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
95,DRR050167,DRX045209,DRS025834,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing ES1 and EGFP,ES1 3,SAMD00044057,,sample name:ES1 EGFP rod 003|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044057,DRX045209,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>105</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>,DRP003043,Ion Torrent PGM sequencing of SAMD00044057,,,,371748120.0,3469843.0,DRR050167,0:107.14,A:107190409;C:79475572;G:83520360;T:101561779;N:0,107,,,,107190409,79475572,83520360,101561779,0,DRX045209,DRS025834,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.81026,,0.26715,,0.86953,,0.52321,,51,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
96,DRR050166,DRX045208,DRS025833,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing ES1 and EGFP,ES1 2,SAMD00044056,,sample name:ES1 EGFP rod 002|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044056,DRX045208,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>128</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>,DRP003043,Ion Torrent PGM sequencing of SAMD00044056,,,,425549011.0,3275261.0,DRR050166,0:129.93,A:126640704;C:86415371;G:90822163;T:121670773;N:0,129,,,,126640704,86415371,90822163,121670773,0,DRX045208,DRS025833,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.80223,,0.31429,,0.85861,,0.5272,,57,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
97,DRR050165,DRX045207,DRS025832,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing ES1 and EGFP,ES1 1,SAMD00044055,,sample name:ES1 EGFP rod 001|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044055,DRX045207,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>147</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>,DRP003043,Ion Torrent PGM sequencing of SAMD00044055,,,,584599765.0,3941083.0,DRR050165,0:148.33,A:164329030;C:129885620;G:136727379;T:153657736;N:0,148,,,,164329030,129885620,136727379,153657736,0,DRX045207,DRS025832,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.83769,,0.25395,,0.83116,,0.52784,,185,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
98,DRR050164,DRX045206,DRS025831,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing EGFP,EGFP 3,SAMD00044054,,sample name:EGFP rod 003|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044054,DRX045206,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>88</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>,DRP003043,Ion Torrent PGM sequencing of SAMD00044054,,,,343014114.0,3827762.0,DRR050164,0:89.61,A:99421434;C:73070267;G:77738821;T:92783592;N:0,89,,,,99421434,73070267,77738821,92783592,0,DRX045206,DRS025831,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.78953,,0.25529,,0.87367,,0.52148,,24,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
99,DRR050163,DRX045205,DRS025830,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing EGFP,EGFP 2,SAMD00044053,,sample name:EGFP rod 002|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044053,DRX045205,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>137</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>,DRP003043,Ion Torrent PGM sequencing of SAMD00044053,,,,533069427.0,3824140.0,DRR050163,0:139.40,A:152608173;C:113928273;G:120051739;T:146481242;N:0,139,,,,152608173,113928273,120051739,146481242,0,DRX045205,DRS025830,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.80412,,0.26768,,0.85338,,0.52255,,245,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
100,DRR050162,DRX045204,DRS025829,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing EGFP,EGFP 1,SAMD00044052,,sample name:EGFP rod 001|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044052,DRX045204,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>113</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>,DRP003043,Ion Torrent PGM sequencing of SAMD00044052,,,,478262965.0,4224064.0,DRR050162,0:113.22,A:136348264;C:104872341;G:113114502;T:123927858;N:0,113,,,,136348264,104872341,113114502,123927858,0,DRX045204,DRS025829,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.86947,,0.29839,,0.83317,,0.51453,,80,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
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
28893,SRR26821448,SRX22518177,SRS19529846,SRP471728,PRJNA1040136,Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs,GSE247669,Transcriptome Analysis,The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.,,pubmed:38385024,,10mT fractured 3,GSM7898626,,source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs|geo loc name:missing|collection date:missing,10mT fractured 3,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,Whole scales,,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs,GSM7898626,GSM7898626: 10mT fractured 3; Danio rerio; RNA Seq,GSM7898626 r1,GSM7898626,1,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471728,,,10mT_fractured_3_R2.fq.gz 10mT_fractured_3_R1.fq.gz,fastq fastq,1301482800.0,4338276.0,GSM7898626 r1,0:150 1:150,A:335087662;C:232566321;G:385245929;T:348358361;N:224527,150,150,,,335087662,232566321,385245929,348358361,224527,SRX22518177,SRS19529846,SRA1750892,Kanazawa University,Kanazawa University,2,0.67547,0.04621,0.23296,0.03359,0.78279,0.99648,0.54124,0.52153,150,150,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2023-11-14,Undetermined,Undetermined,Scale,Surface Structure
28894,SRR26821449,SRX22518176,SRS19529845,SRP471728,PRJNA1040136,Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs,GSE247669,Transcriptome Analysis,The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.,,pubmed:38385024,,10mT fractured 2,GSM7898625,,source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs|geo loc name:missing|collection date:missing,10mT fractured 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,Whole scales,,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs,GSM7898625,GSM7898625: 10mT fractured 2; Danio rerio; RNA Seq,GSM7898625 r1,GSM7898625,1,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471728,,,10mT_fractured_2_R1.fq.gz 10mT_fractured_2_R2.fq.gz,fastq fastq,1507967100.0,5026557.0,GSM7898625 r1,0:150 1:150,A:390969189;C:278659472;G:444481407;T:393553558;N:303474,150,150,,,390969189,278659472,444481407,393553558,303474,SRX22518176,SRS19529845,SRA1750892,Kanazawa University,Kanazawa University,2,0.68061,0.08614,0.31496,0.0705,0.77001,0.99513,0.53747,0.57677,150,150,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2023-11-14,Undetermined,Undetermined,Scale,Surface Structure
