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2,179 rows where devstage_curation_coarse = "Undetermined" and technology = "unknown"

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tissue_curation >10

experiment.library_selection 10

experiment.platform 6

experiment.library_strategy 5

experiment.library_source 2

experiment.library_layout 2

technology 1

  • unknown · 2,179 ✖

devstage_curation_coarse 1

  • Undetermined · 2,179 ✖

devstage_curation 1

Link 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 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 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 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 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 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
100 100 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
147 147 DRR051067 DRX045959 DRS057267 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.     These cells are from the same fish as h62A GFP plus Tel GFP cells from telencephalon of hspGFF62A;UAS:GFP transgenic zebrafish SAMD00044994   sample name:h62A GFP minus Tel|tissue type:brain|genotype:hspGFF62A;UAS:GFP                 Illumina HiSeq 2500 paired end sequencing of SAMD00044994 DRX045959 h62A GFP minus Tel 1 cDNA synthesis : clontech SMARTer v3 > Library prep : Illumina Nextera XT DNA Library Preparation Kits   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 2500 paired end sequencing of SAMD00044994       17913873600.0 89569368.0 DRR051067 0:100 1:100 A:5009629866;C:3957379257;G:3797879751;T:5144366288;N:4618438 100 100     5009629866 3957379257 3797879751 5144366288 4618438 DRX045959 DRS057267 DRA004277 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 2 0.89075 0.89087 0.23044 0.23295 0.69493 0.69769 0.5366 0.54852 100 100 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified nextera bulk unknown unknown   Japan 2018-01-06 Undetermined Undetermined Brain Nervous System
151 151 DRR051063 DRX045955 DRS057266 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.     These cells are from the same fish as 120A GFP plus Tel GFP cells from telencephalon of SAGFFLF120A;UAS:GFP transgenic zebrafish SAMD00044987   sample name:120A GFP minus Tel|tissue type:brain|genotype:SAGFFLF120A;UAS:GFP                 Illumina HiSeq 2500 paired end sequencing of SAMD00044987 DRX045955 120A GFP minus Tel 1 cDNA synthesis : clontech SMARTer v2 > Library prep : Illumina TrunSeq DNA Sample Preparation Kits   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 2500 paired end sequencing of SAMD00044987       15411400120.0 76294060.0 DRR051063 0:101 1:101 A:4583085286;C:3082552426;G:3134669086;T:4606055524;N:5037798 101 101     4583085286 3082552426 3134669086 4606055524 5037798 DRX045955 DRS057266 DRA004273 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 2 0.89184 0.8842 0.30246 0.30334 0.69232 0.705 0.52824 0.51492 101 101 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   Japan 2018-01-06 Undetermined Undetermined Brain Nervous System
5793 5793 ERR1955208 ERX2020800 ERS1697077 ERP017053 PRJEB15333 Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247 Other In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08     Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations SAMEA104033184 EMBL EUROPEAN BIOINFORMATICS INSTITUTE ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033184|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 2|common name:zebrafish|sample name:Zebrafish.Testis 2|scientific name:Danio rerio|strain:AB|tissue type:testis                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP017053 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16 zebrafish_testis_2.conserved.1.fastq.gz zebrafish_testis_2.conserved.2.fastq.gz fastq fastq 46555372886.0 230472143.0 ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16 0:101 1:101 A:12260062264;C:10888457642;G:11605642683;T:11637267744;N:163942553 101 101     12260062264 10888457642 11605642683 11637267744 163942553 ERX2020800 ERS1697077 ERA904389 EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive EMBL EUROPEAN BIOINFORMATICS INSTITUTE 2 0.93165 0.92785 0.29822 0.32141 0.71386 0.71971 0.66173 0.63843 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2017-01-31 Undetermined Undetermined Gonad Reproductive System
5794 5794 ERR1955207 ERX2020799 ERS1697076 ERP017053 PRJEB15333 Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247 Other In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08     Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations SAMEA104033183 EMBL EUROPEAN BIOINFORMATICS INSTITUTE ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033183|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 1|common name:zebrafish|sample name:Zebrafish.Testis 1|scientific name:Danio rerio|strain:AB|tissue type:testis                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP017053 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16 zebrafish_testis_1.conserved.1.fastq.gz zebrafish_testis_1.conserved.2.fastq.gz fastq fastq 41056086708.0 203247954.0 ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15 0:101 1:101 A:10675591750;C:9672762387;G:10139834713;T:10380949257;N:186948601 101 101     10675591750 9672762387 10139834713 10380949257 186948601 ERX2020799 ERS1697076 ERA904389 EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive EMBL EUROPEAN BIOINFORMATICS INSTITUTE 2 0.92308 0.9157 0.30221 0.31293 0.68276 0.68836 0.56114 0.5857 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2017-01-31 Undetermined Undetermined Gonad Reproductive System
9918 9918 ERR5059480 ERX4865549 ERS5523939 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05     aAM 6h rep1 JD AD30 PRPN1970901   ENA FIRST PUBLIC:2022 07 05T12:06:33Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:33Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AD30_PRPN197090.tar.gz nanopore 3739882337.0 3148027.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 0:1188.01 A:1054501690;C:834193435;G:847423060;T:1003764152;N:0 1188       1054501690 834193435 847423060 1003764152 0 ERX4865549 ERS5523939 ERA3206712 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9920 9920 ERR4330695 ERX4277529 ERS4811113 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 2h rep1 WT 2h rep1 SAMEA7050483 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7050483|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD B2 PDBN005727|common name:zebrafish|sample name:JD B2 PDBN005727                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-B2_PDBN005727.tar.gz fastq     ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1                       ERX4277529   ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9921 9921 ERR4327134 ERX4273968 ERS4808634 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep2 WT 4h rep2 SAMEA7048000 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7048000|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD AM39 PDBN042841|common name:zebrafish|sample name:JD AM39 PDBN042841                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AM39_PDBN042841.tar.gz nanopore 719646261.0 897768.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 0:801.59 A:210217908;C:152963718;G:157393834;T:199070801;N:0 801       210217908 152963718 157393834 199070801 0 ERX4273968 ERS4808634 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9922 9922 ERR4330696 ERX4277530 ERS4811114 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep1 WT 4h rep1 JD C3 PDBN006177   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-C3_PDBN006177.tar.gz nanopore 4240799932.0 4331689.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 0:979.02 A:1229803846;C:914476674;G:943703560;T:1152815852;N:0 979       1229803846 914476674 943703560 1152815852 0 ERX4277530 ERS4811114 ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9923 9923 ERR4327135 ERX4273969 ERS4808635 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep1 WT 6h rep1 JD AC29 PDBN024889   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AC29_PDBN024889.tar.gz nanopore 1900324756.0 2013035.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 0:944.01 A:549431032;C:411510218;G:422103800;T:517279706;N:0 944       549431032 411510218 422103800 517279706 0 ERX4273969 ERS4808635 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9924 9924 ERR4326350 ERX4273208 ERS4808398 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   430 LNA 6h rep1 430 LNA 6h rep1 SAMEA7047764 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7047764|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD H8 PDBN059569|common name:zebrafish|sample name:JD H8 PDBN059569                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-H8_PDBN059569.tar.gz nanopore 722817654.0 657296.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 0:1099.68 A:206996491;C:157022109;G:155085437;T:203713617;N:0 1099       206996491 157022109 155085437 203713617 0 ERX4273208 ERS4808398 ERA2764399 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9925 9925 ERR4335436 ERX4282181 ERS4818366 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep2 WT 6h rep2 JD W23 PRPN039928   ENA FIRST PUBLIC:2022 07 05T12:06:24Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:24Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:456 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-W23_PRPN039928.tar.gz nanopore 1268761319.0 1385621.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:457 1 0:915.66 A:366823862;C:275507684;G:284634548;T:341795225;N:0 915       366823862 275507684 284634548 341795225 0 ERX4282181 ERS4818366 ERA2769006 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9926 9926 ERR4321680 ERX4268538 ERS4808125 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 0h rep1 WT 0h rep1 JD A1 GDDN003032   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 GridION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE GridION   ERP122761 GridION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-A1_GDDN003032.tar.gz nanopore 753417826.0 698774.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 0:1078.20 A:214525685;C:165042952;G:171160615;T:202688574;N:0 1078       214525685 165042952 171160615 202688574 0 ERX4268538 ERS4808125 ERA2763718 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
