800715,1587922794,1723479722,0,SRX26420030,SRS22939664,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34057,SRR31034582,SRX26420029,SRS22939659,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,dhps morpholino 2,GSM8579959,,source name:whole body|tissue:whole body|treatment:dhps morpholino|geo loc name:missing|collection date:missing,dhps morpholino 2,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:dhps morpholino,GSM8579959,GSM8579959: dhps morpholino 2; Danio rerio; RNA Seq,GSM8579959 r1,GSM8579959,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,DHPSMO2_1.fq.gz DHPSMO2_2.fq.gz,fastq fastq,6582483600.0,21941612.0,GSM8579959 r1,0:150 1:150,A:1720509810;C:1570278366;G:1585433293;T:1706262131;N:0,150,150,,,1720509810,1570278366,1585433293,1706262131,0,SRX26420029,SRS22939659,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34058,SRR31034583,SRX26420028,SRS22939662,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,dhps morpholino 1,GSM8579958,,source name:whole body|tissue:whole body|treatment:dhps morpholino|geo loc name:missing|collection date:missing,dhps morpholino 1,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:dhps morpholino,GSM8579958,GSM8579958: dhps morpholino 1; Danio rerio; RNA Seq,GSM8579958 r1,GSM8579958,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,DHPSMO1_1.fq.gz DHPSMO1_2.fq.gz,fastq fastq,6596391000.0,21987970.0,GSM8579958 r1,0:150 1:150,A:1725362753;C:1572510096;G:1586851982;T:1711666169;N:0,150,150,,,1725362753,1572510096,1586851982,1711666169,0,SRX26420028,SRS22939662,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34059,SRR31034584,SRX26420027,SRS22939661,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,Control morpholino 3,GSM8579957,,source name:whole body|tissue:whole body|treatment:Control morpholino|geo loc name:missing|collection date:missing,Control morpholino 3,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:Control morpholino,GSM8579957,GSM8579957: Control morpholino 3; Danio rerio; RNA Seq,GSM8579957 r1,GSM8579957,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,CtrlMO3_1.fq.gz CtrlMO3_2.fq.gz,fastq fastq,6625089300.0,22083631.0,GSM8579957 r1,0:150 1:150,A:1728439807;C:1584339137;G:1602988513;T:1709321843;N:0,150,150,,,1728439807,1584339137,1602988513,1709321843,0,SRX26420027,SRS22939661,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34060,SRR31034585,SRX26420026,SRS22939658,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,Control morpholino 2,GSM8579956,,source name:whole body|tissue:whole body|treatment:Control morpholino|geo loc name:missing|collection date:missing,Control morpholino 2,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:Control morpholino,GSM8579956,GSM8579956: Control morpholino 2; Danio rerio; RNA Seq,GSM8579956 r1,GSM8579956,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,CtrlMO2_1.fq.gz CtrlMO2_2.fq.gz,fastq fastq,6823000500.0,22743335.0,GSM8579956 r1,0:150 1:150,A:1777305843;C:1633379395;G:1649025317;T:1763289945;N:0,150,150,,,1777305843,1633379395,1649025317,1763289945,0,SRX26420026,SRS22939658,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34061,SRR31034586,SRX26420025,SRS22939660,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,Control morpholino 1,GSM8579955,,source name:whole body|tissue:whole body|treatment:Control morpholino|geo loc name:missing|collection date:missing,Control morpholino 1,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:Control morpholino,GSM8579955,GSM8579955: Control morpholino 1; Danio rerio; RNA Seq,GSM8579955 r1,GSM8579955,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,CtrlMO1_1.fq.gz CtrlMO1_2.fq.gz,fastq fastq,6625797900.0,22085993.0,GSM8579955 r1,0:150 1:150,A:1738695154;C:1575541452;G:1592240618;T:1719320676;N:0,150,150,,,1738695154,1575541452,1592240618,1719320676,0,SRX26420025,SRS22939660,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34153,SRR31377592,SRX26751157,SRS23239770,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,CCSER1 S Body R6,GSM8637009,,source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing,CCSER1 S Body R6,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:CCSER1 S48Y*,GSM8637009,GSM8637009: CCSER1 S Body R6; Danio rerio; RNA Seq,GSM8637009 r1,GSM8637009,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW041_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW041_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,3891217754.0,12884827.0,GSM8637009 r1,0:151 1:151,A:1016852836;C:927774615;G:947465133;T:998741423;N:383747,151,151,,,1016852836,927774615,947465133,998741423,383747,SRX26751157,SRS23239770,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34154,SRR31377593,SRX26751156,SRS23239769,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,CCSER1 S Body R5,GSM8637008,,source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing,CCSER1 S Body R5,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:CCSER1 S48Y*,GSM8637008,GSM8637008: CCSER1 S Body R5; Danio rerio; RNA Seq,GSM8637008 r1,GSM8637008,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW040_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW040_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,3646264950.0,12073725.0,GSM8637008 r1,0:151 1:151,A:939260848;C:884661915;G:900614466;T:921376437;N:351284,151,151,,,939260848,884661915,900614466,921376437,351284,SRX26751156,SRS23239769,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34155,SRR31377594,SRX26751155,SRS23239768,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,CCSER1 S Body R4,GSM8637007,,source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing,CCSER1 S Body R4,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:CCSER1 S48Y*,GSM8637007,GSM8637007: CCSER1 S Body R4; Danio rerio; RNA Seq,GSM8637007 r1,GSM8637007,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW039_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW039_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,4173716406.0,13820253.0,GSM8637007 r1,0:151 1:151,A:1101647100;C:985852757;G:1008447663;T:1077356024;N:412862,151,151,,,1101647100,985852757,1008447663,1077356024,412862,SRX26751155,SRS23239768,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34156,SRR31377595,SRX26751154,SRS23239766,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,CCSER1 S Body R3,GSM8637006,,source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing,CCSER1 S Body R3,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:CCSER1 S48Y*,GSM8637006,GSM8637006: CCSER1 S Body R3; Danio rerio; RNA Seq,GSM8637006 r1,GSM8637006,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW038_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW038_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,4042195708.0,13384754.0,GSM8637006 r1,0:151 1:151,A:1060347597;C:961319252;G:982742171;T:1037395227;N:391461,151,151,,,1060347597,961319252,982742171,1037395227,391461,SRX26751154,SRS23239766,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34157,SRR31377596,SRX26751153,SRS23239767,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,CCSER1 S Body R2,GSM8637005,,source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing,CCSER1 S Body R2,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:CCSER1 S48Y*,GSM8637005,GSM8637005: CCSER1 S Body R2; Danio rerio; RNA Seq,GSM8637005 r1,GSM8637005,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW037_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW037_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,4273642468.0,14151134.0,GSM8637005 r1,0:151 1:151,A:1128762921;C:1007923026;G:1029470831;T:1107066433;N:419257,151,151,,,1128762921,1007923026,1029470831,1107066433,419257,SRX26751153,SRS23239767,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34158,SRR31377597,SRX26751152,SRS23239764,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,CCSER1 S Body R1,GSM8637004,,source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing,CCSER1 S Body R1,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:CCSER1 S48Y*,GSM8637004,GSM8637004: CCSER1 S Body R1; Danio rerio; RNA Seq,GSM8637004 r1,GSM8637004,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW036_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW036_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,3653975010.0,12099255.0,GSM8637004 r1,0:151 1:151,A:955600414;C:873541559;G:890489547;T:933988860;N:354630,151,151,,,955600414,873541559,890489547,933988860,354630,SRX26751152,SRS23239764,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34159,SRR31377598,SRX26751151,SRS23239765,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,CCSER1 M Body R6,GSM8637003,,source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing,CCSER1 M Body R6,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:CCSER1 P471,GSM8637003,GSM8637003: CCSER1 M Body R6; Danio rerio; RNA Seq,GSM8637003 r1,GSM8637003,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW035_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW035_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,4080528266.0,13511683.0,GSM8637003 r1,0:151 1:151,A:1061173416;C:977476934;G:997386836;T:1044093823;N:397257,151,151,,,1061173416,977476934,997386836,1044093823,397257,SRX26751151,SRS23239765,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34160,SRR31377599,SRX26751150,SRS23239762,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,CCSER1 M Body R5,GSM8637002,,source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing,CCSER1 M Body R5,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:CCSER1 P471,GSM8637002,GSM8637002: CCSER1 M Body R5; Danio rerio; RNA Seq,GSM8637002 r1,GSM8637002,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW034_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW034_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,4337490402.0,14362551.0,GSM8637002 r1,0:151 