28895,SRR26821450,SRX22518175,SRS19529844,SRP471728,PRJNA1040136,Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs,GSE247669,Transcriptome Analysis,The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.,,pubmed:38385024,,10mT fractured 1,GSM7898624,,source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs|geo loc name:missing|collection date:missing,10mT fractured 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,Whole scales,,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs,GSM7898624,GSM7898624: 10mT fractured 1; Danio rerio; RNA Seq,GSM7898624 r1,GSM7898624,1,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471728,,,10mT_fractured_1_R2.fq.gz 10mT_fractured_1_R1.fq.gz,fastq fastq,1718495100.0,5728317.0,GSM7898624 r1,0:150 1:150,A:452779669;C:319880075;G:491162181;T:454320323;N:352852,150,150,,,452779669,319880075,491162181,454320323,352852,SRX22518175,SRS19529844,SRA1750892,Kanazawa University,Kanazawa University,2,0.67153,0.10745,0.32942,0.08781,0.76775,0.99427,0.53417,0.5895,150,150,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2023-11-14,Undetermined,Undetermined,Scale,Surface Structure
28896,SRR26821451,SRX22518174,SRS19529843,SRP471728,PRJNA1040136,Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs,GSE247669,Transcriptome Analysis,The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.,,pubmed:38385024,,0mT fractured 3,GSM7898623,,source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs|geo loc name:missing|collection date:missing,0mT fractured 3,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,Whole scales,,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs,GSM7898623,GSM7898623: 0mT fractured 3; Danio rerio; RNA Seq,GSM7898623 r1,GSM7898623,1,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471728,,,0mT_fractured_3_R1.fq.gz 0mT_fractured_3_R2.fq.gz,fastq fastq,1468748700.0,4895829.0,GSM7898623 r1,0:150 1:150,A:378980971;C:273130967;G:441424422;T:374917129;N:295211,150,150,,,378980971,273130967,441424422,374917129,295211,SRX22518174,SRS19529843,SRA1750892,Kanazawa University,Kanazawa University,2,0.67867,0.10573,0.35963,0.0899,0.75982,0.99508,0.53209,0.48863,150,150,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2023-11-14,Undetermined,Undetermined,Scale,Surface Structure
28897,SRR26821452,SRX22518173,SRS19529842,SRP471728,PRJNA1040136,Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs,GSE247669,Transcriptome Analysis,The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.,,pubmed:38385024,,0mT fractured 2,GSM7898622,,source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs|geo loc name:missing|collection date:missing,0mT fractured 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,Whole scales,,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs,GSM7898622,GSM7898622: 0mT fractured 2; Danio rerio; RNA Seq,GSM7898622 r1,GSM7898622,1,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471728,,,0mT_fractured_2_R1.fq.gz 0mT_fractured_2_R2.fq.gz,fastq fastq,2406885600.0,8022952.0,GSM7898622 r1,0:150 1:150,A:646926387;C:366751040;G:726614721;T:666425874;N:167578,150,150,,,646926387,366751040,726614721,666425874,167578,SRX22518173,SRS19529842,SRA1750892,Kanazawa University,Kanazawa University,2,0.67096,0.06177,0.27169,0.04875,0.77492,0.99805,0.55512,0.62711,150,150,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2023-11-14,Undetermined,Undetermined,Scale,Surface Structure
28898,SRR26821453,SRX22518172,SRS19529841,SRP471728,PRJNA1040136,Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs,GSE247669,Transcriptome Analysis,The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.,,pubmed:38385024,,0mT fractured 1,GSM7898621,,source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs|geo loc name:missing|collection date:missing,0mT fractured 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,Whole scales,,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs,GSM7898621,GSM7898621: 0mT fractured 1; Danio rerio; RNA Seq,GSM7898621 r1,GSM7898621,1,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471728,,,0mT_fractured_1_R1.fq.gz 0mT_fractured_1_R2.fq.gz,fastq fastq,2084550000.0,6948500.0,GSM7898621 r1,0:150 1:150,A:567504433;C:327104215;G:627285267;T:562454734;N:201351,150,150,,,567504433,327104215,627285267,562454734,201351,SRX22518172,SRS19529841,SRA1750892,Kanazawa University,Kanazawa University,2,0.68491,0.14639,0.35327,0.12371,0.76459,0.99584,0.52889,0.52678,150,150,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2023-11-14,Undetermined,Undetermined,Scale,Surface Structure
28899,SRR26821454,SRX22518171,SRS19529840,SRP471728,PRJNA1040136,Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs,GSE247669,Transcriptome Analysis,The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.,,pubmed:38385024,,Int 3,GSM7898620,,source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Intact scales|geo loc name:missing|collection date:missing,Int 3,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,Whole scales,,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,tissue:Whole scales|genotype:Wild type|treatment:Intact scales,GSM7898620,GSM7898620: Int 3; Danio rerio; RNA Seq,GSM7898620 r1,GSM7898620,1,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471728,,,Int_3_R1.fq.gz Int_3_R2.fq.gz,fastq fastq,2081211600.0,6937372.0,GSM7898620 r1,0:150 1:150,A:561341589;C:327618433;G:629445558;T:562620891;N:185129,150,150,,,561341589,327618433,629445558,562620891,185129,SRX22518171,SRS19529840,SRA1750892,Kanazawa University,Kanazawa University,2,0.68553,0.11302,0.32184,0.0937,0.7654,0.99646,0.53135,0.50819,150,150,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2023-11-14,Undetermined,Undetermined,Scale,Surface Structure
28900,SRR26821455,SRX22518170,SRS19529839,SRP471728,PRJNA1040136,Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs,GSE247669,Transcriptome Analysis,The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.,,pubmed:38385024,,Int 2,GSM7898619,,source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Intact scales|geo loc name:missing|collection date:missing,Int 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,Whole scales,,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,tissue:Whole scales|genotype:Wild type|treatment:Intact scales,GSM7898619,GSM7898619: Int 2; Danio rerio; RNA Seq,GSM7898619 r1,GSM7898619,1,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471728,,,Int_2_R1.fq.gz Int_2_R2.fq.gz,fastq fastq,1639167900.0,5463893.0,GSM7898619 r1,0:150 1:150,A:445245908;C:275437900;G:483637484;T:434649575;N:197033,150,150,,,445245908,275437900,483637484,434649575,197033,SRX22518170,SRS19529839,SRA1750892,Kanazawa University,Kanazawa University,2,0.68102,0.1645,0.41429,0.1457,0.76641,0.9964,0.53665,0.50264,150,150,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2023-11-14,Undetermined,Undetermined,Scale,Surface Structure