10170 10170 ERR375749 ERX348126 ERS337052 ERP003756 PRJEB4464 Zebrafish olfactory transcriptomics Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742 Transcriptome Analysis The olfactory gene repertoire is largely species specific shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families iii its biology is well known iv is a commonly used model organism and it is suitable for subsequent functional analysis.         SAMEA2168448 SC ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:06Z|External Id:SAMEA2168448|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:06Z|INSDC status:public|Submitter Id:ZF OE3 sc 2013 08 12T10:36:21Z 1677721|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE3 sc 2013 08 12T10:36:21Z 1677721|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing SC EXP 10586 2#3 7941068 Illumina sequencing of library 7941068 constructed from sample accession ERS337052 for study accession ERP003756. This is part of an Illumina multiplexed sequencing run 10586 2. This submission includes reads tagged with the sequence TTAGGC. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16 10586_2#3.cram cram 11298599000.0 56492995.0 SC RUN 10586 2#3 0:100 1:100 A:3356877540;C:2323057831;G:2299363865;T:3303865798;N:15433966 100 100     3356877540 2323057831 2299363865 3303865798 15433966 ERX348126 ERS337052 ERA267455 SC Wellcome Sanger Institute 2 0.91061 0.90958 0.1659 0.16567 0.68398 0.68645 0.53954 0.54231 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-11-25 Undetermined Undetermined Brain Nervous System
10171 10171 ERR375748 ERX348125 ERS337051 ERP003756 PRJEB4464 Zebrafish olfactory transcriptomics Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742 Transcriptome Analysis The olfactory gene repertoire is largely species specific shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families iii its biology is well known iv is a commonly used model organism and it is suitable for subsequent functional analysis.         SAMEA2168447 SC ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:13Z|External Id:SAMEA2168447|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:13Z|INSDC status:public|Submitter Id:ZF OE2 sc 2013 08 12T10:36:20Z 1677720|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE2 sc 2013 08 12T10:36:20Z 1677720|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing SC EXP 10586 2#2 7941067 Illumina sequencing of library 7941067 constructed from sample accession ERS337051 for study accession ERP003756. This is part of an Illumina multiplexed sequencing run 10586 2. This submission includes reads tagged with the sequence CGATGT. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16 10586_2#2.cram cram 10462424000.0 52312120.0 SC RUN 10586 2#2 0:100 1:100 A:3035632557;C:2208885147;G:2197231235;T:3006145790;N:14529271 100 100     3035632557 2208885147 2197231235 3006145790 14529271 ERX348125 ERS337051 ERA267455 SC Wellcome Sanger Institute 2 0.91417 0.91329 0.15428 0.15477 0.66882 0.66896 0.52191 0.51898 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-11-25 Undetermined Undetermined Brain Nervous System
10172 10172 ERR375747 ERX348124 ERS337050 ERP003756 PRJEB4464 Zebrafish olfactory transcriptomics Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742 Transcriptome Analysis The olfactory gene repertoire is largely species specific shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families iii its biology is well known iv is a commonly used model organism and it is suitable for subsequent functional analysis.         SAMEA2168446 SC ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:06Z|External Id:SAMEA2168446|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:06Z|INSDC status:public|Submitter Id:ZF OE1 sc 2013 08 12T10:36:17Z 1677719|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE1 sc 2013 08 12T10:36:17Z 1677719|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing SC EXP 10586 2#1 7941066 Illumina sequencing of library 7941066 constructed from sample accession ERS337050 for study accession ERP003756. This is part of an Illumina multiplexed sequencing run 10586 2. This submission includes reads tagged with the sequence ATCACG. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16 10586_2#1.cram cram 10377603200.0 51888016.0 SC RUN 10586 2#1 0:100 1:100 A:3021582125;C:2187474575;G:2170525378;T:2983668309;N:14352813 100 100     3021582125 2187474575 2170525378 2983668309 14352813 ERX348124 ERS337050 ERA267455 SC Wellcome Sanger Institute 2 0.90978 0.90815 0.15565 0.15454 0.67322 0.67476 0.52923 0.51842 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-11-25 Undetermined Undetermined Brain Nervous System
10173 10173 ERR375746 ERX348123 ERS337052 ERP003756 PRJEB4464 Zebrafish olfactory transcriptomics Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742 Transcriptome Analysis The olfactory gene repertoire is largely species specific shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families iii its biology is well known iv is a commonly used model organism and it is suitable for subsequent functional analysis.         SAMEA2168448 SC ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:06Z|External Id:SAMEA2168448|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:06Z|INSDC status:public|Submitter Id:ZF OE3 sc 2013 08 12T10:36:21Z 1677721|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE3 sc 2013 08 12T10:36:21Z 1677721|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing SC EXP 10586 1#3 7941068 Illumina sequencing of library 7941068 constructed from sample accession ERS337052 for study accession ERP003756. This is part of an Illumina multiplexed sequencing run 10586 1. This submission includes reads tagged with the sequence TTAGGC. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16 10586_1#3.cram cram 11455059800.0 57275299.0 SC RUN 10586 1#3 0:100 1:100 A:3406564785;C:2353388363;G:2329218644;T:3351844154;N:14043854 100 100     3406564785 2353388363 2329218644 3351844154 14043854 ERX348123 ERS337052 ERA267455 SC Wellcome Sanger Institute 2 0.91087 0.90879 0.16647 0.16616 0.6832 0.68436 0.54098 0.53604 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-11-25 Undetermined Undetermined Brain Nervous System
10174 10174 ERR375745 ERX348122 ERS337051 ERP003756 PRJEB4464 Zebrafish olfactory transcriptomics Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742 Transcriptome Analysis The olfactory gene repertoire is largely species specific shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families iii its biology is well known iv is a commonly used model organism and it is suitable for subsequent functional analysis.         SAMEA2168447 SC ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:13Z|External Id:SAMEA2168447|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:13Z|INSDC status:public|Submitter Id:ZF OE2 sc 2013 08 12T10:36:20Z 1677720|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE2 sc 2013 08 12T10:36:20Z 1677720|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing SC EXP 10586 1#2 7941067 Illumina sequencing of library 7941067 constructed from sample accession ERS337051 for study accession ERP003756. This is part of an Illumina multiplexed sequencing run 10586 1. This submission includes reads tagged with the sequence CGATGT. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16 10586_1#2.cram cram 10636681200.0 53183406.0 SC RUN 10586 1#2 0:100 1:100 A:3088549841;C:2244455059;G:2232424530;T:3058125106;N:13126664 100 100     3088549841 2244455059 2232424530 3058125106 13126664 ERX348122 ERS337051 ERA267455 SC Wellcome Sanger Institute 2 0.9134 0.91251 0.15433 0.154 0.66849 0.66949 0.52089 0.53096 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-11-25 Undetermined Undetermined Brain Nervous System
10175 10175 ERR375744 ERX348121 ERS337050 ERP003756 PRJEB4464 Zebrafish olfactory transcriptomics Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742 Transcriptome Analysis The olfactory gene repertoire is largely species specific shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families iii its biology is well known iv is a commonly used model organism and it is suitable for subsequent functional analysis.         SAMEA2168446 SC ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:06Z|External Id:SAMEA2168446|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:06Z|INSDC status:public|Submitter Id:ZF OE1 sc 2013 08 12T10:36:17Z 1677719|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE1 sc 2013 08 12T10:36:17Z 1677719|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing SC EXP 10586 1#1 7941066 Illumina sequencing of library 7941066 constructed from sample accession ERS337050 for study accession ERP003756. This is part of an Illumina multiplexed sequencing run 10586 1. This submission includes reads tagged with the sequence ATCACG. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16 10586_1#1.cram cram 10534775800.0 52673879.0 SC RUN 10586 1#1 0:100 1:100 A:3069581091;C:2219273001;G:2202030288;T:3030929981;N:12961439 100 100     3069581091 2219273001 2202030288 3030929981 12961439 ERX348121 ERS337050 ERA267455 SC Wellcome Sanger Institute 2 0.91028 0.90986 0.15668 0.15607 0.67456 0.67472 0.52998 0.49845 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-11-25 Undetermined Undetermined Brain Nervous System