1:151,A:1123121935;C:1047421198;G:1062576487;T:1103949606;N:421176,151,151,,,1123121935,1047421198,1062576487,1103949606,421176,SRX26751150,SRS23239762,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34161,SRR31377600,SRX26751149,SRS23239760,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,CCSER1 M Body R4,GSM8637001,,source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing,CCSER1 M Body R4,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:CCSER1 P471,GSM8637001,GSM8637001: CCSER1 M Body R4; Danio rerio; RNA Seq,GSM8637001 r1,GSM8637001,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW033_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW033_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,3844091862.0,12728781.0,GSM8637001 r1,0:151 1:151,A:991817790;C:930869770;G:945916630;T:975114794;N:372878,151,151,,,991817790,930869770,945916630,975114794,372878,SRX26751149,SRS23239760,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34162,SRR31377601,SRX26751148,SRS23239763,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,CCSER1 M Body R3,GSM8637000,,source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing,CCSER1 M Body R3,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:CCSER1 P471,GSM8637000,GSM8637000: CCSER1 M Body R3; Danio rerio; RNA Seq,GSM8637000 r1,GSM8637000,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW032_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW032_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,3561535830.0,11793165.0,GSM8637000 r1,0:151 1:151,A:925501870;C:854996726;G:868955460;T:911732180;N:349594,151,151,,,925501870,854996726,868955460,911732180,349594,SRX26751148,SRS23239763,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34163,SRR31377602,SRX26751147,SRS23239761,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,CCSER1 M Body R2,GSM8636999,,source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing,CCSER1 M Body R2,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:CCSER1 P471,GSM8636999,GSM8636999: CCSER1 M Body R2; Danio rerio; RNA Seq,GSM8636999 r1,GSM8636999,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW031_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW031_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,4010996088.0,13281444.0,GSM8636999 r1,0:151 1:151,A:1041141909;C:965136690;G:981220550;T:1023106736;N:390203,151,151,,,1041141909,965136690,981220550,1023106736,390203,SRX26751147,SRS23239761,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34164,SRR31377603,SRX26751146,SRS23239759,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,CCSER1 M Body R1,GSM8636998,,source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing,CCSER1 M Body R1,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:CCSER1 P471,GSM8636998,GSM8636998: CCSER1 M Body R1; Danio rerio; RNA Seq,GSM8636998 r1,GSM8636998,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW030_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW030_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,3897705620.0,12906310.0,GSM8636998 r1,0:151 1:151,A:1018200154;C:931829100;G:950742174;T:996554508;N:379684,151,151,,,1018200154,931829100,950742174,996554508,379684,SRX26751146,SRS23239759,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34165,SRR31377604,SRX26751145,SRS23239758,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,WT Body R6,GSM8636997,,source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing,WT Body R6,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:WT,GSM8636997,GSM8636997: WT Body R6; Danio rerio; RNA Seq,GSM8636997 r1,GSM8636997,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW029_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW029_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,3865866666.0,12800883.0,GSM8636997 r1,0:151 1:151,A:1011251980;C:922495324;G:940649850;T:991092479;N:377033,151,151,,,1011251980,922495324,940649850,991092479,377033,SRX26751145,SRS23239758,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34166,SRR31377605,SRX26751144,SRS23239756,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,WT Body R5,GSM8636996,,source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing,WT Body R5,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:WT,GSM8636996,GSM8636996: WT Body R5; Danio rerio; RNA Seq,GSM8636996 r1,GSM8636996,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW028_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW028_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,4063620192.0,13455696.0,GSM8636996 r1,0:151 1:151,A:1059319911;C:972296744;G:990411694;T:1041199642;N:392201,151,151,,,1059319911,972296744,990411694,1041199642,392201,SRX26751144,SRS23239756,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34167,SRR31377606,SRX26751143,SRS23239757,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,WT Body R4,GSM8636995,,source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing,WT Body R4,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:WT,GSM8636995,GSM8636995: WT Body R4; Danio rerio; RNA Seq,GSM8636995 r1,GSM8636995,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW027_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW027_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,3813832368.0,12628584.0,GSM8636995 r1,0:151 1:151,A:1000392936;C:909932334;G:925952997;T:977190341;N:363760,151,151,,,1000392936,909932334,925952997,977190341,363760,SRX26751143,SRS23239757,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34168,SRR31377607,SRX26751142,SRS23239754,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,WT Body R3,GSM8636994,,source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing,WT Body R3,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:WT,GSM8636994,GSM8636994: WT Body R3; Danio rerio; RNA Seq,GSM8636994 r1,GSM8636994,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW026_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW026_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,4006681716.0,13267158.0,GSM8636994 r1,0:151 1:151,A:1048048089;C:954759070;G:972606862;T:1030876175;N:391520,151,151,,,1048048089,954759070,972606862,1030876175,391520,SRX26751142,SRS23239754,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34169,SRR31377608,SRX26751141,SRS23239755,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,WT Body R2,GSM8636993,,source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing,WT Body R2,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:WT,GSM8636993,GSM8636993: WT Body R2; Danio rerio; RNA Seq,GSM8636993 r1,GSM8636993,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW025_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW025_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,4208402314.0,13935107.0,GSM8636993 r1,0:151 1:151,A:1096841306;C:1009718849;G:1025250660;T:1076184256;N:407243,151,151,,,1096841306,1009718849,1025250660,1076184256,407243,SRX26751141,SRS23239755,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
34170,SRR31377609,SRX26751140,SRS23239752,SRP545865,PRJNA1187491,CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.,GSE282155,Transcriptome Analysis,CCSER1  a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways  including calcium signaling and neuroactive ligand receptor interaction  in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior  as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases  such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1   CCSER1 P471 or CCSER1 M  and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains  homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,,,WT Body R1,GSM8636992,,source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing,WT Body R1,Raw reads were first processed by Novogene AIT to remove adapter  poly N sequences  and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software  v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner  default parameters  and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned,whole body,,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,tissue:whole body|genotype:WT,GSM8636992,GSM8636992: WT Body R1; Danio rerio; RNA Seq,GSM8636992 r1,GSM8636992,1,The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP545865,,,RZW024_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW024_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz,fastq fastq,4407394644.0,14594022.0,GSM8636992 r1,0:151 1:151,A:1153185021;C:1053968670;G:1069220613;T:1130594464;N:425876,151,151,,,1153185021,1053968670,1069220613,1130594464,425876,SRX26751140,SRS23239752,SRA2016812,"ASM Lab, Physiology, NUS","ASM Lab, Physiology, NUS",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2024-11-18,Undetermined,Adult,Trunk,Surface Structure
36272,SRR298567,SRX079845,SRS212651,SRP007331,PRJNA141525,Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.,GSE29418,Transcriptome Analysis,RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.,,pubmed:21743441,,ZiliIPTes,GSM727524,,tissue:RNA obtained from immunoprecipitation with Zili antibody|strain:TL,ZiliIPTes,three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.,RNA obtained from immunoprecipitation with Zili antibody,,Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen  3 or 6 testes  and Zili antibody in a total volume of 500 µl.  RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis  adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.,,strain:TL,GSM727524,GSM727524: ZiliIPTes,GSM727524: ZiliIPTes,GSM727524: ZiliIPTes,1,,GEO Accession:GSM727524,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>,SRP007331,,read name barcode proc directive:ignore,ZiliIPTes.fastq,fastq,995759064.0,27659974.0,GSM727524 1,0:36,,36,,,,,,,,,SRX079845,SRS212651,SRA039167,GEO,"European Research Institute for the Biology of Ageing, University Medical Center Groningen",1,0.0537,,0.03117,,0.95856,,0.42091,,36,,B,,usable mapping rate,illumina,early_illumina,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Netherlands,2011-05-20,Undetermined,Undetermined,Trunk,Surface Structure