28901,SRR26821456,SRX22518169,SRS19529838,SRP471728,PRJNA1040136,Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs,GSE247669,Transcriptome Analysis,The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.,,pubmed:38385024,,Int 1,GSM7898618,,source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Intact scales|geo loc name:missing|collection date:missing,Int 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,Whole scales,,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,tissue:Whole scales|genotype:Wild type|treatment:Intact scales,GSM7898618,GSM7898618: Int 1; Danio rerio; RNA Seq,GSM7898618 r1,GSM7898618,1,Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471728,,,Int_1_R1.fq.gz Int_1_R2.fq.gz,fastq fastq,2309186700.0,7697289.0,GSM7898618 r1,0:150 1:150,A:625174483;C:362587163;G:697384210;T:623845956;N:194888,150,150,,,625174483,362587163,697384210,623845956,194888,SRX22518169,SRS19529838,SRA1750892,Kanazawa University,Kanazawa University,2,0.68814,0.09858,0.30026,0.08284,0.77315,0.99768,0.53387,0.50406,150,150,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2023-11-14,Undetermined,Undetermined,Scale,Surface Structure
29197,SRR27321690,SRX22998813,SRS19963383,SRP479569,PRJNA1055522,Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin,GSE251828,Transcriptome Analysis,This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal  bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition  the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings  together with the identification of novel fin regenerate markers  advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration  we harvested single cells and FACS enriched for siam+  shha+  osterix+  RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.,,pubmed:38318374,,4th round of regeneration,GSM7988809,,source name:Fin|tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing,4th round of regeneration,A reference based on GRCz10  Ensembl annotation e98 was created  by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format.,Fin,Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa  cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS  Roche #10269638001 for 10 min at 28°C. The sample was pipetted slowly up and down with an elongated  flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2  Gibco #12082739. post centrifugation 15 minutes  1800 rpm  4°C  the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM  Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet  GFP and mCherry+ cells were collected in 50 µl 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system  10X library preparation according to the manufacturer's instructions.,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3’ RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer’s guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation,GSM7988809,GSM7988809: 4th round of regeneration; Danio rerio; RNA Seq,GSM7988809 r1,GSM7988809,1,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP479569,,,L33268_osteoblasts_reg4_R2.fastq.gz L33268_osteoblasts_reg4_R1.fastq.gz,fastq fastq,7429523805.0,89512335.0,GSM7988809 r1,0:26 1:57,A:2056160949;C:1638835280;G:1683264344;T:2047119393;N:4143839,26,57,,,2056160949,1638835280,1683264344,2047119393,4143839,SRX22998813,SRS19963383,SRA1774238,"Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden","Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden",2,0.00833,0.93478,0.00199,0.12451,0.9849,0.82418,0.46227,0.53386,26,57,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-12-21,Undetermined,Undetermined,Fin,Surface Structure
29198,SRR27321691,SRX22998812,SRS19963382,SRP479569,PRJNA1055522,Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin,GSE251828,Transcriptome Analysis,This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal  bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition  the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings  together with the identification of novel fin regenerate markers  advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration  we harvested single cells and FACS enriched for siam+  shha+  osterix+  RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.,,pubmed:38318374,,3rd round of regeneration,GSM7988808,,source name:Fin|tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing,3rd round of regeneration,A reference based on GRCz10  Ensembl annotation e98 was created  by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format.,Fin,Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa  cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS  Roche #10269638001 for 10 min at 28°C. The sample was pipetted slowly up and down with an elongated  flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2  Gibco #12082739. post centrifugation 15 minutes  1800 rpm  4°C  the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM  Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet  GFP and mCherry+ cells were collected in 50 µl 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system  10X library preparation according to the manufacturer's instructions.,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3’ RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer’s guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation,GSM7988808,GSM7988808: 3rd round of regeneration; Danio rerio; RNA Seq,GSM7988808 r1,GSM7988808,1,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP479569,,,L33267_osteoblasts_reg3_R1.fastq.gz L33267_osteoblasts_reg3_R2.fastq.gz,fastq fastq,5171923722.0,62312334.0,GSM7988808 r1,0:26 1:57,A:1429339406;C:1125953827;G:1205184308;T:1408611366;N:2834815,26,57,,,1429339406,1125953827,1205184308,1408611366,2834815,SRX22998812,SRS19963382,SRA1774238,"Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden","Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden",2,0.01041,0.92057,0.00236,0.13516,0.98198,0.82244,0.45267,0.53338,26,57,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-12-21,Undetermined,Undetermined,Fin,Surface Structure