10206 10206 ERR6474244 ERX6101519 ERS7377049 ERP131171 PRJEB46937 RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E-MTAB-10834 Other RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq. ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11   Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour o… InputFISH E MTAB 10834:InputFISH   isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11                 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E MTAB 10834:InputFISH p InputFISH p RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubati… Experimental Factor: immunoprecipitate:input DNA|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 550   ERP131171 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11 InputFISH.R1.fastq.gz InputFISH.R2.fastq.gz fastq fastq 2014534500.0 24271500.0 E MTAB 10834:InputFISH.R 0:40 1:43 A:435725523;C:539145149;G:601092466;T:438298953;N:272409 40 43     435725523 539145149 601092466 438298953 272409 ERX6101519 ERS7377049 ERA5607540 Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive 2 0.394 0.34957 0.09053 0.09378 0.96485 0.97323 0.73467 0.62676 40 43 B B biological fallback assumption illumina nextseq unknown small_rna unknown bulk unknown unknown   Sweden 2023-08-11 Undetermined Undetermined Multi-tissue Multi-system
10207 10207 ERR6474223 ERX6101498 ERS7377028 ERP131171 PRJEB46937 RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E-MTAB-10834 Other RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq. ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11   Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour o… hsHuRFISH rep2 E MTAB 10834:hsHuRFISH rep2   isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11                 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E MTAB 10834:hsHuRFISH rep2 p hsHuRFISH rep2 p RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubati… Experimental Factor: immunoprecipitate:anti hsHuR|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 550   ERP131171 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11 hsHuRFISH_rep2.R2.fastq.gz hsHuRFISH_rep2.R1.fastq.gz fastq fastq 2106598100.0 25380700.0 E MTAB 10834:hsHuRFISH rep2.R 0:40 1:43 A:503141361;C:548220448;G:569927989;T:485014455;N:293847 40 43     503141361 548220448 569927989 485014455 293847 ERX6101498 ERS7377028 ERA5607540 Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive 2 0.76055 0.70626 0.18785 0.18742 0.92387 0.93533 0.72831 0.65481 40 43 B B biological fallback assumption illumina nextseq unknown small_rna unknown bulk unknown unknown   Sweden 2023-08-11 Undetermined Undetermined Multi-tissue Multi-system
10208 10208 ERR6474222 ERX6101497 ERS7377027 ERP131171 PRJEB46937 RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E-MTAB-10834 Other RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq. ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11   Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour o… hsHuRFISH rep1 E MTAB 10834:hsHuRFISH rep1   isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11                 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E MTAB 10834:hsHuRFISH rep1 p hsHuRFISH rep1 p RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubati… Experimental Factor: immunoprecipitate:anti hsHuR|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 550   ERP131171 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11 hsHuRFISH_rep1.R1.fastq.gz hsHuRFISH_rep1.R2.fastq.gz fastq fastq 2520623431.0 30368957.0 E MTAB 10834:hsHuRFISH rep1.R 0:40 1:43 A:604086659;C:653262791;G:679919989;T:582992802;N:361190 40 43     604086659 653262791 679919989 582992802 361190 ERX6101497 ERS7377027 ERA5607540 Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive 2 0.76096 0.70783 0.18844 0.18848 0.92101 0.93275 0.7333 0.62616 40 43 B B biological fallback assumption illumina nextseq unknown small_rna unknown bulk unknown unknown   Sweden 2023-08-11 Undetermined Undetermined Multi-tissue Multi-system
10209 10209 ERR6474221 ERX6101496 ERS7377026 ERP131171 PRJEB46937 RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E-MTAB-10834 Other RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq. ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11   Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour o… HaloFISH E MTAB 10834:HaloFISH   isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11                 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E MTAB 10834:HaloFISH p HaloFISH p RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubati… Experimental Factor: immunoprecipitate:anti HaloTag|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 550   ERP131171 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11 HaloFISH.R2.fastq.gz HaloFISH.R1.fastq.gz fastq fastq 2353027590.0 28349730.0 E MTAB 10834:HaloFISH.R 0:40 1:43 A:522964401;C:650152942;G:677020220;T:502555313;N:334714 40 43     522964401 650152942 677020220 502555313 334714 ERX6101496 ERS7377026 ERA5607540 Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive 2 0.82307 0.78117 0.18309 0.18609 0.93888 0.94627 0.73861 0.63812 40 43 B B biological fallback assumption illumina nextseq unknown small_rna unknown bulk unknown unknown   Sweden 2023-08-11 Undetermined Undetermined Multi-tissue Multi-system
10210 10210 ERR6474216 ERX6101492 ERS7377022 ERP131171 PRJEB46937 RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E-MTAB-10834 Other RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq. ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11   Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour o… drHuRFISH rep2 E MTAB 10834:drHuRFISH rep2   isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11                 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E MTAB 10834:drHuRFISH rep2 p drHuRFISH rep2 p RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubati… Experimental Factor: immunoprecipitate:anti drHuR|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 550   ERP131171 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11 drHuRFISH_rep2.R1.fastq.gz drHuRFISH_rep2.R2.fastq.gz fastq fastq 2408024386.0 29012342.0 E MTAB 10834:drHuRFISH rep2.R 0:40 1:43 A:566287649;C:627743498;G:663052609;T:550604982;N:335648 40 43     566287649 627743498 663052609 550604982 335648 ERX6101492 ERS7377022 ERA5607540 Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive 2 0.68524 0.62721 0.16916 0.1656 0.93501 0.94541 0.7028 0.64738 40 43 B B biological fallback assumption illumina nextseq unknown small_rna unknown bulk unknown unknown   Sweden 2023-08-11 Undetermined Undetermined Multi-tissue Multi-system
10211 10211 ERR6474215 ERX6101491 ERS7377021 ERP131171 PRJEB46937 RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E-MTAB-10834 Other RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq. ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11   Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour o… drHuRFISH rep1 E MTAB 10834:drHuRFISH rep1   isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11                 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA E MTAB 10834:drHuRFISH rep1 p drHuRFISH rep1 p RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubati… Experimental Factor: immunoprecipitate:anti drHuR|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 550   ERP131171 NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11 drHuRFISH_rep1.R1.fastq.gz drHuRFISH_rep1.R2.fastq.gz fastq fastq 3025188980.0 36448060.0 E MTAB 10834:drHuRFISH rep1.R 0:40 1:43 A:720153781;C:784188971;G:824077525;T:696330222;N:438481 40 43     720153781 784188971 824077525 696330222 438481 ERX6101491 ERS7377021 ERA5607540 Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive 2 0.7001 0.64217 0.17626 0.1728 0.93154 0.94249 0.72494 0.65821 40 43 B B biological fallback assumption illumina nextseq unknown small_rna unknown bulk unknown unknown   Sweden 2023-08-11 Undetermined Undetermined Multi-tissue Multi-system
10383 10383 ERR8517249 ERX8083723 ERS10517669 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Modifier control hnRNPK 003 SAMEA12918519 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918519|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 003|common name:zebrafish|sample name:hnRNPK 003                 NextSeq 500 paired end sequencing; Raw reads: hnRNPK 003 webin reads hnRNPK 003   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: hnRNPK 003 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 hnRNPK_003_R1.fastq.gz hnRNPK_003_R2.fastq.gz fastq fastq 2931486932.0 19421721.0 webin reads hnRNPK 003 0:75.51 1:75.43 A:759548162;C:700272829;G:700149526;T:770783019;N:733396 75 75     759548162 700272829 700149526 770783019 733396 ERX8083723 ERS10517669 ERA8937191 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.9621 0.96378 0.06994 0.06876 0.68757 0.68998 0.46746 0.47041 76 75 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10384 10384 ERR8517226 ERX8083700 ERS10517665 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Modifier control hnRNPK 001 SAMEA12918515 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918515|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 001|common name:zebrafish|sample name:hnRNPK 001                 NextSeq 500 paired end sequencing; Raw reads: hnRNPK 001 webin reads hnRNPK 001   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: hnRNPK 001 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 hnRNPK_001_R1.fastq.gz hnRNPK_001_R2.fastq.gz fastq fastq 2728299749.0 18074835.0 webin reads hnRNPK 001 0:75.51 1:75.43 A:710869412;C:649804308;G:644363972;T:722599378;N:662679 75 75     710869412 649804308 644363972 722599378 662679 ERX8083700 ERS10517665 ERA8936710 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96092 0.96336 0.07296 0.07144 0.68862 0.69209 0.47036 0.47104 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10385 10385 ERR8517194 ERX8083668 ERS10517668 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 RNA control GFP 003 SAMEA12918518 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918518|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 003|common name:zebrafish|sample name:GFP 003                 NextSeq 500 paired end sequencing; Raw reads: GFP 003 webin reads GFP 003   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: GFP 003 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 GFP_003_R1.fastq.gz GFP_003_R2.fastq.gz fastq fastq 2845571506.0 18850866.0 webin reads GFP 003 0:75.52 1:75.43 A:737412560;C:678774596;G:684567775;T:744108157;N:708418 75 75     737412560 678774596 684567775 744108157 708418 ERX8083668 ERS10517668 ERA8936242 