40162,SRR2937381,SRX1440089,SRS1170438,SRP066406,PRJNA302080,Danio rerio Raw sequence reads,PRJNA302080,Whole Genome Sequencing,The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon,,,,,T,,strain:AB strain|age:0|dev stage:embryo|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon,T,T,cDNA/Total RNA was extracted from 50 homogenized zebrafish embryos treated with and without xxx  respectively  by using Trizol regent Invitrogen  USA according to the manufacturer’s instruction and treated with RNase free DNase I Takara Biotechnology  China. RNA integrity was confirmed with a minimum RNA integrated number value of 8 by the 2100 bio analyzer Agilent. PolyA mRNA was enriched with oligo dT beads and then was fragmented. The cleaved RNA fragments were transcribed into first strand cDNA using reverse transcriptase and random hexamer primers  which was followed by second  strand cDNA synthesis. The double stranded cDNA was further subjected to end repair  phosphorylation  3’ adenylation and adaptor ligation in sequence. Adaptor ligated fragments were selected according to the size 250 to 350 bp  and the desired range of cDNA fragments were excised from the gel. The fragments were enriched by PCR amplification. The quality and quantity of the two libraries one library was treated with TDF but the other one did not were determined g on an Agilent 2100 Bioanalyzer and ABI StepOnePlus Real Time PCR System. Subsequently  the cDNA library was sequenced on a flow cell using Illumina HiSeq2000.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>,SRP066406,,,T.fq.gz,fastq,587807332.0,11996068.0,T,0:49,A:146199755;C:143635765;G:149348442;T:148593898;N:29472,49,,,,146199755,143635765,149348442,148593898,29472,SRX1440089,SRS1170438,SRA312474,National Central University|Chen-Ssu-Ching lab,National Central University,1,0.95023,,0.02672,,0.77889,,0.46839,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Taiwan,2016-11-20,Undetermined,Embryo,Trunk,Surface Structure
40163,SRR2924938,SRX1438257,SRS1168908,SRP066406,PRJNA302080,Danio rerio Raw sequence reads,PRJNA302080,Whole Genome Sequencing,The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon,,,,,D,,strain:AB strain|age:0|dev stage:embryo|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon,D,D,cDNA/Total RNA was extracted from 50 homogenized zebrafish embryos treated with and without xxx  respectively  by using Trizol regent Invitrogen  USA according to the manufacturer’s instruction and treated with RNase free DNase I Takara Biotechnology  China. RNA integrity was confirmed with a minimum RNA integrated number value of 8 by the 2100 bio analyzer Agilent. PolyA mRNA was enriched with oligo dT beads and then was fragmented. The cleaved RNA fragments were transcribed into first strand cDNA using reverse transcriptase and random hexamer primers  which was followed by second  strand cDNA synthesis. The double stranded cDNA was further subjected to end repair  phosphorylation  3’ adenylation and adaptor ligation in sequence. Adaptor ligated fragments were selected according to the size 250 to 350 bp  and the desired range of cDNA fragments were excised from the gel. The fragments were enriched by PCR amplification. The quality and quantity of the two libraries one library was treated with TDF but the other one did not were determined g on an Agilent 2100 Bioanalyzer and ABI StepOnePlus Real Time PCR System. Subsequently  the cDNA library was sequenced on a flow cell using Illumina HiSeq2000.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>,SRP066406,,,D.fq.gz,fastq,535039673.0,10919177.0,D,0:49,A:135797892;C:127799155;G:132966868;T:138440725;N:35033,49,,,,135797892,127799155,132966868,138440725,35033,SRX1438257,SRS1168908,SRA312306,National Central University|Chen-Ssu-Ching lab,National Central University,1,0.93993,,0.0586,,0.73391,,0.46855,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Taiwan,2016-11-19,Undetermined,Embryo,Trunk,Surface Structure
42197,SRR5485641,SRX2768777,SRS2152486,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,A 3.0.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,A 3.0.2,A 3.0.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_4.A_R1.fastq.gz HI.4096.008.Index_4.A_R1.fastq.gz,fastq fastq,2072387100.0,20723871.0,HI.4079.001.Index 4.A R1.fastq.gz,0:100 1:0,A:539231555;C:478779687;G:466992364;T:587014266;N:369228,100,0,,,539231555,478779687,466992364,587014266,369228,SRX2768777,SRS2152486,SRA557480,Brandon University|Biology,Brandon University,1,0.94094,,0.13282,,0.67566,,0.46135,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42198,SRR5485640,SRX2768776,SRS2152485,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,B 3.5.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,B 3.5.2,B 3.5.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_5.B_R1.fastq.gz HI.4096.008.Index_5.B_R1.fastq.gz,fastq fastq,2236492200.0,22364922.0,HI.4079.001.Index 5.B R1.fastq.gz,0:100 1:0,A:580646206;C:518191209;G:502712894;T:634542622;N:399269,100,0,,,580646206,518191209,502712894,634542622,399269,SRX2768776,SRS2152485,SRA557480,Brandon University|Biology,Brandon University,1,0.94188,,0.13073,,0.67653,,0.4635,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42199,SRR5485639,SRX2768775,SRS2152484,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,C 3.20.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,C 3.20.2,C 3.20.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_12.C_R1.fastq.gz HI.4096.008.Index_12.C_R1.fastq.gz,fastq fastq,1979628000.0,19796280.0,HI.4079.001.Index 12.C R1.fastq.gz,0:100 1:0,A:519406228;C:453563284;G:442115002;T:564195493;N:347993,100,0,,,519406228,453563284,442115002,564195493,347993,SRX2768775,SRS2152484,SRA557480,Brandon University|Biology,Brandon University,1,0.93946,,0.14364,,0.6759,,0.46247,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42200,SRR5485638,SRX2768774,SRS2152483,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,D 3.0.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,D 3.0.14,D 3.0.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_19.D_R1.fastq.gz HI.4096.008.Index_19.D_R1.fastq.gz,fastq fastq,1856095600.0,18560956.0,HI.4079.001.Index 19.D R1.fastq.gz,0:100 1:0,A:492424946;C:416504198;G:409645413;T:537196088;N:324955,100,0,,,492424946,416504198,409645413,537196088,324955,SRX2768774,SRS2152483,SRA557480,Brandon University|Biology,Brandon University,1,0.9288,,0.15497,,0.69232,,0.46842,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42201,SRR5485637,SRX2768773,SRS2152481,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,E 3.5.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,E 3.5.14,E 3.5.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4096.008.Index_1.E_R1.fastq.gz HI.4079.001.Index_1.E_R1.fastq.gz,fastq fastq,2936761500.0,29367615.0,HI.4079.001.Index 1.E R1.fastq.gz,0:100 1:0,A:762661816;C:675701333;G:661832769;T:836033713;N:531869,100,0,,,762661816,675701333,661832769,836033713,531869,SRX2768773,SRS2152481,SRA557480,Brandon University|Biology,Brandon University,1,0.93957,,0.12499,,0.67714,,0.4697,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2017-05-08,Undetermined,Multi-stage,Trunk,Surface Structure
42202,SRR5485636,SRX2768772,SRS2152480,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,F 3.20.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,F 3.20.14,F 3.20.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_3.F_R1.fastq.gz HI.4096.008.Index_3.F_R1.fastq.gz,fastq fastq,2169884500.0,21698845.0,HI.4079.001.Index 3.F R1.fastq.gz,0:100 1:0,A:566808272;C:496620769;G:487930959;T:618144722;N:379778,100,0,,,566808272,496620769,487930959,618144722,379778,SRX2768772,SRS2152480,SRA557480,Brandon University|Biology,Brandon University,1,0.93678,,0.13131,,0.67635,,0.47972,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42203,SRR5485635,SRX2768771,SRS2152482,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,G 4.0.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,G 4.0.2,G 4.0.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_9.G_R1.fastq.gz HI.4096.008.Index_9.G_R1.fastq.gz,fastq fastq,2008051800.0,20080518.0,HI.4079.001.Index 9.G R1.fastq.gz,0:100 1:0,A:518304309;C:466602325;G:455957803;T:566834696;N:352667,100,0,,,518304309,466602325,455957803,566834696,352667,SRX2768771,SRS2152482,SRA557480,Brandon University|Biology,Brandon University,1,0.94445,,0.12419,,0.68201,,0.46743,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42204,SRR5485634,SRX2768770,SRS2152479,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,H 4.5.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,H 4.5.2,H 4.5.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_8.H_R1.fastq.gz HI.4096.008.Index_8.H_R1.fastq.gz,fastq fastq,1908097900.0,19080979.0,HI.4079.001.Index 8.H R1.fastq.gz,0:100 1:0,A:494318032;C:441931870;G:431477592;T:540030651;N:339755,100,0,,,494318032,441931870,431477592,540030651,339755,SRX2768770,SRS2152479,SRA557480,Brandon University|Biology,Brandon University,1,0.94216,,0.1306,,0.68195,,0.45834,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42205,SRR5485633,SRX2768769,SRS2152477,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,I 4.20.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.20.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,I 4.20.2,I 4.20.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_10.I_R1.fastq.gz HI.4096.008.Index_10.I_R1.fastq.gz,fastq fastq,2059931100.0,20599311.0,HI.4079.001.Index 10.I R1.fastq.gz,0:100 1:0,A:536731862;C:475769707;G:462890515;T:584183211;N:355805,100,0,,,536731862,475769707,462890515,584183211,355805,SRX2768769,SRS2152477,SRA557480,Brandon University|Biology,Brandon University,1,0.93561,,0.13393,,0.68225,,0.46489,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42206,SRR5485632,SRX2768768,SRS2152478,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,J 4.0.