29199,SRR27321692,SRX22998811,SRS19963381,SRP479569,PRJNA1055522,Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin,GSE251828,Transcriptome Analysis,This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal  bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition  the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings  together with the identification of novel fin regenerate markers  advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration  we harvested single cells and FACS enriched for siam+  shha+  osterix+  RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.,,pubmed:38318374,,2nd round of regeneration,GSM7988807,,source name:Fin|tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing,2nd round of regeneration,A reference based on GRCz10  Ensembl annotation e98 was created  by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format.,Fin,Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa  cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS  Roche #10269638001 for 10 min at 28°C. The sample was pipetted slowly up and down with an elongated  flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2  Gibco #12082739. post centrifugation 15 minutes  1800 rpm  4°C  the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM  Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet  GFP and mCherry+ cells were collected in 50 µl 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system  10X library preparation according to the manufacturer's instructions.,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3’ RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer’s guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation,GSM7988807,GSM7988807: 2nd round of regeneration; Danio rerio; RNA Seq,GSM7988807 r1,GSM7988807,1,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP479569,,,L32508_osteoblasts_reg2_R1.fastq.gz L32508_osteoblasts_reg2_R2.fastq.gz,fastq fastq,6922720659.0,83406273.0,GSM7988807 r1,0:26 1:57,A:1901173243;C:1540845413;G:1598673449;T:1877295749;N:4732805,26,57,,,1901173243,1540845413,1598673449,1877295749,4732805,SRX22998811,SRS19963381,SRA1774238,"Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden","Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden",2,0.00257,0.93924,0.00083,0.10412,0.99474,0.83023,0.47435,0.51839,26,57,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-12-21,Undetermined,Undetermined,Fin,Surface Structure
29200,SRR27321693,SRX22998810,SRS19963380,SRP479569,PRJNA1055522,Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin,GSE251828,Transcriptome Analysis,This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal  bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition  the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings  together with the identification of novel fin regenerate markers  advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration  we harvested single cells and FACS enriched for siam+  shha+  osterix+  RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.,,pubmed:38318374,,1st round of regeneration,GSM7988806,,source name:Fin|tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing,1st round of regeneration,A reference based on GRCz10  Ensembl annotation e98 was created  by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format.,Fin,Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa  cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS  Roche #10269638001 for 10 min at 28°C. The sample was pipetted slowly up and down with an elongated  flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2  Gibco #12082739. post centrifugation 15 minutes  1800 rpm  4°C  the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM  Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet  GFP and mCherry+ cells were collected in 50 µl 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system  10X library preparation according to the manufacturer's instructions.,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3’ RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer’s guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation,GSM7988806,GSM7988806: 1st round of regeneration; Danio rerio; RNA Seq,GSM7988806 r1,GSM7988806,1,For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP479569,,,L32023_osteoblasts_reg1_R1.fastq.gz L32023_osteoblasts_reg1_R2.fastq.gz,fastq fastq,15070528207.0,181572629.0,GSM7988806 r1,0:26 1:57,A:4238593010;C:3314457079;G:3500292725;T:4013398538;N:3786855,26,57,,,4238593010,3314457079,3500292725,4013398538,3786855,SRX22998810,SRS19963380,SRA1774238,"Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden","Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden",2,0.01031,0.92947,0.00392,0.17331,0.98526,0.81815,0.4321,0.54688,26,57,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-12-21,Undetermined,Undetermined,Fin,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
32858,SRR29482326,SRX24993370,SRS21694834,SRP515140,PRJNA1126247,Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq],GSE270356,Other,Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics  we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly  melanoma only develops from melanocytes lining internal organs  analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression  consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors  allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma  our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations.  Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.,,,,Internal melanocytes,GSM8340241,,source name:Internal melanocytes|tissue:Internal melanocytes|cell type:melanocytes|genotype:mitfa / ; roy /  fish injected with mitfa:GFP|geo loc name:missing|collection date:missing,Internal melanocytes,BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq,Internal melanocytes,,Respective tissues were mechanically dissociated  digested in TrypLE for 45 min Invitrogen  12563011  40uM filtered  spun down  and resuspended in FACs buffer dPBS Mg+/Ca+ free  with 2% FBS  pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification  library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.,mitfa / ; roy /  zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues,tissue:Internal melanocytes|cell type:melanocytes|genotype:mitfa / ; roy /  fish injected with mitfa:GFP,GSM8340241,GSM8340241: Internal melanocytes; Danio rerio; OTHER,GSM8340241 r1,GSM8340241,1,Respective tissues were mechanically dissociated  digested in TrypLE for 45 min Invitrogen  12563011  40uM filtered  spun down  and resuspended in FACs buffer dPBS Mg+/Ca+ free  with 2% FBS  pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification  library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP515140,,,HAR-MI-002_H5GCWBGXF_R2.fastq.gz HAR-MI-002_H5GCWBGXF_R1.fastq.gz,fastq fastq,2957975418.0,34395063.0,GSM8340241 r1,0:26 1:60,A:738954503;C:560052455;G:520746060;T:1137116132;N:1106268,26,60,,,738954503,560052455,520746060,1137116132,1106268,SRX24993370,SRS21694834,SRA1904773,"Insco Lab, Medical Oncology, Dana Farber Cancer Institute","Insco Lab, Medical Oncology, Dana Farber Cancer Institute",2,0.11637,0.84116,0.10894,0.31188,0.98851,0.71526,0.6688,0.60221,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,United States,2024-06-20,Undetermined,Adult,Skin,Surface Structure
32859,SRR29482327,SRX24993369,SRS21694833,SRP515140,PRJNA1126247,Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq],GSE270356,Other,Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics  we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly  melanoma only develops from melanocytes lining internal organs  analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression  consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors  allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma  our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations.  Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.,,,,Cutaneous melanocytes,GSM8340240,,source name:Cutaneous melanocytes|tissue:Cutaneous melanocytes|cell type:melanocytes|genotype:mitfa / ; roy /  fish injected with mitfa:GFP|geo loc name:missing|collection date:missing,Cutaneous melanocytes,BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq,Cutaneous melanocytes,,Respective tissues were mechanically dissociated  digested in TrypLE for 45 min Invitrogen  12563011  40uM filtered  spun down  and resuspended in FACs buffer dPBS Mg+/Ca+ free  with 2% FBS  pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification  library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.,mitfa / ; roy /  zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues,tissue:Cutaneous melanocytes|cell type:melanocytes|genotype:mitfa / ; roy /  fish injected with mitfa:GFP,GSM8340240,GSM8340240: Cutaneous melanocytes; Danio rerio; OTHER,GSM8340240 r1,GSM8340240,1,Respective tissues were mechanically dissociated  digested in TrypLE for 45 min Invitrogen  12563011  40uM filtered  spun down  and resuspended in FACs buffer dPBS Mg+/Ca+ free  with 2% FBS  pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification  library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP515140,,,HAR-MI-001_H5GCWBGXF_R2.fastq.gz HAR-MI-001_H5GCWBGXF_R1.fastq.gz,fastq fastq,2680460212.0,31168142.0,GSM8340240 r1,0:26 1:60,A:704357434;C:519158361;G:467098420;T:988838604;N:1007393,26,60,,,704357434,519158361,467098420,988838604,1007393,SRX24993369,SRS21694833,SRA1904773,"Insco Lab, Medical Oncology, Dana Farber Cancer Institute","Insco Lab, Medical Oncology, Dana Farber Cancer Institute",2,0.11679,0.81545,0.10693,0.5033,0.9808,0.76404,0.44749,0.57623,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,United States,2024-06-20,Undetermined,Adult,Skin,Surface Structure
33894,SRR30866028,SRX26263941,SRS22803195,SRP536275,PRJNA1168148,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq],GSE278653,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.,,,,m4b mut melanoma  biol rep 2,GSM8552314,,source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing,m4b mut melanoma  biol rep 2,Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample,skin,,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI,GSM8552314,GSM8552314: m4b mut melanoma  biol rep 2; Danio rerio; RNA Seq,GSM8552314 r1,GSM8552314,1,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,MKO2_S39_R1_001.fastq.gz MKO2_S39_R2_001.fastq.gz,fastq fastq,3705364625.0,14164066.0,GSM8552314 r1,0:126.72 1:134.89,A:785806700;C:949078797;G:1178279032;T:784972987;N:7227109,126,134,,,785806700,949078797,1178279032,784972987,7227109,SRX26263941,SRS22803195,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,India,2024-10-02,Undetermined,Undetermined,Skin,Surface Structure
33895,SRR30866029,SRX26263940,SRS22803194,SRP536275,PRJNA1168148,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq],GSE278653,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.,,,,m4b mut melanoma  biol rep 1,GSM8552313,,source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing,m4b mut melanoma  biol rep 1,Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample,skin,,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI,GSM8552313,GSM8552313: m4b mut melanoma  biol rep 1; Danio rerio; RNA Seq,GSM8552313 r1,GSM8552313,1,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,MKO1_S38_R1_001.fastq.gz MKO1_S38_R2_001.fastq.gz,fastq fastq,4779377372.0,18058294.0,GSM8552313 r1,0:128.72 1:135.94,A:1016908920;C:1236613888;G:1502465334;T:1018053808;N:5335422,128,135,,,1016908920,1236613888,1502465334,1018053808,5335422,SRX26263940,SRS22803194,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,India,2024-10-02,Undetermined,Undetermined,Skin,Surface Structure
33896,SRR30866030,SRX26263939,SRS22803193,SRP536275,PRJNA1168148,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq],GSE278653,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.,,,,wild type melanoma control  biol rep 2,GSM8552312,,source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing,wild type melanoma control  biol rep 2,Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample,skin,,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI,GSM8552312,GSM8552312: wild type melanoma control  biol rep 2; Danio rerio; RNA Seq,GSM8552312 r1,GSM8552312,1,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,EV2_S37_R1_001.fastq.gz EV2_S37_R2_001.fastq.gz,fastq fastq,5427379509.0,19981504.0,GSM8552312 r1,0:133.16 1:138.46,A:1136639418;C:1414638483;G:1736492639;T:1137614638;N:1994331,133,138,,,1136639418,1414638483,1736492639,1137614638,1994331,SRX26263939,SRS22803193,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,India,2024-10-02,Undetermined,Undetermined,Skin,Surface Structure