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96279 0.96355 0.06774 0.06607 0.68864 0.69183 0.469 0.46906 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10386 10386 ERR8517159 ERX8083633 ERS10517664 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 RNA control GFP 001 SAMEA12918514 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918514|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 001|common name:zebrafish|sample name:GFP 001                 NextSeq 500 paired end sequencing; Raw reads: GFP 001 webin reads GFP 001   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: GFP 001 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 GFP_001_R1.fastq.gz GFP_001_R2.fastq.gz fastq fastq 2873485447.0 19035162.0 webin reads GFP 001 0:75.52 1:75.44 A:746120172;C:687054955;G:682142981;T:757435799;N:731540 75 75     746120172 687054955 682142981 757435799 731540 ERX8083633 ERS10517664 ERA8935703 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96176 0.96461 0.07014 0.06932 0.68672 0.68913 0.47006 0.46794 75 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10387 10387 ERR8517115 ERX8083589 ERS10517671 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Modifier rescue 91S hnRNPK 003 SAMEA12918521 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918521|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 003|common name:zebrafish|sample name:91S hnRNPK 003                 NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 003 webin reads 91S hnRNPK 003   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: 91S hnRNPK 003 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 91S_hnRNPK_003_R1.fastq.gz 91S_hnRNPK_003_R2.fastq.gz fastq fastq 2853403405.0 18902398.0 webin reads 91S hnRNPK 003 0:75.52 1:75.44 A:739541111;C:681340573;G:681790014;T:750013318;N:718389 75 75     739541111 681340573 681790014 750013318 718389 ERX8083589 ERS10517671 ERA8935191 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96234 0.96429 0.0679 0.06627 0.68984 0.69126 0.46434 0.47087 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10388 10388 ERR8517082 ERX8083556 ERS10517667 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Modifier rescue 91S hnRNPK 001 SAMEA12918517 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918517|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 001|common name:zebrafish|sample name:91S hnRNPK 001                 NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 001 webin reads 91S hnRNPK 001   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: 91S hnRNPK 001 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 91S_hnRNPK_001_R1.fastq.gz 91S_hnRNPK_001_R2.fastq.gz fastq fastq 2795603091.0 18519699.0 webin reads 91S hnRNPK 001 0:75.52 1:75.43 A:722724564;C:672552332;G:664566386;T:735058575;N:701234 75 75     722724564 672552332 664566386 735058575 701234 ERX8083556 ERS10517667 ERA8934579 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96307 0.96547 0.06551 0.06458 0.68714 0.68856 0.46817 0.46555 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10389 10389 ERR8517039 ERX8083513 ERS10517670 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Toxic condition 91S GFP 003 SAMEA12918520 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918520|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 003|common name:zebrafish|sample name:91S GFP 003                 NextSeq 500 paired end sequencing; Raw reads: 91S GFP 003 webin reads 91S GFP 003   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: 91S GFP 003 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 91S_GFP_003_R1.fastq.gz 91S_GFP_003_R2.fastq.gz fastq fastq 2946600193.0 19521826.0 webin reads 91S GFP 003 0:75.51 1:75.43 A:763284580;C:704439363;G:702989767;T:775149110;N:737373 75 75     763284580 704439363 702989767 775149110 737373 ERX8083513 ERS10517670 ERA8933888 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96151 0.96295 0.06621 0.06481 0.68807 0.69092 0.46928 0.46982 75 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10390 10390 ERR8516998 ERX8083472 ERS10517666 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Toxic condition 91S GFP 001 SAMEA12918516 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918516|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 001|common name:zebrafish|sample name:91S GFP 001                 NextSeq 500 paired end sequencing; Raw reads: 91S GFP 001 webin reads 91S GFP 001   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: 91S GFP 001 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 91S_GFP_001_R1.fastq.gz 91S_GFP_001_R2.fastq.gz fastq fastq 2821113913.0 18686946.0 webin reads 91S GFP 001 0:75.52 1:75.44 A:726676187;C:676899384;G:676400816;T:740427303;N:710223 75 75     726676187 676899384 676400816 740427303 710223 ERX8083472 ERS10517666 ERA8933211 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96147 0.96465 0.07106 0.06991 0.68822 0.69556 0.47261 0.47451 75 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
11143 11143 ERR10034092 ERX9574496 ERS12562207 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   Postmetamorphic posterior tissue including caudal fin from Danio rerio Drerio postmetamorphic 5 SAMEA110464179 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464179|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:SAMPLE45|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE45|sex:not provided|tissue type:posterior trunk including caudal fin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:841 19218 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 S879Nr45.1.fastq.gz S879Nr45.2.fastq.gz fastq fastq 31205725028.0 155856846.0 ena RUN TAB 05 08 2022 14:25:08:841 19219 0:100.11 1:100.11 A:8165930827;C:7529482042;G:7775787815;T:7734109822;N:414522 100 100     8165930827 7529482042 7775787815 7734109822 414522 ERX9574496 ERS12562207 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.97305 0.97331 0.04336 0.04353 0.73728 0.74324 0.47532 0.4806 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Multi-tissue Multi-system
11144 11144 ERR10034091 ERX9574495 ERS12562206 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   Postmetamorphic posterior tissue including caudal fin from Danio rerio Drerio postmetamorphic 4 SAMEA110464178 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464178|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:SAMPLE44|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE44|sex:not provided|tissue type:posterior trunk including caudal fin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:841 19216 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 S879Nr44.1.fastq.gz S879Nr44.2.fastq.gz fastq fastq 12791868714.0 63868301.0 ena RUN TAB 05 08 2022 14:25:08:841 19217 0:100.14 1:100.14 A:3327645062;C:3095411506;G:3211023712;T:3157616450;N:171984 100 100     3327645062 3095411506 3211023712 3157616450 171984 ERX9574495 ERS12562206 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.97212 0.97067 0.04428 0.04445 0.74548 0.75114 0.47785 0.49354 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Multi-tissue Multi-system
11145 11145 ERR10034090 ERX9574494 ERS12562205 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   Postmetamorphic posterior tissue including caudal fin from Danio rerio Drerio postmetamorphic 3 SAMEA110464177 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464177|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:SAMPLE43|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE43|sex:not provided|tissue type:posterior trunk including caudal fin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:840 19214 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 S879Nr43.1.fastq.gz S879Nr43.2.fastq.gz fastq fastq 8220676412.0 40976395.0 ena RUN TAB 05 08 2022 14:25:08:840 19215 0:100.31 1:100.31 A:2152497687;C:1985765652;G:2020897890;T:2061403084;N:112099 100 100     2152497687 1985765652 2020897890 2061403084 112099 ERX9574494 ERS12562205 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.97126 0.97279 0.04717 0.04683 0.74223 0.74479 0.47471 0.49071 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Multi-tissue Multi-system
11146 11146 ERR10034089 ERX9574493 ERS12562204 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   Postmetamorphic posterior tissue including caudal fin from Danio rerio Drerio postmetamorphic 2 SAMEA110464176 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464176|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:SAMPLE42|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE42|sex:not provided|tissue type:posterior trunk including caudal fin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:840 19212 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 S879Nr42.1.fastq.gz S879Nr42.2.fastq.gz fastq fastq 9426020714.0 47021406.0 ena RUN TAB 05 08 2022 14:25:08:840 19213 0:100.23 1:100.23 A:2487913802;C:2263414842;G:2331327650;T:2343237033;N:127387 100 100     2487913802 2263414842 2331327650 2343237033 127387 ERX9574493 ERS12562204 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.97197 0.97222 0.04546 0.04553 0.74235 0.7485 0.48841 0.48446 93 93 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Multi-tissue Multi-system
11147 11147 ERR10034088 ERX9574492 ERS12562203 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   Postmetamorphic posterior tissue including caudal fin from Danio rerio Drerio postmetamorphic 1 SAMEA110464175 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464175|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:SAMPLE41|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE41|sex:not provided|tissue type:posterior trunk including caudal fin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:840 19210 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 S879Nr41.1.fastq.gz S879Nr41.2.fastq.gz fastq fastq 10220995994.0 50953819.0 ena RUN TAB 05 08 2022 14:25:08:840 19211 0:100.30 1:100.30 A:2679378092;C:2474435843;G:2537496182;T:2529546220;N:139657 100 100     2679378092 2474435843 2537496182 2529546220 139657 ERX9574492 ERS12562203 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.97322 0.97339 0.05421 0.05374 0.73693 0.74194 0.50642 0.50631 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Multi-tissue Multi-system