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,J 4.0.14,J 4.0.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_11.J_R1.fastq.gz HI.4096.008.Index_11.J_R1.fastq.gz,fastq fastq,2199504800.0,21995048.0,HI.4079.001.Index 11.J R1.fastq.gz,0:100 1:0,A:579625731;C:499663817;G:489173373;T:630657278;N:384601,100,0,,,579625731,499663817,489173373,630657278,384601,SRX2768768,SRS2152478,SRA557480,Brandon University|Biology,Brandon University,1,0.93523,,0.13836,,0.68655,,0.47839,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42207,SRR5485631,SRX2768767,SRS2152475,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,K 4.5.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,K 4.5.14,K 4.5.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_20.K_R1.fastq.gz HI.4096.008.Index_20.K_R1.fastq.gz,fastq fastq,2154282200.0,21542822.0,HI.4079.001.Index 20.K R1.fastq.gz,0:100 1:0,A:563358732;C:494058898;G:482596638;T:613890813;N:377119,100,0,,,563358732,494058898,482596638,613890813,377119,SRX2768767,SRS2152475,SRA557480,Brandon University|Biology,Brandon University,1,0.93863,,0.12932,,0.67801,,0.46426,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42208,SRR5485630,SRX2768766,SRS2152476,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,L 4.20.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.20.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,L 4.20.14,L 4.20.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4096.008.Index_22.L_R1.fastq.gz HI.4079.001.Index_22.L_R1.fastq.gz,fastq fastq,2702515700.0,27025157.0,HI.4079.001.Index 22.L R1.fastq.gz,0:100 1:0,A:708045960;C:615042366;G:603133757;T:775807969;N:485648,100,0,,,708045960,615042366,603133757,775807969,485648,SRX2768766,SRS2152476,SRA557480,Brandon University|Biology,Brandon University,1,0.93316,,0.14421,,0.68915,,0.47027,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2017-05-08,Undetermined,Multi-stage,Trunk,Surface Structure
42209,SRR5485629,SRX2768765,SRS2152474,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,M 5.0.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,M 5.0.2,M 5.0.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_25.M_R1.fastq.gz HI.4096.008.Index_25.M_R1.fastq.gz,fastq fastq,1999183400.0,19991834.0,HI.4079.001.Index 25.M R1.fastq.gz,0:100 1:0,A:526344986;C:456726468;G:447467581;T:568292150;N:352215,100,0,,,526344986,456726468,447467581,568292150,352215,SRX2768765,SRS2152474,SRA557480,Brandon University|Biology,Brandon University,1,0.9374,,0.14185,,0.67665,,0.47249,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42210,SRR5485628,SRX2768764,SRS2152473,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,N 5.5.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,N 5.5.2,N 5.5.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_21.N_R1.fastq.gz HI.4096.008.Index_21.N_R1.fastq.gz,fastq fastq,2097386100.0,20973861.0,HI.4079.001.Index 21.N R1.fastq.gz,0:100 1:0,A:551586521;C:479609380;G:467572413;T:598246436;N:371350,100,0,,,551586521,479609380,467572413,598246436,371350,SRX2768764,SRS2152473,SRA557480,Brandon University|Biology,Brandon University,1,0.93984,,0.13949,,0.68219,,0.46921,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42211,SRR5485627,SRX2768763,SRS2152472,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,O 5.20.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,O 5.20.2,O 5.20.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_23.O_R1.fastq.gz HI.4096.008.Index_23.O_R1.fastq.gz,fastq fastq,2003835800.0,20038358.0,HI.4079.001.Index 23.O R1.fastq.gz,0:100 1:0,A:529075084;C:456810826;G:444441300;T:573155538;N:353052,100,0,,,529075084,456810826,444441300,573155538,353052,SRX2768763,SRS2152472,SRA557480,Brandon University|Biology,Brandon University,1,0.93635,,0.15287,,0.67712,,0.45807,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42212,SRR5485626,SRX2768762,SRS2152471,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,P 5.0.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,P 5.0.14,P 5.0.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_27.P_R1.fastq.gz HI.4096.008.Index_27.P_R1.fastq.gz,fastq fastq,1799355500.0,17993555.0,HI.4079.001.Index 27.P R1.fastq.gz,0:100 1:0,A:485156399;C:399414298;G:389730888;T:524733869;N:320046,100,0,,,485156399,399414298,389730888,524733869,320046,SRX2768762,SRS2152471,SRA557480,Brandon University|Biology,Brandon University,1,0.92813,,0.15749,,0.67943,,0.47424,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42213,SRR5485625,SRX2768761,SRS2152470,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,Q 5.5.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,Q 5.5.14,Q 5.5.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_2.Q_R1.fastq.gz HI.4096.008.Index_2.Q_R1.fastq.gz,fastq fastq,2260494100.0,22604941.0,HI.4079.001.Index 2.Q R1.fastq.gz,0:100 1:0,A:602519260;C:506296484;G:495685951;T:655587703;N:404702,100,0,,,602519260,506296484,495685951,655587703,404702,SRX2768761,SRS2152470,SRA557480,Brandon University|Biology,Brandon University,1,0.92524,,0.14979,,0.6859,,0.47957,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42214,SRR5485624,SRX2768760,SRS2152469,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,R 5.20.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,R 5.20.14,R 5.20.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_13.R_R1.fastq.gz HI.4096.008.Index_13.R_R1.fastq.gz,fastq fastq,1975297900.0,19752979.0,HI.4079.001.Index 13.R R1.fastq.gz,0:100 1:0,A:527732232;C:440160233;G:430962427;T:576091914;N:351094,100,0,,,527732232,440160233,430962427,576091914,351094,SRX2768760,SRS2152469,SRA557480,Brandon University|Biology,Brandon University,1,0.92785,,0.15864,,0.6814,,0.47773,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42215,SRR5485623,SRX2768759,SRS2152468,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,S 6.0.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:S 6.0.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,S 6.0.2,S 6.0.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_6.S_R1.fastq.gz HI.4096.008.Index_6.S_R1.fastq.gz,fastq fastq,2690628500.0,26906285.0,HI.4079.001.Index 6.S R1.fastq.gz,0:100 1:0,A:713021693;C:609779787;G:594591832;T:772745072;N:490116,100,0,,,713021693,609779787,594591832,772745072,490116,SRX2768759,SRS2152468,SRA557480,Brandon University|Biology,Brandon University,1,0.93405,,0.15472,,0.68505,,0.45796,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42216,SRR5485622,SRX2768758,SRS2152466,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,T 6.5.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,T 6.5.2,T 6.5.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_15.T_R1.fastq.gz HI.4096.008.Index_15.T_R1.fastq.gz,fastq fastq,1949043500.0,19490435.0,HI.4079.001.Index 15.T R1.fastq.gz,0:100 1:0,A:515794596;C:441198348;G:430323928;T:561379111;N:347517,100,0,,,515794596,441198348,430323928,561379111,347517,SRX2768758,SRS2152466,SRA557480,Brandon University|Biology,Brandon University,1,0.93579,,0.16207,,0.68473,,0.44993,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42217,SRR5485621,SRX2768757,SRS2152467,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,U 6.20.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,U 6.20.2,U 6.20.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_7.U_R1.fastq.gz HI.4096.008.Index_7.U_R1.fastq.gz,fastq fastq,1754851900.0,17548519.0,HI.4079.001.Index 7.U R1.fastq.gz,0:100 1:0,A:464191451;C:397313933;G:387262108;T:505777499;N:306909,100,0,,,464191451,397313933,387262108,505777499,306909,SRX2768757,SRS2152467,SRA557480,Brandon University|Biology,Brandon University,1,0.93016,,0.16163,,0.68329,,0.47088,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42218,SRR5485620,SRX2768756,SRS2152463,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,V 6.0.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.0.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,V 6.0.14,V 6.0.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_18.V_R1.fastq.gz HI.4096.008.Index_18.V_R1.fastq.gz,fastq fastq,2027423200.0,20274232.0,HI.4079.001.Index 18.V R1.fastq.gz,0:100 1:0,A:542440452;C:449399743;G:440389586;T:594839784;N:353635,100,0,,,542440452,449399743,440389586,594839784,353635,SRX2768756,SRS2152463,SRA557480,Brandon University|Biology,Brandon University,1,0.92441,,0.16974,,0.6842,,0.48209,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42219,SRR5485619,SRX2768755,SRS2152464,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,W 6.5.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,W 6.5.14,W 6.5.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_14.W_R1.fastq.gz HI.4096.008.Index_14.W_R1.fastq.gz,fastq fastq,2139528300.0,21395283.0,HI.4079.001.Index 14.W R1.fastq.gz,0:100 1:0,A:569259910;C:478055273;G:469309420;T:622525486;N:378211,100,0,,,569259910,478055273,469309420,622525486,378211,SRX2768755,SRS2152464,SRA557480,Brandon University|Biology,Brandon University,1,0.92551,,0.15358,,0.68136,,0.47093,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42220,SRR5485618,SRX2768754,SRS2152465,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,X 6.20.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,X 6.20.14,X 6.20.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_16.X_R1.fastq.gz HI.4096.008.Index_16.X_R1.fastq.gz,fastq fastq,1768110400.0,17681104.0,HI.4079.001.Index 16.X R1.fastq.gz,0:100 1:0,A:472810124;C:392555880;G:382616900;T:519817796;N:309700,100,0,,,472810124,392555880,382616900,519817796,309700,SRX2768754,SRS2152465,SRA557480,Brandon University|Biology,Brandon University,1,0.92486,,0.16073,,0.69041,,0.48403,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