33897,SRR30866031,SRX26263938,SRS22803192,SRP536275,PRJNA1168148,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq],GSE278653,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.,,,,wild type melanoma control  biol rep 1,GSM8552311,,source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing,wild type melanoma control  biol rep 1,Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample,skin,,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI,GSM8552311,GSM8552311: wild type melanoma control  biol rep 1; Danio rerio; RNA Seq,GSM8552311 r1,GSM8552311,1,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,EV1_S36_R1_001.fastq.gz EV1_S36_R2_001.fastq.gz,fastq fastq,5248108957.0,19087024.0,GSM8552311 r1,0:135.12 1:139.84,A:1112163842;C:1354895660;G:1658732932;T:1120342985;N:1973538,135,139,,,1112163842,1354895660,1658732932,1120342985,1973538,SRX26263938,SRS22803192,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,India,2024-10-02,Undetermined,Undetermined,Skin,Surface Structure
33898,SRR30866032,SRX26263937,SRS22803191,SRP536275,PRJNA1168148,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq],GSE278653,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.,,,,melanophore  biol rep 2,GSM8552310,,source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing,melanophore  biol rep 2,Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample,skin,,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,tissue:skin|cell type:melanophore|genotype:WT|treatment:No,GSM8552310,GSM8552310: melanophore  biol rep 2; Danio rerio; RNA Seq,GSM8552310 r1,GSM8552310,1,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,WT2_S41_R1_001.fastq.gz WT2_S41_R2_001.fastq.gz,fastq fastq,4636631881.0,16340506.0,GSM8552310 r1,0:140.47 1:143.28,A:1114533149;C:1104066636;G:1293649625;T:1122672029;N:1710442,140,143,,,1114533149,1104066636,1293649625,1122672029,1710442,SRX26263937,SRS22803191,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,India,2024-10-02,Undetermined,Undetermined,Skin,Surface Structure
33899,SRR30866033,SRX26263936,SRS22803190,SRP536275,PRJNA1168148,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq],GSE278653,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.,,,,melanophore  biol rep 1,GSM8552309,,source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing,melanophore  biol rep 1,Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample,skin,,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,tissue:skin|cell type:melanophore|genotype:WT|treatment:No,GSM8552309,GSM8552309: melanophore  biol rep 1; Danio rerio; RNA Seq,GSM8552309 r1,GSM8552309,1,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,WT1_S40_R1_001.fastq.gz WT1_S40_R2_001.fastq.gz,fastq fastq,5185761246.0,18118534.0,GSM8552309 r1,0:141.81 1:144.40,A:1231235669;C:1235759770;G:1476864583;T:1240636871;N:1264353,141,144,,,1231235669,1235759770,1476864583,1240636871,1264353,SRX26263936,SRS22803190,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,India,2024-10-02,Undetermined,Undetermined,Skin,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
34143,SRR31364121,SRX26737888,SRS23227909,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset3 BMPi LDN RFP,GSM8635057,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|treatment:LDN|geo loc name:missing|collection date:missing,dataset3 BMPi LDN RFP,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type|treatment:LDN,GSM8635057,GSM8635057: dataset3 BMPi LDN RFP; Danio rerio; RNA Seq,GSM8635057 r1,GSM8635057,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,LDN_RFP_S4_L001_I1_001.fastq.gz LDN_RFP_S4_L001_I2_001.fastq.gz LDN_RFP_S4_L001_R1_001.fastq.gz LDN_RFP_S4_L001_R2_001.fastq.gz,fastq fastq fastq fastq,4755245952.0,34458304.0,GSM8635057 r1,0:10 1:10 2:28 3:90,A:926644119;C:661476939;G:733308280;T:779560094;N:257928,10,10,28,90,926644119,661476939,733308280,779560094,257928,SRX26737888,SRS23227909,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34144,SRR31364122,SRX26737887,SRS23227908,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset3 BMPi LDN no RFP,GSM8635056,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|treatment:LDN|geo loc name:missing|collection date:missing,dataset3 BMPi LDN no RFP,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type|treatment:LDN,GSM8635056,GSM8635056: dataset3 BMPi LDN no RFP; Danio rerio; RNA Seq,GSM8635056 r1,GSM8635056,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,LDN_noRFP_S3_L001_I1_001.fastq.gz LDN_noRFP_S3_L001_I2_001.fastq.gz LDN_noRFP_S3_L001_R1_001.fastq.gz LDN_noRFP_S3_L001_R2_001.fastq.gz,fastq fastq fastq fastq,5062759908.0,36686666.0,GSM8635056 r1,0:10 1:10 2:28 3:90,A:992393338;C:660757137;G:728422640;T:919955090;N:271735,10,10,28,90,992393338,660757137,728422640,919955090,271735,SRX26737887,SRS23227908,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34145,SRR31364123,SRX26737886,SRS23227906,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset3 BMPi DMSO RFP,GSM8635055,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|treatment:DMSO|geo loc name:missing|collection date:missing,dataset3 BMPi DMSO RFP,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type|treatment:DMSO,GSM8635055,GSM8635055: dataset3 BMPi DMSO RFP; Danio rerio; RNA Seq,GSM8635055 r1,GSM8635055,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,DMSO_RFP_S2_L001_I1_001.fastq.gz DMSO_RFP_S2_L001_I2_001.fastq.gz DMSO_RFP_S2_L001_R1_001.fastq.gz DMSO_RFP_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,4298328228.0,31147306.0,GSM8635055 r1,0:10 1:10 2:28 3:90,A:816881516;C:611689038;G:673484940;T:700975488;N:226558,10,10,28,90,816881516,611689038,673484940,700975488,226558,SRX26737886,SRS23227906,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34146,SRR31364124,SRX26737885,SRS23227907,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset3 BMPi DMSO no RFP,GSM8635054,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|treatment:DMSO|geo loc name:missing|collection date:missing,dataset3 BMPi DMSO no RFP,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type|treatment:DMSO,GSM8635054,GSM8635054: dataset3 BMPi DMSO no RFP; Danio rerio; RNA Seq,GSM8635054 r1,GSM8635054,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,DMSO_noRFP_S1_L001_I1_001.fastq.gz