11148 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 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 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 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 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
11158 11158 ERR10047721 ERX9587609 ERS12570320 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Female 4 MF4 SAMEA110472297 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472297|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29737|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29737|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85553 MF4 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EF12_1.fq.gz EF12_2.fq.gz fastq fastq 9295860000.0 30986200.0 ena RUN TAB 10 08 2022 10:54:39:372 85554 0:150 1:150 A:2456629138;C:2211534829;G:2202795083;T:2424808616;N:92334 150 150     2456629138 2211534829 2202795083 2424808616 92334 ERX9587609 ERS12570320 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.94791 0.94821 0.05293 0.05316 0.71285 0.71267 0.5054 0.50686 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11159 11159 ERR10047720 ERX9587608 ERS12570319 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Female 3 MF3 SAMEA110472296 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472296|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29736|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29736|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85551 MF3 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EF11_1.fq.gz EF11_2.fq.gz fastq fastq 9515997600.0 31719992.0 ena RUN TAB 10 08 2022 10:54:39:372 85552 0:150 1:150 A:2541032543;C:2239204827;G:2227356932;T:2508310635;N:92663 150 150     2541032543 2239204827 2227356932 2508310635 92663 ERX9587608 ERS12570319 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95512 0.95547 0.06023 0.06014 0.70721 0.70658 0.51615 0.50766 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11160 11160 ERR10047719 ERX9587607 ERS12570318 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Female 2 MF2 SAMEA110472295 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472295|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29735|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29735|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85549 MF2 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EF10_1.fq.gz EF10_2.fq.gz fastq fastq 10394476500.0 34648255.0 ena RUN TAB 10 08 2022 10:54:39:372 85550 0:150 1:150 A:2789547305;C:2438564969;G:2423744267;T:2742517499;N:102460 150 150     2789547305 2438564969 2423744267 2742517499 102460 ERX9587607 ERS12570318 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95582 0.95591 0.06231 0.06252 0.70565 0.70715 0.51407 0.51477 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11161 11161 ERR10047718 ERX9587606 ERS12570317 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Female 1 MF1 SAMEA110472294 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472294|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29734|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29734|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85547 MF1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EF9_1.fq.gz EF9_2.fq.gz fastq fastq 9531565200.0 31771884.0 ena RUN TAB 10 08 2022 10:54:39:372 85548 0:150 1:150 A:2534403521;C:2257857645;G:2242329348;T:2496889068;N:85618 150 150     2534403521 2257857645 2242329348 2496889068 85618 ERX9587606 ERS12570317 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95744 0.95773 0.05406 0.054 0.70703 0.70627 0.49691 0.49886 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11162 11162 ERR10047717 ERX9587605 ERS12570316 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Male 4 MM4 SAMEA110472293 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472293|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29733|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29733|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85545 MM4 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EM16_1.fq.gz EM16_2.fq.gz fastq fastq 9801781200.0 32672604.0 ena RUN TAB 10 08 2022 10:54:39:371 85546 0:150 1:150 A:2617469644;C:2307347982;G:2294965646;T:2581792895;N:205033 150 150     2617469644 2307347982 2294965646 2581792895 205033 ERX9587605 ERS12570316 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95755 0.95764 0.0539 0.05338 0.71587 0.71484 0.51048 0.52067 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11163 11163 ERR10047716 ERX9587604 ERS12570315 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Male 3 MM3 SAMEA110472292 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472292|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29732|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29732|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85543 MM3 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EM15_1.fq.gz EM15_2.fq.gz fastq fastq 9922431900.0 33074773.0 ena RUN TAB 10 08 2022 10:54:39:371 85544 0:150 1:150 A:2640289295;C:2345938205;G:2336699617;T:2599294368;N:210415 150 150     2640289295 2345938205 2336699617 2599294368 210415 ERX9587604 ERS12570315 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95894 0.95898 0.04903 0.04914 0.71346 0.71388 0.51462 0.51356 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11164 11164 ERR10047715 ERX9587603 ERS12570314 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Male 2 MM2 SAMEA110472291 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472291|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29731|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29731|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85541 MM2 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EM14_1.fq.gz EM14_2.fq.gz fastq fastq 9470081700.0 31566939.0 ena RUN TAB 10 08 2022 10:54:39:371 85542 0:150 1:150 A:2518757590;C:2239498890;G:2227790286;T:2483847148;N:187786 150 150     2518757590 2239498890 2227790286 2483847148 187786 ERX9587603 ERS12570314 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95826 0.95753 0.05166 0.05151 0.71827 0.71725 0.50776 0.50874 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11165 11165 ERR10047714 ERX9587602 ERS12570313 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Mutant Male 1 MM1 SAMEA110472290 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472290|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29730|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29730|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85539 MM1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 EM13_1.fq.gz EM13_2.fq.gz fastq fastq 9896066100.0 32986887.0 ena RUN TAB 10 08 2022 10:54:39:371 85540 0:150 1:150 A:2615586694;C:2355549418;G:2345987621;T:2578734637;N:207730 150 150     2615586694 2355549418 2345987621 2578734637 207730 ERX9587602 ERS12570313 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.96075 0.9607 0.04898 0.04814 0.71914 0.71762 0.50604 0.51092 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11166 11166 ERR10047713 ERX9587601 ERS12570312 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Female 4 WF4 SAMEA110472289 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472289|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29729|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29729|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85537 WF4 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WF4_1.fq.gz WF4_2.fq.gz fastq fastq 8902470600.0 29674902.0 ena RUN TAB 10 08 2022 10:54:39:370 85538 0:150 1:150 A:2387064218;C:2088721835;G:2083589487;T:2343005357;N:89703 150 150     2387064218 2088721835 2083589487 2343005357 89703 ERX9587601 ERS12570312 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95676 0.95666 0.0593 0.05927 0.70092 0.70337 0.49608 0.49899 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11167 11167 ERR10047712 ERX9587600 ERS12570311 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Female 3 WF3 SAMEA110472288 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472288|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29728|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29728|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85535 WF3 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WF3_1.fq.gz WF3_2.fq.gz fastq fastq 9063103800.0 30210346.0 ena RUN TAB 10 08 2022 10:54:39:370 85536 0:150 1:150 A:2432312114;C:2123240631;G:2111227574;T:2396247669;N:75812 150 150     2432312114 2123240631 2111227574 2396247669 75812 ERX9587600 ERS12570311 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95482 0.95494 0.06998 0.07003 0.70122 0.70228 0.50936 0.50507 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11168 11168 ERR10047711 ERX9587599 ERS12570310 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Female 2 WF2 SAMEA110472287 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472287|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29727|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29727|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85533 WF2 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WF2_1.fq.gz WF2_2.fq.gz fastq fastq 11904985800.0 39683286.0 ena RUN TAB 10 08 2022 10:54:39:370 85534 0:150 1:150 A:3185302826;C:2804829029;G:2783464897;T:3131272515;N:116533 150 150     3185302826 2804829029 2783464897 3131272515 116533 ERX9587599 ERS12570310 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95589 0.95646 0.058 0.05797 0.70457 0.70492 0.51464 0.5143 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11169 11169 ERR10047710 ERX9587598 ERS12570309 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Female 1 WF1 SAMEA110472286 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472286|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29726|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29726|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85531 WF1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WF1_1.fq.gz