43420,SRR5931502,SRX3091760,SRS2429123,SRP115384,PRJNA398194,Regulation of posterior body and ectodermal morphogenesis in zebrafish by localized Yap1 and  Wwtr1,GSE102606,Transcriptome Analysis,The vertebrate embryo undergoes a series of dramatic morphological changes as the body extends to form the complete anterior posterior  axis during the somite forming stages. The molecular mechanisms regulating these complex processes are still largely unknown. We show that  the Hippo pathway transcriptional coactivators Yap1 and Wwtr1 are specifically localized to the ectoderm and notochord  and play a critical and  unexpected role in posterior body extension by regulating the assembly of Fibronectin underneath the ectoderm and surrounding the notochord.  We also find that Yap1/Wwtr1  also acting through Fibronectin  have an essential role in the ectodermal morphogenesis necessary to form the  initial dorsal and ventral fins  a process that had been thought to involve bending of an epithelial sheet  but which we now show involves active  cell migration. Our results reveal how the Hippo pathway transcriptional program  localized to two specific tissues  acts to control essential  morphological events in the vertebrate embryo. Overall design: two biological replicates of tails of yap1/wwtr1 double homozygous mutants and siblings 24 each at 16 18 somite stage were collected for RNAseq.  Tails are tissues of the posterior end until the third newest somite S III.,,pubmed:29283341,,mutants replicate2,GSM2741693,,source name:tails|developmental stage:16 18ss|tissue:posterior body up to S III|genotype/variation:yap1/wwtr1 double homozygous mutants,mutants replicate2,Reads trimming: Trimmomatic v0.33 LEADING:3 TRAILING:3 SLIDINGWINDOW:5:20 CROP:500 MINLEN:15 Alignment: STAR 2.4.0a   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 30   outFilterMultimapNmax 999   alignEndsProtrude 10 ConcordantPair normalization and statistics: Cufflinks suite v2.2.1 standard parameters Genome build: Zv10 Supplementary files format and content: fpkm tracking,tails,,RNA extraction was performed with Qiagen miRNeasy kit Library was prepared with Truseq Stranded mRNA library preparation kit,,developmental stage:16 18ss|tissue:posterior body up to S III|genotype/variation:yap1/wwtr1 double homozygous mutants,GSM2741693,GSM2741693: mutants replicate2; Danio rerio; RNA Seq,GSM2741693,,1,RNA extraction was performed with Qiagen miRNeasy kit Library was prepared with Truseq Stranded mRNA library preparation kit,GEO Accession:GSM2741693,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP115384,,,jason_tail_mut3_R1.fastq jason_tail_mut3_R2.fastq,fastq fastq,1785197177.0,11988655.0,GSM2741693 r1,0:74.51 1:74.41,A:448190563;C:437837221;G:441820983;T:457307048;N:41362,74,74,,,448190563,437837221,441820983,457307048,41362,SRX3091760,SRS2429123,SRA598978,GEO,"Stainier Lab, Developmental Genetics, Max Planck Institute For Heart and Lung Research",2,0.96703,0.96894,0.08442,0.08379,0.722,0.72506,0.48663,0.48673,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2017-08-14,Undetermined,Embryo,Trunk,Surface Structure
43421,SRR5931501,SRX3091759,SRS2429122,SRP115384,PRJNA398194,Regulation of posterior body and ectodermal morphogenesis in zebrafish by localized Yap1 and  Wwtr1,GSE102606,Transcriptome Analysis,The vertebrate embryo undergoes a series of dramatic morphological changes as the body extends to form the complete anterior posterior  axis during the somite forming stages. The molecular mechanisms regulating these complex processes are still largely unknown. We show that  the Hippo pathway transcriptional coactivators Yap1 and Wwtr1 are specifically localized to the ectoderm and notochord  and play a critical and  unexpected role in posterior body extension by regulating the assembly of Fibronectin underneath the ectoderm and surrounding the notochord.  We also find that Yap1/Wwtr1  also acting through Fibronectin  have an essential role in the ectodermal morphogenesis necessary to form the  initial dorsal and ventral fins  a process that had been thought to involve bending of an epithelial sheet  but which we now show involves active  cell migration. Our results reveal how the Hippo pathway transcriptional program  localized to two specific tissues  acts to control essential  morphological events in the vertebrate embryo. Overall design: two biological replicates of tails of yap1/wwtr1 double homozygous mutants and siblings 24 each at 16 18 somite stage were collected for RNAseq.  Tails are tissues of the posterior end until the third newest somite S III.,,pubmed:29283341,,mutants replicate1,GSM2741692,,source name:tails|developmental stage:16 18ss|tissue:posterior body up to S III|genotype/variation:yap1/wwtr1 double homozygous mutants,mutants replicate1,Reads trimming: Trimmomatic v0.33 LEADING:3 TRAILING:3 SLIDINGWINDOW:5:20 CROP:500 MINLEN:15 Alignment: STAR 2.4.0a   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 30   outFilterMultimapNmax 999   alignEndsProtrude 10 ConcordantPair normalization and statistics: Cufflinks suite v2.2.1 standard parameters Genome build: Zv10 Supplementary files format and content: fpkm tracking,tails,,RNA extraction was performed with Qiagen miRNeasy kit Library was prepared with Truseq Stranded mRNA library preparation kit,,developmental stage:16 18ss|tissue:posterior body up to S III|genotype/variation:yap1/wwtr1 double homozygous mutants,GSM2741692,GSM2741692: mutants replicate1; Danio rerio; RNA Seq,GSM2741692,,1,RNA extraction was performed with Qiagen miRNeasy kit Library was prepared with Truseq Stranded mRNA library preparation kit,GEO Accession:GSM2741692,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP115384,,,jason_tail_mut2_R1.fastq jason_tail_mut2_R2.fastq,fastq fastq,1330843114.0,8934569.0,GSM2741692 r1,0:74.53 1:74.43,A:334692975;C:325256311;G:332297545;T:338565318;N:30965,74,74,,,334692975,325256311,332297545,338565318,30965,SRX3091759,SRS2429122,SRA598978,GEO,"Stainier Lab, Developmental Genetics, Max Planck Institute For Heart and Lung Research",2,0.96799,0.96959,0.07645,0.07614,0.72115,0.72508,0.48043,0.48512,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2017-08-14,Undetermined,Embryo,Trunk,Surface Structure
43422,SRR5931500,SRX3091758,SRS2429121,SRP115384,PRJNA398194,Regulation of posterior body and ectodermal morphogenesis in zebrafish by localized Yap1 and  Wwtr1,GSE102606,Transcriptome Analysis,The vertebrate embryo undergoes a series of dramatic morphological changes as the body extends to form the complete anterior posterior  axis during the somite forming stages. The molecular mechanisms regulating these complex processes are still largely unknown. We show that  the Hippo pathway transcriptional coactivators Yap1 and Wwtr1 are specifically localized to the ectoderm and notochord  and play a critical and  unexpected role in posterior body extension by regulating the assembly of Fibronectin underneath the ectoderm and surrounding the notochord.  We also find that Yap1/Wwtr1  also acting through Fibronectin  have an essential role in the ectodermal morphogenesis necessary to form the  initial dorsal and ventral fins  a process that had been thought to involve bending of an epithelial sheet  but which we now show involves active  cell migration. Our results reveal how the Hippo pathway transcriptional program  localized to two specific tissues  acts to control essential  morphological events in the vertebrate embryo. Overall design: two biological replicates of tails of yap1/wwtr1 double homozygous mutants and siblings 24 each at 16 18 somite stage were collected for RNAseq.  Tails are tissues of the posterior end until the third newest somite S III.,,pubmed:29283341,,siblings replicate2,GSM2741691,,source name:tails|developmental stage:16 18ss|tissue:posterior body up to S III|genotype/variation:siblings,siblings replicate2,Reads trimming: Trimmomatic v0.33 LEADING:3 TRAILING:3 SLIDINGWINDOW:5:20 CROP:500 MINLEN:15 Alignment: STAR 2.4.0a   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 30   outFilterMultimapNmax 999   alignEndsProtrude 10 ConcordantPair normalization and statistics: Cufflinks suite v2.2.1 standard parameters Genome build: Zv10 Supplementary files format and content: fpkm tracking,tails,,RNA extraction was performed with Qiagen miRNeasy kit Library was prepared with Truseq Stranded mRNA library preparation kit,,developmental stage:16 18ss|tissue:posterior body up to S III|genotype/variation:siblings,GSM2741691,GSM2741691: siblings replicate2; Danio rerio; RNA Seq,GSM2741691,,1,RNA extraction was performed with Qiagen miRNeasy kit Library was prepared with Truseq Stranded mRNA library preparation kit,GEO Accession:GSM2741691,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP115384,,loader:fastq load.py,jason_tail_sib3_R1.fastq jason_tail_sib3_R2.fastq,fastq fastq,1386240386.0,9329727.0,GSM2741691 r1,,A:344948794;C:340444989;G:350180888;T:350634293;N:31422,,,,,344948794,340444989,350180888,350634293,31422,SRX3091758,SRS2429121,SRA598978,GEO,"Stainier Lab, Developmental Genetics, Max Planck Institute For Heart and Lung Research",2,0.96936,0.97056,0.07005,0.07004,0.71894,0.72352,0.47017,0.47369,74,73,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2017-08-14,Undetermined,Embryo,Trunk,Surface Structure