DMSO_noRFP_S1_L001_I2_001.fastq.gz DMSO_noRFP_S1_L001_R1_001.fastq.gz DMSO_noRFP_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,4086026820.0,29608890.0,GSM8635054 r1,0:10 1:10 2:28 3:90,A:794711851;C:543564325;G:594229898;T:732076441;N:217585,10,10,28,90,794711851,543564325,594229898,732076441,217585,SRX26737885,SRS23227907,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34147,SRR31364125,SRX26737884,SRS23227904,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset2 positions base,GSM8635053,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing,dataset2 positions base,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type,GSM8635053,GSM8635053: dataset2 positions base; Danio rerio; RNA Seq,GSM8635053 r1,GSM8635053,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,tip_rest_S3_L001_I1_001.fastq.gz tip_rest_S3_L001_R1_001.fastq.gz tip_rest_S3_L001_R2_001.fastq.gz,fastq fastq fastq,2562938024.0,27858022.0,GSM8635053 r1,0:8 1:28 2:56,A:465025810;C:315982726;G:357090865;T:420656906;N:1292925,8,28,56,,465025810,315982726,357090865,420656906,1292925,SRX26737884,SRS23227904,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34148,SRR31364126,SRX26737883,SRS23227905,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset2 positions edge,GSM8635052,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing,dataset2 positions edge,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type,GSM8635052,GSM8635052: dataset2 positions edge; Danio rerio; RNA Seq,GSM8635052 r1,GSM8635052,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,tip_white_S2_L001_I1_001.fastq.gz tip_white_S2_L001_R1_001.fastq.gz tip_white_S2_L001_R2_001.fastq.gz,fastq fastq fastq,3561960136.0,38716958.0,GSM8635052 r1,0:8 1:28 2:56,A:640222776;C:444619403;G:502208963;T:579280385;N:1818121,8,28,56,,640222776,444619403,502208963,579280385,1818121,SRX26737883,SRS23227905,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34149,SRR31364127,SRX26737882,SRS23227903,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset1 stages rep4,GSM8635051,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing,dataset1 stages rep4,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type,GSM8635051,GSM8635051: dataset1 stages rep4; Danio rerio; RNA Seq,GSM8635051 r1,GSM8635051,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,dorsal_4_S4_L001_I1_001.fastq.gz dorsal_4_S4_L001_R1_001.fastq.gz dorsal_4_S4_L001_R2_001.fastq.gz,fastq fastq fastq,2719423400.0,29558950.0,GSM8635051 r1,0:8 1:28 2:56,A:491347530;C:348666057;G:386184840;T:428683151;N:419622,8,28,56,,491347530,348666057,386184840,428683151,419622,SRX26737882,SRS23227903,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34150,SRR31364128,SRX26737881,SRS23227902,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset1 stages rep3,GSM8635050,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing,dataset1 stages rep3,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type,GSM8635050,GSM8635050: dataset1 stages rep3; Danio rerio; RNA Seq,GSM8635050 r1,GSM8635050,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,dorsal_3_S3_L001_I1_001.fastq.gz dorsal_3_S3_L001_R1_001.fastq.gz dorsal_3_S3_L001_R2_001.fastq.gz,fastq fastq fastq,2602160384.0,28284352.0,GSM8635050 r1,0:8 1:28 2:56,A:469841004;C:333542050;G:367823398;T:412316065;N:401195,8,28,56,,469841004,333542050,367823398,412316065,401195,SRX26737881,SRS23227902,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34151,SRR31364129,SRX26737880,SRS23227901,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset1 stages rep2,GSM8635049,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing,dataset1 stages rep2,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type,GSM8635049,GSM8635049: dataset1 stages rep2; Danio rerio; RNA Seq,GSM8635049 r1,GSM8635049,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,dorsal_2_S2_L001_I1_001.fastq.gz dorsal_2_S2_L001_R1_001.fastq.gz dorsal_2_S2_L001_R2_001.fastq.gz,fastq fastq fastq,3187245056.0,34643968.0,GSM8635049 r1,0:8 1:28 2:56,A:584729856;C:395297406;G:447424733;T:512111292;N:498921,8,28,56,,584729856,395297406,447424733,512111292,498921,SRX26737880,SRS23227901,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34152,SRR31364130,SRX26737879,SRS23227900,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset1 stages rep1,GSM8635048,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing,dataset1 stages rep1,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type,GSM8635048,GSM8635048: dataset1 stages rep1; Danio rerio; RNA Seq,GSM8635048 r1,GSM8635048,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,dorsal_1_S1_L001_I1_001.fastq.gz dorsal_1_S1_L001_R1_001.fastq.gz dorsal_1_S1_L001_R2_001.fastq.gz,fastq fastq fastq,2963326992.0,32210076.0,GSM8635048 r1,0:8 1:28 2:56,A:550098255;C:357880179;G:398034107;T:497290530;N:461185,8,28,56,,550098255,357880179,398034107,497290530,461185,SRX26737879,SRS23227900,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,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
40334,SRR3086895,SRX1518389,SRS1236744,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF Uninjured Fin 2,GSM2028020,,tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1,ZF Uninjured Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Uninjured fins,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:N1,GSM2028020,GSM2028020: ZF Uninjured Fin 2; Danio rerio; RNA Seq,GSM2028020,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Un2-1.fastq.gz,fastq,800000000.0,16000000.0,GSM2028020 r1,0:50,A:210926663;C:190496048;G:184518152;T:213985916;N:73221,50,,,,210926663,190496048,184518152,213985916,73221,SRX1518389,SRS1236744,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.91126,,0.08857,,0.72054,,0.44807,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40335,SRR3086896,SRX1518389,SRS1236744,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF Uninjured Fin 2,GSM2028020,,tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1,ZF Uninjured Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Uninjured fins,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:N1,GSM2028020,GSM2028020: ZF Uninjured Fin 2; Danio rerio; RNA Seq,GSM2028020,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Un2-2.fastq.gz,fastq,800000000.0,16000000.0,GSM2028020 