WF1_2.fq.gz fastq fastq 9491977800.0 31639926.0 ena RUN TAB 10 08 2022 10:54:39:370 85532 0:150 1:150 A:2540140444;C:2236702404;G:2215435797;T:2499606420;N:92735 150 150     2540140444 2236702404 2215435797 2499606420 92735 ERX9587598 ERS12570309 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95868 0.95935 0.05681 0.05651 0.70487 0.70538 0.50749 0.50617 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11170 11170 ERR10047709 ERX9587597 ERS12570308 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Male 4 WM4 SAMEA110472285 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472285|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29725|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29725|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:369 85529 WM4 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WM8_1.fq.gz WM8_2.fq.gz fastq fastq 9911994300.0 33039981.0 ena RUN TAB 10 08 2022 10:54:39:369 85530 0:150 1:150 A:2647417182;C:2332033790;G:2324021308;T:2608423782;N:98238 150 150     2647417182 2332033790 2324021308 2608423782 98238 ERX9587597 ERS12570308 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95754 0.95758 0.05322 0.05309 0.71936 0.71898 0.52558 0.52697 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11171 11171 ERR10047708 ERX9587596 ERS12570307 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Male 3 WM3 SAMEA110472284 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472284|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29724|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29724|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:369 85527 WM3 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WM7_1.fq.gz WM7_2.fq.gz fastq fastq 10756015500.0 35853385.0 ena RUN TAB 10 08 2022 10:54:39:369 85528 0:150 1:150 A:2882486379;C:2526051573;G:2510570253;T:2836803943;N:103352 150 150     2882486379 2526051573 2510570253 2836803943 103352 ERX9587596 ERS12570307 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95343 0.9538 0.055 0.05491 0.71784 0.71883 0.53419 0.52955 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11172 11172 ERR10047707 ERX9587595 ERS12570306 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Male 2 WM2 SAMEA110472283 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472283|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29723|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29723|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:369 85525 WM2 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WM6_1.fq.gz WM6_2.fq.gz fastq fastq 8944434000.0 29814780.0 ena RUN TAB 10 08 2022 10:54:39:369 85526 0:150 1:150 A:2384550098;C:2112886362;G:2095147407;T:2351765069;N:85064 150 150     2384550098 2112886362 2095147407 2351765069 85064 ERX9587595 ERS12570306 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95717 0.95759 0.05527 0.05526 0.72009 0.72011 0.52634 0.52832 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
11173 11173 ERR10047706 ERX9587594 ERS12570305 ERP140136 PRJEB55250 Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease 0ed9a471-a4ab-4ec7-8113-a41cfa1601b4 Other Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity the accumulation of glycosphingolipids is used as a marker. However recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes. ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15   RNA seq Wild type Male 1 WM1 SAMEA110472282 Computational Biology Unit ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472282|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29722|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29722|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 10 08 2022 10:54:39:368 85523 WM1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140136 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15 WM5_1.fq.gz WM5_2.fq.gz fastq fastq 9558564300.0 31861881.0 ena RUN TAB 10 08 2022 10:54:39:369 85524 0:150 1:150 A:2556941509;C:2249230277;G:2236855770;T:2515442411;N:94333 150 150     2556941509 2249230277 2236855770 2515442411 94333 ERX9587594 ERS12570305 ERA16825549 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 2 0.95505 0.95484 0.05372 0.05318 0.71798 0.71898 0.52584 0.52042 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Unknown 2022-09-15 Undetermined Undetermined Kidney Renal System
19143 19143 ERR14086559 ERX13488933 ERS21188923 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F2 T2 ZF Con 72h F2 T2 SAMEA116144982 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 72h F2 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F2 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:221 27805 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F2_T2.pair1.truncated ZF_Con_72h_F2_T2.pair2.truncated fastq fastq 10806719947.0 36110242.0 ena RUN TAB 19 12 2024 10:07:07:222 27806 0:149.64 1:149.64 A:2965060471;C:2438948465;G:2454160636;T:2948358895;N:191480 149 149     2965060471 2438948465 2454160636 2948358895 191480 ERX13488933 ERS21188923 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19144 19144 ERR14086546 ERX13488920 ERS21188910 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F2 T1 ZF Con 2h F2 T1 SAMEA116144969 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 2h F2 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F2 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:206 27779 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F2_T1.pair1.truncated ZF_Con_2h_F2_T1.pair2.truncated fastq fastq 14857999358.0 49760457.0 ena RUN TAB 19 12 2024 10:07:07:207 27780 0:149.30 1:149.29 A:4063197170;C:3359903309;G:3389720319;T:4045034265;N:144295 149 149     4063197170 3359903309 3389720319 4045034265 144295 ERX13488920 ERS21188910 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19145 19145 ERR14086581 ERX13488955 ERS21188945 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F2 T1 ZF Inf 72h F2 T1 SAMEA116145004 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 72h F2 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F2 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:243 27849 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F2_T1.pair1.truncated ZF_Inf_72h_F2_T1.pair2.truncated fastq fastq 13688478236.0 45721242.0 ena RUN TAB 19 12 2024 10:07:07:244 27850 0:149.69 1:149.69 A:3754535055;C:3089295285;G:3114000296;T:3730455705;N:191895 149 149     3754535055 3089295285 3114000296 3730455705 191895 ERX13488955 ERS21188945 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19146 19146 ERR14086540 ERX13488914 ERS21188904 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F1 T2 ZF Con 24h F1 T2 SAMEA116144963 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 24h F1 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F1 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:199 27767 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F1_T2.pair1.truncated ZF_Con_24h_F1_T2.pair2.truncated fastq fastq 10450579058.0 34942794.0 ena RUN TAB 19 12 2024 10:07:07:200 27768 0:149.54 1:149.54 A:2875878023;C:2351334168;G:2367670600;T:2855687426;N:8841 149 149     2875878023 2351334168 2367670600 2855687426 8841 ERX13488914 ERS21188904 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19147 19147 ERR14086555 ERX13488929 ERS21188919 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F5 T1 ZF Con 48h F5 T1 SAMEA116144978 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 48h F5 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F5 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:216 27797 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F5_T1.pair1.truncated ZF_Con_48h_F5_T1.pair2.truncated fastq fastq 12970550968.0 43346641.0 ena RUN TAB 19 12 2024 10:07:07:217 27798 0:149.61 1:149.61 A:3556627514;C:2927267468;G:2954512353;T:3531914408;N:229225 149 149     3556627514 2927267468 2954512353 3531914408 229225 ERX13488929 ERS21188919 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19148 19148 ERR14086548 ERX13488922 ERS21188912 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F3 T1 ZF Con 2h F3 T1 SAMEA116144971 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 2h F3 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F3 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:208 27783 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F3_T1.pair1.truncated ZF_Con_2h_F3_T1.pair2.truncated fastq fastq 9796047940.0 32778493.0 ena RUN TAB 19 12 2024 10:07:07:209 27784 0:149.43 1:149.43 A:2712516144;C:2185151856;G:2203905915;T:2694465752;N:8273 149 149     2712516144 2185151856 2203905915 2694465752 8273 ERX13488922 ERS21188912 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19149 19149 ERR14086576 ERX13488950 ERS21188940 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F2 T1 ZF Inf 48h F2 T1 SAMEA116144999 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 48h F2 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F2 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:239 27839 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F2_T1.pair1.truncated ZF_Inf_48h_F2_T1.pair2.truncated fastq fastq 10400268770.0 34736762.0 ena RUN TAB 19 12 2024 10:07:07:239 27840 0:149.70 1:149.70 A:2850649951;C:2367895411;G:2362604415;T:2819029152;N:89841 149 149     2850649951 2367895411 2362604415 2819029152 89841 ERX13488950 ERS21188940 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19150 19150 ERR14086580 ERX13488954 ERS21188944 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F5 T2 ZF Inf 48h F5 T2 SAMEA116145003 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 48h F5 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F5 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:242 27847 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F5_T2.pair1.truncated ZF_Inf_48h_F5_T2.pair2.truncated fastq fastq 11541953511.0 38615622.0 ena RUN TAB 19 12 2024 10:07:07:243 27848 0:149.45 1:149.45 A:3149621954;C:2617992293;G:2634267865;T:3139910090;N:161309 149 149     3149621954 2617992293 2634267865 3139910090 161309 ERX13488954 ERS21188944 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19151 19151 ERR14086547 ERX13488921 ERS21188911 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F2 T2 ZF Con 2h F2 T2 SAMEA116144970 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 2h F2 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F2 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:207 27781 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F2_T2.pair1.truncated ZF_Con_2h_F2_T2.pair2.truncated fastq fastq 13863272461.0 46344391.0 ena RUN TAB 19 12 2024 10:07:07:208 27782 0:149.57 1:149.57 A:3792400588;C:3136237717;G:3165201062;T:3769186938;N:246156 149 149     3792400588 3136237717 3165201062 3769186938 246156 ERX13488921 ERS21188911 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19152 19152 ERR14086550 ERX13488924 ERS21188914 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F5 T2 ZF Con 2h F5 T2 SAMEA116144973 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 2h F5 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F5 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:210 27787 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F5_T2.pair1.truncated ZF_Con_2h_F5_T2.pair2.truncated fastq fastq 12875582522.0 43072753.0 ena RUN TAB 19 12 2024 10:07:07:211 27788 0:149.46 1:149.46 A:3497197102;C:2940877881;G:2959759457;T:3477623582;N:124500 149 149     3497197102 2940877881 2959759457 3477623582 124500 ERX13488924 ERS21188914 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19153 19153 ERR14086586 ERX13488960 ERS21188950 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F7 T2 ZF Inf 72h F7 T2 SAMEA116145009 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 72h F7 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F7 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:248 27859 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F7_T2.pair1.truncated ZF_Inf_72h_F7_T2.pair2.truncated fastq fastq 13295980347.0 44467065.0 ena RUN TAB 19 12 2024 10:07:07:249 27860 0:149.50 1:149.50 A:3621424205;C:3027543860;G:3042454743;T:3604321654;N:235885 149 149     3621424205 3027543860 3042454743 3604321654 235885 ERX13488960 ERS21188950 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19154 19154 ERR14086561 ERX13488935 ERS21188925 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F4 T1 ZF Con 72h F4 T1 SAMEA116144984 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 72h F4 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F4 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:224 27809 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F4_T1.pair1.truncated ZF_Con_72h_F4_T1.pair2.truncated fastq fastq 9938081497.0 33212946.0 ena RUN TAB 19 12 2024 10:07:07:224 27810 0:149.61 1:149.61 A:2721489962;C:2248630062;G:2262566481;T:2705255710;N:139282 149 149     2721489962 2248630062 2262566481 2705255710 139282 ERX13488935 ERS21188925 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19155 19155 ERR14086579 ERX13488953 ERS21188943 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F5 T1 ZF Inf 48h F5 T1 SAMEA116145002 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 48h F5 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F5 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:241 27845 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F5_T1.pair1.truncated ZF_Inf_48h_F5_T1.pair2.truncated fastq fastq 12222927812.0 40990200.0 ena RUN TAB 19 12 2024 10:07:07:242 27846 0:149.10 1:149.10 A:3396661594;C:2718183404;G:2739192225;T:3368673043;N:217546 149 149     3396661594 2718183404 2739192225 3368673043 217546 ERX13488953 ERS21188943 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19156 19156 ERR14086573 ERX13488947 ERS21188937 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F5 T1 ZF Inf 2h F5 T1 SAMEA116144996 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 2h F5 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F5 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:236 27833 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F5_T1.pair1.truncated ZF_Inf_2h_F5_T1.pair2.truncated fastq fastq 10449733742.0 35250991.0 ena RUN TAB 19 12 2024 10:07:07:236 27834 0:148.22 1:148.22 A:2804774831;C:2419904968;G:2439597584;T:2785285420;N:170939 148 148     2804774831 2419904968 2439597584 2785285420 170939 ERX13488947 ERS21188937 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19157 19157 ERR14086568 ERX13488942 ERS21188932 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F5 T2 ZF Inf 24h F5 T2 SAMEA116144991 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 24h F5 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F5 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:231 27823 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F5_T2.pair1.truncated ZF_Inf_24h_F5_T2.pair2.truncated fastq fastq 12646844136.0 42337796.0 ena RUN TAB 19 12 2024 10:07:07:231 27824 0:149.36 1:149.36 A:3482695386;C:2837435668;G:2870976079;T:3455511927;N:225076 149 149     3482695386 2837435668 2870976079 3455511927 225076 ERX13488942 ERS21188932 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19158 19158 ERR14086544 ERX13488918 ERS21188908 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F5 T2 ZF Con 24h F5 T2 SAMEA116144967 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 24h F5 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F5 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:204 27775 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F5_T2.pair1.truncated ZF_Con_24h_F5_T2.pair2.truncated fastq fastq 14844040377.0 49765280.0 ena RUN TAB 19 12 2024 10:07:07:204 27776 0:149.14 1:149.14 A:4064105817;C:3361019988;G:3386488696;T:4032154980;N:270896 149 149     4064105817 3361019988 3386488696 4032154980 270896 ERX13488918 ERS21188908 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19159 19159 ERR14086571 ERX13488945 ERS21188935 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F4 T1 ZF Inf 2h F4 T1 SAMEA116144994 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 2h F4 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F4 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:234 27829 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F4_T1.pair1.truncated ZF_Inf_2h_F4_T1.pair2.truncated fastq fastq 12838150223.0 42953821.0 ena RUN TAB 19 12 2024 10:07:07:234 27830 0:149.44 1:149.44 A:3519614186;C:2900824893;G:2922740944;T:3494741243;N:228957 149 149     3519614186 2900824893 2922740944 3494741243 228957 ERX13488945 ERS21188935 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19160 19160 ERR14086549 ERX13488923 ERS21188913 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F5 T1 ZF Con 2h F5 T1 SAMEA116144972 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 2h F5 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F5 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:209 27785 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F5_T1.pair1.truncated ZF_Con_2h_F5_T1.pair2.truncated fastq fastq 11835612468.0 39584841.0 ena RUN TAB 19 12 2024 10:07:07:210 27786 0:149.50 1:149.50 A:3269078282;C:2648809055;G:2674404587;T:3243109727;N:210817 149 149     3269078282 2648809055 2674404587 3243109727 210817 ERX13488923 ERS21188913 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19161 19161 ERR14086542 ERX13488916 ERS21188906 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F4 T2 ZF Con 24h F4 T2 SAMEA116144965 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 24h F4 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F4 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:202 27771 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F4_T2.pair1.truncated ZF_Con_24h_F4_T2.pair2.truncated fastq fastq 13798422139.0 46177289.0 ena RUN TAB 19 12 2024 10:07:07:202 27772 0:149.41 1:149.41 A:3775147943;C:3126239757;G:3146905685;T:3749874746;N:254008 149 149     3775147943 3126239757 3146905685 3749874746 254008 ERX13488916 ERS21188906 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19162 19162 ERR14086552 ERX13488926 ERS21188916 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F2 T2 ZF Con 48h F2 T2 SAMEA116144975 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 48h F2 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F2 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:213 27791 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F2_T2.pair1.truncated ZF_Con_48h_F2_T2.pair2.truncated fastq fastq 13264338841.0 44308876.0 ena RUN TAB 19 12 2024 10:07:07:213 27792 0:149.68 1:149.68 A:3659186141;C:2980901976;G:3004156932;T:3619853492;N:240300 149 149     3659186141 2980901976 3004156932 3619853492 240300 ERX13488926 ERS21188916 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19163 19163 ERR14086564 ERX13488938 ERS21188928 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F3 T1 ZF Inf 24h F3 T1 SAMEA116144987 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 24h F3 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F3 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:227 27815 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F3_T1.pair1.truncated ZF_Inf_24h_F3_T1.pair2.truncated fastq fastq 10381791769.0 34725644.0 ena RUN TAB 19 12 2024 10:07:07:227 27816 0:149.48 1:149.48 A:2873405143;C:2324734677;G:2341512339;T:2841957730;N:181880 149 149     2873405143 2324734677 2341512339 2841957730 181880 ERX13488938 ERS21188928 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19164 19164 ERR14086578 ERX13488952 ERS21188942 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F3 T2 ZF Inf 48h F3 T2 SAMEA116145001 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 48h F3 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F3 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:240 27843 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F3_T2.pair1.truncated ZF_Inf_48h_F3_T2.pair2.truncated fastq fastq 11607933528.0 38797282.0 ena RUN TAB 19 12 2024 10:07:07:241 27844 0:149.60 1:149.60 A:3157510185;C:2647554101;G:2661033132;T:3141630885;N:205225 149 149     3157510185 2647554101 2661033132 3141630885 205225 ERX13488952 ERS21188942 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19165 19165 ERR14086585 ERX13488959 ERS21188949 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F6 T2 ZF Inf 72h F6 T2 SAMEA116145008 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 72h F6 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F6 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:247 27857 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F6_T2.pair1.truncated ZF_Inf_72h_F6_T2.pair2.truncated fastq fastq 14586616716.0 48786392.0 ena RUN TAB 19 12 2024 10:07:07:248 27858 0:149.49 1:149.49 A:4004810052;C:3292146107;G:3307969966;T:3981432519;N:258072 149 149     4004810052 3292146107 3307969966 3981432519 258072 ERX13488959 ERS21188949 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19166 19166 ERR14086569 ERX13488943 ERS21188933 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F3 T1 ZF Inf 2h F3 T1 SAMEA116144992 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 2h F3 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F3 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:232 27825 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F3_T1.pair1.truncated ZF_Inf_2h_F3_T1.pair2.truncated fastq fastq 11019441647.0 36982136.0 ena RUN TAB 19 12 2024 10:07:07:232 27826 0:148.98 1:148.98 A:3037955689;C:2470815294;G:2485099673;T:3025375051;N:195940 148 148     3037955689 2470815294 2485099673 3025375051 195940 ERX13488943 ERS21188933 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19167 19167 ERR14086565 ERX13488939 ERS21188929 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F3 T2 ZF Inf 24h F3 T2 SAMEA116144988 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 24h F3 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F3 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:228 27817 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F3_T2.pair1.truncated ZF_Inf_24h_F3_T2.pair2.truncated fastq fastq 9871958838.0 32967513.0 ena RUN TAB 19 12 2024 10:07:07:229 27818 0:149.72 1:149.72 A:2712574707;C:2241323417;G:2237990565;T:2680027600;N:42549 149 149     2712574707 2241323417 2237990565 2680027600 42549 ERX13488939 ERS21188929 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19168 19168 ERR14086556 ERX13488930 ERS21188920 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F5 T2 ZF Con 48h F5 T2 SAMEA116144979 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 48h F5 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F5 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:217 27799 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F5_T2.pair1.truncated ZF_Con_48h_F5_T2.pair2.truncated fastq fastq 11861470651.0 39639855.0 ena RUN TAB 19 12 2024 10:07:07:218 27800 0:149.62 1:149.62 A:3258887757;C:2673190405;G:2689128055;T:3240053301;N:211133 149 149     3258887757 2673190405 2689128055 3240053301 211133 ERX13488930 ERS21188920 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19169 19169 ERR14086543 ERX13488917 ERS21188907 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F5 T1 ZF Con 24h F5 T1 SAMEA116144966 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 24h F5 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F5 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:203 27773 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F5_T1.pair1.truncated ZF_Con_24h_F5_T1.pair2.truncated fastq fastq 13831914606.0 46241530.0 ena RUN TAB 19 12 2024 10:07:07:203 27774 0:149.56 1:149.56 A:3799248185;C:3123745954;G:3140306544;T:3768364222;N:249701 149 149     3799248185 3123745954 3140306544 3768364222 249701 ERX13488917 ERS21188907 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19170 19170 ERR14086554 ERX13488928 ERS21188918 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F3 T2 ZF Con 48h F3 T2 SAMEA116144977 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 48h F3 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F3 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:215 27795 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F3_T2.pair1.truncated ZF_Con_48h_F3_T2.pair2.truncated fastq fastq 12448461131.0 41602782.0 ena RUN TAB 19 12 2024 10:07:07:215 27796 0:149.61 1:149.61 A:3389327765;C:2836108569;G:2854509891;T:3368293555;N:221351 149 149     3389327765 2836108569 2854509891 3368293555 221351 ERX13488928 ERS21188918 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19171 19171 ERR14086551 ERX13488925 ERS21188915 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F1 T1 ZF Con 48h F1 T1 SAMEA116144974 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 48h F1 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F1 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:211 27789 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F1_T1.pair1.truncated ZF_Con_48h_F1_T1.pair2.truncated fastq fastq 12344084376.0 54459157.0 ena RUN TAB 19 12 2024 10:07:07:212 27790 0:113.33 1:113.33 A:3422797649;C:2748327064;G:2785936911;T:3386774171;N:248581 113 113     3422797649 2748327064 2785936911 3386774171 248581 ERX13488925 ERS21188915 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19172 19172 ERR14086539 ERX13488913 ERS21188903 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F1 T1 ZF Con 24h F1 T1 SAMEA116144962 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 24h F1 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F1 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:197 27765 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F1_T1.pair1.truncated ZF_Con_24h_F1_T1.pair2.truncated fastq fastq 10290290855.0 34422082.0 ena RUN TAB 19 12 2024 10:07:07:198 27766 0:149.47 1:149.47 A:2828748546;C:2322992474;G:2336279187;T:2802084735;N:185913 149 149     2828748546 2322992474 2336279187 2802084735 185913 ERX13488913 ERS21188903 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19173 19173 ERR14086563 ERX13488937 ERS21188927 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F2 T2 ZF Inf 24h F2 T2 SAMEA116144986 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 24h F2 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F2 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:226 27813 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F2_T2.pair1.truncated ZF_Inf_24h_F2_T2.pair2.truncated fastq fastq 13536477558.0 45257672.0 ena RUN TAB 19 12 2024 10:07:07:226 27814 0:149.55 1:149.55 A:3725663504;C:3050152384;G:3076823290;T:3683598880;N:239500 149 149     3725663504 3050152384 3076823290 3683598880 239500 ERX13488937 ERS21188927 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19174 19174 ERR14086545 ERX13488919 ERS21188909 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F1 T2 ZF Con 2h F1 T2 SAMEA116144968 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 2h F1 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F1 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:205 27777 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F1_T2.pair1.truncated ZF_Con_2h_F1_T2.pair2.truncated fastq fastq 11201747073.0 37461080.0 ena RUN TAB 19 12 2024 10:07:07:206 27778 0:149.51 1:149.51 A:3081962381;C:2520875203;G:2541328205;T:3057571709;N:9575 149 149     3081962381 2520875203 2541328205 3057571709 9575 ERX13488919 ERS21188909 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19175 19175 ERR14086577 ERX13488951 ERS21188941 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F3 T1 ZF Inf 48h F3 T1 SAMEA116145000 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 48h F3 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F3 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:239 27841 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F3_T1.pair1.truncated ZF_Inf_48h_F3_T1.pair2.truncated fastq fastq 11531780443.0 49868909.0 ena RUN TAB 19 12 2024 10:07:07:240 27842 0:115.62 1:115.62 A:3218054358;C:2544627851;G:2576550932;T:3192371527;N:175775 115 115     3218054358 2544627851 2576550932 3192371527 175775 ERX13488951 ERS21188941 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19176 19176 ERR14086566 ERX13488940 ERS21188930 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F4 T1 ZF Inf 24h F4 T1 SAMEA116144989 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 24h F4 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F4 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:229 27819 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F4_T1.pair1.truncated ZF_Inf_24h_F4_T1.pair2.truncated fastq fastq 11576629501.0 38725250.0 ena RUN TAB 19 12 2024 10:07:07:230 27820 0:149.47 1:149.47 A:3206545757;C:2592097810;G:2606700733;T:3171079624;N:205577 149 149     3206545757 2592097810 2606700733 3171079624 205577 ERX13488940 ERS21188930 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19177 19177 ERR14086582 ERX13488956 ERS21188946 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F5 T1 ZF Inf 72h F5 T1 SAMEA116145005 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 72h F5 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F5 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:244 27851 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F5_T1.pair1.truncated ZF_Inf_72h_F5_T1.pair2.truncated fastq fastq 12397801507.0 41450013.0 ena RUN TAB 19 12 2024 10:07:07:245 27852 0:149.55 1:149.55 A:3389701418;C:2810670716;G:2824520271;T:3372689235;N:219867 149 149     3389701418 2810670716 2824520271 3372689235 219867 ERX13488956 ERS21188946 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19178 19178 ERR14086562 ERX13488936 ERS21188926 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F7 T2 ZF Con 72h F7 T2 SAMEA116144985 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 72h F7 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F7 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:225 27811 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F7_T2.pair1.truncated ZF_Con_72h_F7_T2.pair2.truncated fastq fastq 11568689281.0 38694416.0 ena RUN TAB 19 12 2024 10:07:07:225 27812 0:149.49 1:149.49 A:3162387247;C:2620210879;G:2638016970;T:3147868485;N:205700 149 149     3162387247 2620210879 2638016970 3147868485 205700 ERX13488936 ERS21188926 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;