43423,SRR5931499,SRX3091757,SRS2429120,SRP115384,PRJNA398194,Regulation of posterior body and ectodermal morphogenesis in zebrafish by localized Yap1 and  Wwtr1,GSE102606,Transcriptome Analysis,The vertebrate embryo undergoes a series of dramatic morphological changes as the body extends to form the complete anterior posterior  axis during the somite forming stages. The molecular mechanisms regulating these complex processes are still largely unknown. We show that  the Hippo pathway transcriptional coactivators Yap1 and Wwtr1 are specifically localized to the ectoderm and notochord  and play a critical and  unexpected role in posterior body extension by regulating the assembly of Fibronectin underneath the ectoderm and surrounding the notochord.  We also find that Yap1/Wwtr1  also acting through Fibronectin  have an essential role in the ectodermal morphogenesis necessary to form the  initial dorsal and ventral fins  a process that had been thought to involve bending of an epithelial sheet  but which we now show involves active  cell migration. Our results reveal how the Hippo pathway transcriptional program  localized to two specific tissues  acts to control essential  morphological events in the vertebrate embryo. Overall design: two biological replicates of tails of yap1/wwtr1 double homozygous mutants and siblings 24 each at 16 18 somite stage were collected for RNAseq.  Tails are tissues of the posterior end until the third newest somite S III.,,pubmed:29283341,,siblings replicate1,GSM2741690,,source name:tails|developmental stage:16 18ss|tissue:posterior body up to S III|genotype/variation:siblings,siblings replicate1,Reads trimming: Trimmomatic v0.33 LEADING:3 TRAILING:3 SLIDINGWINDOW:5:20 CROP:500 MINLEN:15 Alignment: STAR 2.4.0a   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 30   outFilterMultimapNmax 999   alignEndsProtrude 10 ConcordantPair normalization and statistics: Cufflinks suite v2.2.1 standard parameters Genome build: Zv10 Supplementary files format and content: fpkm tracking,tails,,RNA extraction was performed with Qiagen miRNeasy kit Library was prepared with Truseq Stranded mRNA library preparation kit,,developmental stage:16 18ss|tissue:posterior body up to S III|genotype/variation:siblings,GSM2741690,GSM2741690: siblings replicate1; Danio rerio; RNA Seq,GSM2741690,,1,RNA extraction was performed with Qiagen miRNeasy kit Library was prepared with Truseq Stranded mRNA library preparation kit,GEO Accession:GSM2741690,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP115384,,loader:fastq load.py,jason_tail_sib1_R1.fastq jason_tail_sib1_R2.fastq,fastq fastq,2017415692.0,13564988.0,GSM2741690 r1,,A:510314991;C:491044635;G:495080141;T:520928709;N:47216,,,,,510314991,491044635,495080141,520928709,47216,SRX3091757,SRS2429120,SRA598978,GEO,"Stainier Lab, Developmental Genetics, Max Planck Institute For Heart and Lung Research",2,0.96646,0.96801,0.08565,0.08558,0.72001,0.72285,0.48252,0.48043,75,74,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2017-08-14,Undetermined,Embryo,Trunk,Surface Structure
44015,SRR6211474,SRX3320751,SRS2626325,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Time course 10h24h mRNA,GSM2830047,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Embryo|time point:10h  24h,Time course 10h24h mRNA,Library strategy: Targeted amplification Embryos were injected with Cas9 and sgRNA at the 1 cell stage. post 1  2  3  4  6  8  10  and 24 hours  2 3 embryos were collected and RNA and/or DNA were extracted using TRIzol Reagent according to the manufacturer’s protocols. Bulk scar libraries were produced similarly to the bulk libraries for the scar probabilities. For each sample  we calculated the percentage of unscarred RFP. We fit a negative exponential to this data  assuming that the fraction of unscarred RFP at t=0 was one. Genome build: N/A Supplementary files format and content: List of scar sequences with CIGAR and cell barcode.,Full organism,,Trizol extraction of RNA. CEL seq,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Embryo|time point:10h  24h,GSM2830047,GSM2830047: Time course 10h24h mRNA; Danio rerio; OTHER,GSM2830047,,1,Trizol extraction of RNA. CEL seq,GEO Accession:GSM2830047,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,dyn_RNA_10h24h_S13_R2_001.fastq.gz dyn_RNA_10h24h_S13_R1_001.fastq.gz,fastq fastq,1456176300.0,9707842.0,GSM2830047 r1,0:100 1:50,A:216943159;C:398650961;G:516656316;T:323899428;N:26436,100,50,,,216943159,398650961,516656316,323899428,26436,SRX3320751,SRS2626325,SRA623333,GEO,Max Delbrück Center,2,3e-05,0.00111,0.0,0.0011,0.99995,1.0,0.75,,100,50,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,sc,single_cell_plate,celseq,,Germany,2017-10-24,Undetermined,Embryo,Trunk,Surface Structure
44016,SRR6211473,SRX3320750,SRS2626324,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Time course 3h6h8h mRNA,GSM2830046,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Embryo|time point:3h  6h  8h,Time course 3h6h8h mRNA,Library strategy: Targeted amplification Embryos were injected with Cas9 and sgRNA at the 1 cell stage. post 1  2  3  4  6  8  10  and 24 hours  2 3 embryos were collected and RNA and/or DNA were extracted using TRIzol Reagent according to the manufacturer’s protocols. Bulk scar libraries were produced similarly to the bulk libraries for the scar probabilities. For each sample  we calculated the percentage of unscarred RFP. We fit a negative exponential to this data  assuming that the fraction of unscarred RFP at t=0 was one. Genome build: N/A Supplementary files format and content: List of scar sequences with CIGAR and cell barcode.,Full organism,,Trizol extraction of RNA. CEL seq,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Embryo|time point:3h  6h  8h,GSM2830046,GSM2830046: Time course 3h6h8h mRNA; Danio rerio; OTHER,GSM2830046,,1,Trizol extraction of RNA. CEL seq,GEO Accession:GSM2830046,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,dyn_RNA_3h6h8h_S12_R1_001.fastq.gz dyn_RNA_3h6h8h_S12_R2_001.fastq.gz,fastq fastq,1382400000.0,9216000.0,GSM2830046 r1,0:100 1:50,A:219040774;C:378529638;G:475287684;T:309516830;N:25074,100,50,,,219040774,378529638,475287684,309516830,25074,SRX3320750,SRS2626324,SRA623333,GEO,Max Delbrück Center,2,5e-05,0.00116,0.0,0.00115,0.99987,1.0,0.5,,100,50,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,sc,single_cell_plate,celseq,,Germany,2017-10-24,Undetermined,Embryo,Trunk,Surface Structure
49175,SRR7764540,SRX4620156,SRS3722694,SRP159053,PRJNA488354,Molecularly distinct models of zebrafish Myc induced B cell leukemia,GSE119173,Transcriptome Analysis,The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish  expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.,,pubmed:30573774,,hMYC 14,GSM3360022,,tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line,hMYC 14,Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al.  2018 PMID 29749398.  Briefly  reads were aligned using STAR Dobin et al.  2013 to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts Liao et al.  2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples,GFP+ FACS purified ALL from total body,,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:rag2:hMYC;lck:eGFP double transgenic line,GSM3360022,GSM3360022: hMYC 14; Danio rerio; RNA Seq,GSM3360022,,1,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3360022,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP159053,,,MCB_14_d_R2_001.fastq.gz MCB_14_d_R1_001.fastq.gz,fastq fastq,8041956188.0,26628994.0,GSM3360022 r1,0:151 1:151,A:2169107009;C:1867732731;G:1838645489;T:2164562982;N:1907977,151,151,,,2169107009,1867732731,1838645489,2164562982,1907977,SRX4620156,SRS3722694,SRA764101,GEO,"Pediatrics, University of Oklahoma Health Sciences Center",2,0.90129,0.90181,0.17265,0.16628,0.77914,0.78571,0.51437,0.51601,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-08-29,Undetermined,Undetermined,Trunk,Surface Structure
49176,SRR7764539,SRX4620155,SRS3722693,SRP159053,PRJNA488354,Molecularly distinct models of zebrafish Myc induced B cell leukemia,GSE119173,Transcriptome Analysis,The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish  expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.,,pubmed:30573774,,hMYC 13,GSM3360021,,tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line,hMYC 13,Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al.  2018 PMID 29749398.  Briefly  reads were aligned using STAR Dobin et al.  2013 to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts Liao et al.  2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples,GFP+ FACS purified ALL from total body,,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:rag2:hMYC;lck:eGFP double transgenic line,GSM3360021,GSM3360021: hMYC 13; Danio rerio; RNA Seq,GSM3360021,,1,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3360021,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP159053,,,MCB_13_d_R1_001.fastq.gz MCB_13_d_R2_001.fastq.gz,fastq fastq,8396214872.0,27802036.0,GSM3360021 r1,0:151 1:151,A:2241185626;C:1969096150;G:1937906595;T:2246030255;N:1996246,151,151,,,2241185626,1969096150,1937906595,2246030255,1996246,SRX4620155,SRS3722693,SRA764101,GEO,"Pediatrics, University of Oklahoma Health Sciences Center",2,0.9263,0.92555,0.1672,0.16003,0.7754,0.78143,0.50818,0.50565,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-08-29,Undetermined,Undetermined,Trunk,Surface Structure
49177,SRR7764538,SRX4620154,SRS3722692,SRP159053,PRJNA488354,Molecularly distinct models of zebrafish Myc induced B cell leukemia,GSE119173,Transcriptome Analysis,The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish  expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.,,pubmed:30573774,,hMYC 12,GSM3360020,,tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line,hMYC 12,Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al.  2018 PMID 29749398.  Briefly  reads were aligned using STAR Dobin et al.  2013 to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts Liao et al.  2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples,GFP+ FACS purified ALL from total body,,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:rag2:hMYC;lck:eGFP double transgenic line,GSM3360020,GSM3360020: hMYC 12; Danio rerio; RNA Seq,GSM3360020,,1,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3360020,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP159053,,,MCB_12_d_R2_001.fastq.gz MCB_12_d_R1_001.fastq.gz,fastq fastq,8640985570.0,28612535.0,GSM3360020 r1,0:151 1:151,A:2320458014;C:2008991633;G:1983687859;T:2325784420;N:2063644,151,151,,,2320458014,2008991633,1983687859,2325784420,2063644,SRX4620154,SRS3722692,SRA764101,GEO,"Pediatrics, University of Oklahoma Health Sciences Center",2,0.91667,0.9169,0.20552,0.19745,0.77137,0.77768,0.51563,0.51361,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-08-29,Undetermined,Undetermined,Trunk,Surface Structure
49178,SRR7764537,SRX4620153,SRS3722691,SRP159053,PRJNA488354,Molecularly distinct models of zebrafish Myc induced B cell leukemia,GSE119173,Transcriptome Analysis,The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish  expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.,,pubmed:30573774,,hMYC 11,GSM3360019,,tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line,hMYC 11,Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al.  2018 PMID 29749398.  Briefly  reads were aligned using STAR Dobin et al.  2013 to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts Liao et al.  2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples,GFP+ FACS purified ALL from total body,,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:rag2:hMYC;lck:eGFP double transgenic line,GSM3360019,GSM3360019: hMYC 11; Danio rerio; RNA Seq,GSM3360019,,1,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3360019,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP159053,,,MCB_11_d_R1_001.fastq.gz MCB_11_d_R2_001.fastq.gz,fastq fastq,10375306338.0,34355319.0,GSM3360019 r1,0:151 1:151,A:2774834850;C:2433110341;G:2384852893;T:2780049207;N:2459047,151,151,,,2774834850,2433110341,2384852893,2780049207,2459047,SRX4620153,SRS3722691,SRA764101,GEO,"Pediatrics, University of Oklahoma Health Sciences Center",2,0.92646,0.92634,0.25883,0.24912,0.80667,0.81294,0.52396,0.4604,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-08-29,Undetermined,Undetermined,Trunk,Surface Structure
49179,SRR7764536,SRX4620152,SRS3722690,SRP159053,PRJNA488354,Molecularly distinct models of zebrafish Myc induced B cell leukemia,GSE119173,Transcriptome Analysis,The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish  expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.,,pubmed:30573774,,hMYC 10,GSM3360018,,tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line,hMYC 10,Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al.  2018 PMID 29749398.  Briefly  reads were aligned using STAR Dobin et al.  2013 to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts Liao et al.  2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples,GFP+ FACS purified ALL from total body,,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:rag2:hMYC;lck:eGFP double transgenic line,GSM3360018,GSM3360018: hMYC 10; Danio rerio; RNA Seq,GSM3360018,,1,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3360018,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP159053,,,MCB_10_d_R1_001.fastq.gz MCB_10_d_R2_001.fastq.gz,fastq fastq,9103054630.0,30142565.0,GSM3360018 r1,0:151 1:151,A:2444515359;C:2120625212;G:2086999932;T:2448748127;N:2166000,151,151,,,2444515359,2120625212,2086999932,2448748127,2166000,SRX4620152,SRS3722690,SRA764101,GEO,"Pediatrics, University of Oklahoma Health Sciences Center",2,0.919,0.91974,0.20589,0.19901,0.78169,0.78855,0.51136,0.5163,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-08-29,Undetermined,Undetermined,Trunk,Surface Structure
49180,SRR7764535,SRX4620151,SRS3722689,SRP159053,PRJNA488354,Molecularly distinct models of zebrafish Myc induced B cell leukemia,GSE119173,Transcriptome Analysis,The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish  expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.,,pubmed:30573774,,hMYC 9,GSM3360017,,tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line,hMYC 9,Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al.  2018 PMID 29749398.  Briefly  reads were aligned using STAR Dobin et al.  2013 to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts Liao et al.  2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples,GFP+ FACS purified ALL from total body,,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:rag2:hMYC;lck:eGFP double transgenic line,GSM3360017,GSM3360017: hMYC 9; Danio rerio; RNA Seq,GSM3360017,,1,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3360017,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP159053,,,MCB_9_d_R1_001.fastq.gz MCB_9_d_R2_001.fastq.gz,fastq fastq,9781069696.0,32387648.0,GSM3360017 r1,0:151 1:151,A:2593768575;C:2312524357;G:2270896742;T:2601565073;N:2314949,151,151,,,2593768575,2312524357,2270896742,2601565073,2314949,SRX4620151,SRS3722689,SRA764101,GEO,"Pediatrics, University of Oklahoma Health Sciences Center",2,0.9302,0.9302,0.16677,0.16095,0.78486,0.79105,0.51234,0.50852,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-08-29,Undetermined,Undetermined,Trunk,Surface Structure
49181,SRR7764534,SRX4620150,SRS3722687,SRP159053,PRJNA488354,Molecularly distinct models of zebrafish Myc induced B cell leukemia,GSE119173,Transcriptome Analysis,The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish  expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.,,pubmed:30573774,,hMYC 8,GSM3360016,,tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line,hMYC 8,Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al.  2018 PMID 29749398.  Briefly  reads were aligned using STAR Dobin et al.  2013 to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts Liao et al.  2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples,GFP+ FACS purified ALL from total body,,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:rag2:hMYC;lck:eGFP double transgenic line,GSM3360016,GSM3360016: hMYC 8; Danio rerio; RNA Seq,GSM3360016,,1,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3360016,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP159053,,,MCB_8_c_GCCAAT_R1_concat.fastq.gz MCB_8_c_GCCAAT_R2_concat.fastq.gz,fastq fastq,5631730306.0,27879853.0,GSM3360016 r1,0:101 1:101,A:1502650481;C:1306810950;G:1314705252;T:1500209887;N:7353736,101,101,,,1502650481,1306810950,1314705252,1500209887,7353736,SRX4620150,SRS3722687,SRA764101,GEO,"Pediatrics, University of Oklahoma Health Sciences Center",2,0.93418,0.93562,0.20662,0.20876,0.78175,0.78455,0.51374,0.50871,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-08-29,Undetermined,Undetermined,Trunk,Surface Structure
49182,SRR7764533,SRX4620149,SRS3722688,SRP159053,PRJNA488354,Molecularly distinct models of zebrafish Myc induced B cell leukemia,GSE119173,Transcriptome Analysis,The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish  expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.,,pubmed:30573774,,hMYC 6,GSM3360015,,tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line,hMYC 6,Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al.  2018 PMID 29749398.  Briefly  reads were aligned using STAR Dobin et al.  2013 to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts Liao et al.  2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples,GFP+ FACS purified ALL from total body,,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:rag2:hMYC;lck:eGFP double transgenic line,GSM3360015,GSM3360015: hMYC 6; Danio rerio; RNA Seq,GSM3360015,,1,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3360015,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP159053,,,MCB_6_c_TGACCA_R1_concat.fastq.gz MCB_6_c_TGACCA_R2_concat.fastq.gz,fastq fastq,5005976120.0,24782060.0,GSM3360015 r1,0:101 1:101,A:1337000499;C:1160240242;G:1164651573;T:1337549504;N:6534302,101,101,,,1337000499,1160240242,1164651573,1337549504,6534302,SRX4620149,SRS3722688,SRA764101,GEO,"Pediatrics, University of Oklahoma Health Sciences Center",2,0.93447,0.93694,0.24013,0.24194,0.78569,0.78843,0.51039,0.51234,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-08-29,Undetermined,Undetermined,Trunk,Surface Structure
49183,SRR7764532,SRX4620148,SRS3722686,SRP159053,PRJNA488354,Molecularly distinct models of zebrafish Myc induced B cell leukemia,GSE119173,Transcriptome Analysis,The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish  expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.,,pubmed:30573774,,hMYC 5,GSM3360014,,tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line,hMYC 5,Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al.  2018 PMID 29749398.  Briefly  reads were aligned using STAR Dobin et al.  2013 to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts Liao et al.  2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples,GFP+ FACS purified ALL from total body,,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:rag2:hMYC;lck:eGFP double transgenic line,GSM3360014,GSM3360014: hMYC 5; Danio rerio; RNA Seq,GSM3360014,,1,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3360014,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP159053,,,MCB_5_c_TTAGGC_R1_concat.fastq.gz MCB_5_c_TTAGGC_R2_concat.fastq.gz,fastq fastq,4977608654.0,24641627.0,GSM3360014 r1,0:101 1:101,A:1314910590;C:1165984454;G:1181974120;T:1308322261;N:6417229,101,101,,,1314910590,1165984454,1181974120,1308322261,6417229,SRX4620148,SRS3722686,SRA764101,GEO,"Pediatrics, University of Oklahoma Health Sciences Center",2,0.92362,0.92695,0.10675,0.10794,0.76698,0.76873,0.50174,0.50838,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-08-29,Undetermined,Undetermined,Trunk,Surface Structure
49184,SRR7764531,SRX4620147,SRS3722684,SRP159053,PRJNA488354,Molecularly distinct models of zebrafish Myc induced B cell leukemia,GSE119173,Transcriptome Analysis,The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish  expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.,,pubmed:30573774,,hMYC 4,GSM3360013,,tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line,hMYC 4,Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al.  2018 PMID 29749398.  Briefly  reads were aligned using STAR Dobin et al.  2013 to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts Liao et al.  2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples,GFP+ FACS purified ALL from total body,,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:rag2:hMYC;lck:eGFP double transgenic line,GSM3360013,GSM3360013: hMYC 4; Danio rerio; RNA Seq,GSM3360013,,1,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3360013,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP159053,,,MCB_4_c_AGTCAA_R1_concat.fastq.gz MCB_4_c_AGTCAA_R2_concat.fastq.gz,fastq fastq,4643314814.0,22986707.0,GSM3360013 r1,0:101 1:101,A:1230639467;C:1085508722;G:1095255741;T:1225853845;N:6057039,101,101,,,1230639467,1085508722,1095255741,1225853845,6057039,SRX4620147,SRS3722684,SRA764101,GEO,"Pediatrics, University of Oklahoma Health Sciences Center",2,0.92296,0.92585,0.14279,0.14414,0.76232,0.76392,0.51322,0.51626,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-08-29,Undetermined,Undetermined,Trunk,Surface Structure
49185,SRR7764530,SRX4620146,SRS3722683,SRP159053,PRJNA488354,Molecularly distinct models of zebrafish Myc induced B cell leukemia,GSE119173,Transcriptome Analysis,The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish  expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.,,pubmed:30573774,,hMYC 3,GSM3360012,,tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line,hMYC 3,Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al.  2018 PMID 29749398.  Briefly  reads were aligned using STAR Dobin et al.  2013 to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts Liao et al.  2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples,GFP+ FACS purified ALL from total body,,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:rag2:hMYC;lck:eGFP double transgenic line,GSM3360012,GSM3360012: hMYC 3; Danio rerio; RNA Seq,GSM3360012,,1,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3360012,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP159053,,,MCB_3_c_AGTTCC_R1_concat.fastq.gz MCB_3_c_AGTTCC_R2_concat.fastq.gz,fastq fastq,4554953954.0,22549277.0,GSM3360012 r1,0:101 1:101,A:1189333550;C:1082661290;G:1094370390;T:1182606305;N:5982419,101,101,,,1189333550,1082661290,1094370390,1182606305,5982419,SRX4620146,SRS3722683,SRA764101,GEO,"Pediatrics, University of Oklahoma Health Sciences Center",2,0.92378,0.92708,0.10269,0.10292,0.76051,0.76199,0.51083,0.50811,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-08-29,Undetermined,Undetermined,Trunk,Surface Structure
49186,SRR7764529,SRX4620145,SRS3722685,SRP159053,PRJNA488354,Molecularly distinct models of zebrafish Myc induced B cell leukemia,GSE119173,Transcriptome Analysis,The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish  expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.,,pubmed:30573774,,hMYC 2,GSM3360011,,tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line,hMYC 2,Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al.  2018 PMID 29749398.  Briefly  reads were aligned using STAR Dobin et al.  2013 to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts Liao et al.  2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples,GFP+ FACS purified ALL from total body,,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:rag2:hMYC;lck:eGFP double transgenic line,GSM3360011,GSM3360011: hMYC 2; Danio rerio; RNA Seq,GSM3360011,,1,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3360011,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP159053,,,MCB_2_c_CTTGTA_R1_concat.fastq.gz MCB_2_c_CTTGTA_R2_concat.fastq.gz,fastq fastq,4765708230.0,23592615.0,GSM3360011 r1,0:101 1:101,A:1281598432;C:1095469903;G:1100358193;T:1282017533;N:6264169,101,101,,,1281598432,1095469903,1100358193,1282017533,6264169,SRX4620145,SRS3722685,SRA764101,GEO,"Pediatrics, University of Oklahoma Health Sciences Center",2,0.9366,0.93502,0.29149,0.28598,0.81834,0.81611,0.51036,0.50798,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-08-29,Undetermined,Undetermined,Trunk,Surface Structure
49187,SRR7764528,SRX4620144,SRS3722682,SRP159053,PRJNA488354,Molecularly distinct models of zebrafish Myc induced B cell leukemia,GSE119173,Transcriptome Analysis,The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish  expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.,,pubmed:30573774,,hMYC 1,GSM3360010,,tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line,hMYC 1,Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al.  2018 PMID 29749398.  Briefly  reads were aligned using STAR Dobin et al.  2013 to GRCz10.  Picard was used to filter out potential PCR duplicates.  Counts were assigned to each gene using featureCounts Liao et al.  2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples,GFP+ FACS purified ALL from total body,,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:rag2:hMYC;lck:eGFP double transgenic line,GSM3360010,GSM3360010: hMYC 1; Danio rerio; RNA Seq,GSM3360010,,1,Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3360010,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP159053,,,MCB_1_c_CGATGT_R1_concan.fastq.gz MCB_1_c_CGATGT_R2_concan.fastq.gz,fastq fastq,4646978084.0,23004842.0,GSM3360010 r1,0:101 1:101,A:1211324194;C:1106543328;G:1120164021;T:1202883527;N:6063014,101,101,,,1211324194,1106543328,1120164021,1202883527,6063014,SRX4620144,SRS3722682,SRA764101,GEO,"Pediatrics, University of Oklahoma Health Sciences Center",2,0.92808,0.9305,0.10385,0.10435,0.76485,0.76627,0.51885,0.51967,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-08-29,Undetermined,Undetermined,Trunk,Surface Structure
60021,SRR12103084,SRX8627422,SRS6915731,SRP269070,PRJNA642405,Changes of m6A RNA methylation following spinal cord injury,PRJNA642405,Other,Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury,,,,,SCI IP,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:SCI IP|BioSampleModel:Model organism or animal,,,,,,,,,IP library sequencing data of treated sample,SCIIP BKDL192540807 1a,SCIIP BKDL192540807 1a,IP library sequencing data of treated sample,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP269070,,,SCIIP_BKDL192540807-1a_1.fq.gz SCIIP_BKDL192540807-1a_2.fq.gz,fastq fastq,7110503700.0,23701679.0,SCIIP BKDL192540807 1a 1.fq.gz,0:150 1:150,A:1520693228;C:1953670419;G:2215620460;T:1420407690;N:111903,150,150,,,1520693228,1953670419,2215620460,1420407690,111903,SRX8627422,SRS6915731,SRA1091926,Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and,Nantong University,2,0.9115,0.9147,0.19936,0.2033,0.81864,0.81919,0.66838,0.6677,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-06-28,Undetermined,Larval,Trunk,Surface Structure
60022,SRR12103085,SRX8627421,SRS6915730,SRP269070,PRJNA642405,Changes of m6A RNA methylation following spinal cord injury,PRJNA642405,Other,Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury,,,,,SCI Input,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:SCI Input|BioSampleModel:Model organism or animal,,,,,,,,,Input library sequencing data of treated sample,SCIIN BKDL192540809 1a,SCIIN BKDL192540809 1a,Input library sequencing data of treated sample,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP269070,,,SCIIN_BKDL192540809-1a_2.fq.gz SCIIN_BKDL192540809-1a_1.fq.gz,fastq fastq,7774587300.0,25915291.0,SCIIN BKDL192540809 1a 1.fq.gz,0:150 1:150,A:1595151855;C:2243828590;G:2397611978;T:1537918306;N:76571,150,150,,,1595151855,2243828590,2397611978,1537918306,76571,SRX8627421,SRS6915730,SRA1091926,Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and,Nantong University,2,0.96018,0.96291,0.23754,0.23744,0.84904,0.85245,0.74661,0.74738,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-06-28,Undetermined,Larval,Trunk,Surface Structure
60023,SRR12103086,SRX8627420,SRS6915729,SRP269070,PRJNA642405,Changes of m6A RNA methylation following spinal cord injury,PRJNA642405,Other,Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury,,,,,Control IP,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:Control IP|BioSampleModel:Model organism or animal,,,,,,,,,IP library sequencing data of control sample,controlIP BKDL192540808 1a,controlIP BKDL192540808 1a,IP library sequencing data of control sample,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP269070,,,controlIP_BKDL192540808-1a_2.fq.gz controlIP_BKDL192540808-1a_1.fq.gz,fastq fastq,7359972600.0,24533242.0,controlIP BKDL192540808 1a 1.fq.gz,0:150 1:150,A:1569051886;C:2002692591;G:2333418000;T:1454676484;N:133639,150,150,,,1569051886,2002692591,2333418000,1454676484,133639,SRX8627420,SRS6915729,SRA1091926,Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and,Nantong University,2,0.92004,0.92293,0.20272,0.20739,0.83254,0.83291,0.68471,0.65224,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-06-28,Undetermined,Larval,Trunk,Surface Structure
60024,SRR12103087,SRX8627419,SRS6915728,SRP269070,PRJNA642405,Changes of m6A RNA methylation following spinal cord injury,PRJNA642405,Other,Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury,,,,,Control Input,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:Control Input|BioSampleModel:Model organism or animal,,,,,,,,,Input library sequencing data of control sample,controlIN BKDL192540810 1a,controlIN BKDL192540810 1a,Input library sequencing data of control sample,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP269070,,,controlIN_BKDL192540810-1a_1.fq.gz controlIN_BKDL192540810-1a_2.fq.gz,fastq fastq,7830123600.0,26100412.0,controlIN BKDL192540810 1a 1.fq.gz,0:150 1:150,A:1589371287;C:2296547915;G:2409439612;T:1534684151;N:80635,150,150,,,1589371287,2296547915,2409439612,1534684151,80635,SRX8627419,SRS6915728,SRA1091926,Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and,Nantong University,2,0.97501,0.97626,0.23177,0.23578,0.89497,0.8971,0.78501,0.77674,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-06-28,Undetermined,Larval,Trunk,Surface Structure