r2,0:50,A:210822728;C:190175530;G:185124231;T:213867287;N:10224,50,,,,210822728,190175530,185124231,213867287,10224,SRX1518389,SRS1236744,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.90559,,0.08872,,0.7194,,0.43319,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40336,SRR3086897,SRX1518389,SRS1236744,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF Uninjured Fin 2,GSM2028020,,tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1,ZF Uninjured Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Uninjured fins,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:N1,GSM2028020,GSM2028020: ZF Uninjured Fin 2; Danio rerio; RNA Seq,GSM2028020,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Un2-3.fastq.gz,fastq,46067800.0,921356.0,GSM2028020 r3,0:50,A:12182398;C:10879021;G:10673094;T:12333021;N:266,50,,,,12182398,10879021,10673094,12333021,266,SRX1518389,SRS1236744,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.89253,,0.08727,,0.72094,,0.45046,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40337,SRR3086892,SRX1518388,SRS1236746,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF Uninjured Fin 1,GSM2028019,,tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1,ZF Uninjured Fin 1,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Uninjured fins,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:N1,GSM2028019,GSM2028019: ZF Uninjured Fin 1; Danio rerio; RNA Seq,GSM2028019,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Un1-1.fastq.gz,fastq,800000000.0,16000000.0,GSM2028019 r1,0:50,A:206270357;C:193369997;G:191677237;T:208652195;N:30214,50,,,,206270357,193369997,191677237,208652195,30214,SRX1518388,SRS1236746,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.91334,,0.07414,,0.73034,,0.44343,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40338,SRR3086893,SRX1518388,SRS1236746,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF Uninjured Fin 1,GSM2028019,,tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1,ZF Uninjured Fin 1,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Uninjured fins,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:N1,GSM2028019,GSM2028019: ZF Uninjured Fin 1; Danio rerio; RNA Seq,GSM2028019,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Un1-2.fastq.gz,fastq,493137350.0,9862747.0,GSM2028019 r2,0:50,A:127272457;C:119005858;G:118176094;T:128679179;N:3762,50,,,,127272457,119005858,118176094,128679179,3762,SRX1518388,SRS1236746,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.90901,,0.07418,,0.73085,,0.44107,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40339,SRR3086894,SRX1518388,SRS1236746,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF Uninjured Fin 1,GSM2028019,,tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1,ZF Uninjured Fin 1,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Uninjured fins,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:N1,GSM2028019,GSM2028019: ZF Uninjured Fin 1; Danio rerio; RNA Seq,GSM2028019,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Un1-3.fastq.gz,fastq,800000000.0,16000000.0,GSM2028019 r3,0:50,A:206410293;C:193573258;G:191140232;T:208806339;N:69878,50,,,,206410293,193573258,191140232,208806339,69878,SRX1518388,SRS1236746,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.91744,,0.07298,,0.72847,,0.44383,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40340,SRR3086888,SRX1518387,SRS1236747,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF 4dpa Fin 2,GSM2028018,,tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation,ZF 4dpa Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Fins 4d post amputation,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:Fin Amputation,GSM2028018,GSM2028018: ZF 4dpa Fin 2; Danio rerio; RNA Seq,GSM2028018,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Reg2-1.fastq.gz,fastq,800000000.0,16000000.0,GSM2028018 r1,0:50,A:208862526;C:192270727;G:188582591;T:210215639;N:68517,50,,,,208862526,192270727,188582591,210215639,68517,SRX1518387,SRS1236747,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.92514,,0.07091,,0.70638,,0.46239,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40341,SRR3086889,SRX1518387,SRS1236747,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF 4dpa Fin 2,GSM2028018,,tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation,ZF 4dpa Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Fins 4d post amputation,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:Fin Amputation,GSM2028018,GSM2028018: ZF 4dpa Fin 2; Danio rerio; RNA Seq,GSM2028018,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Reg2-2.fastq.gz,fastq,800000000.0,16000000.0,GSM2028018 r2,0:50,A:208854177;C:192161932;G:188871135;T:210062448;N:50308,50,,,,208854177,192161932,188871135,210062448,50308,SRX1518387,SRS1236747,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.92252,,0.07056,,0.70694,,0.45392,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40342,SRR3086890,SRX1518387,SRS1236747,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF 4dpa Fin 2,GSM2028018,,tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation,ZF 4dpa Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Fins 4d post amputation,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:Fin Amputation,GSM2028018,GSM2028018: ZF 4dpa Fin 2; Danio rerio; RNA Seq,GSM2028018,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Reg2-3.fastq.gz,fastq,800000000.0,16000000.0,GSM2028018 r3,0:50,A:208765699;C:191936198;G:189409194;T:209878960;N:9949,50,,,,208765699,191936198,189409194,209878960,9949,SRX1518387,SRS1236747,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.91451,,0.06995,,0.70741,,0.45822,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40343,SRR3086891,SRX1518387,SRS1236747,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF 4dpa Fin 2,GSM2028018,,tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation,ZF 4dpa Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Fins 4d post amputation,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:Fin Amputation,GSM2028018,GSM2028018: ZF 4dpa Fin 2; Danio rerio; RNA Seq,GSM2028018,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Reg2-4.fastq.gz,fastq,123651950.0,2473039.0,GSM2028018 r4,0:50,A:32365652;C:29515195;G:29236871;T:32533508;N:724,50,,,,32365652,29515195,29236871,32533508,724,SRX1518387,SRS1236747,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.91437,,0.07079,,0.70867,,0.46558,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure