RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

99 rows where devstage_curation_coarse = "Adult" and tissue_curation = "Trunk"

✎ View and edit SQL

This data as json, CSV (advanced)

experiment.library_selection 5

technology 3

experiment.platform 3

experiment.library_strategy 3

experiment.library_layout 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Trunk · 99 ✖

experiment.library_source 1

devstage_curation_coarse 1

  • Adult · 99 ✖
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
9170 9170 ERR216332 ERX190997 ERS094086 ERP001234 PRJEB2894 ZF adult transcriptome ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.         SAMEA1689285 SC ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689285|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:29Z 1355130|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:29Z 1355130|scientific name:Danio rerio|strain:SAT                 1 SC EXP 7896 6#6 4927108 Illumina sequencing of library 4927108 constructed from sample accession ERS094086 for study accession ERP001234. This is part of an Illumina multiplexed sequencing run 7896 6. This submission includes reads tagged with the sequence GCCAATGT. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001234 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16 7896_6#6.bam bam 3849223200.0 25661488.0 SC RUN 7896 6#6 0:75 1:75 A:1052343872;C:867977827;G:867966925;T:1060514703;N:419873 75 75     1052343872 867977827 867966925 1060514703 419873 ERX190997 ERS094086 ERA182034 SC Wellcome Sanger Institute 2 0.94843 0.9504 0.09374 0.09366 0.71421 0.71916 0.5306 0.52809 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-01-07 Adult Adult Trunk Surface Structure
9171 9171 ERR216331 ERX190996 ERS094085 ERP001234 PRJEB2894 ZF adult transcriptome ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.         SAMEA1689286 SC ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:15Z|External Id:SAMEA1689286|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:15Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355129|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355129|scientific name:Danio rerio|strain:SAT                 1 SC EXP 7896 6#5 4927107 Illumina sequencing of library 4927107 constructed from sample accession ERS094085 for study accession ERP001234. This is part of an Illumina multiplexed sequencing run 7896 6. This submission includes reads tagged with the sequence ACAGTGGT. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001234 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16 7896_6#5.bam bam 5957027700.0 39713518.0 SC RUN 7896 6#5 0:75 1:75 A:1634176455;C:1344899134;G:1345048404;T:1632256963;N:646744 75 75     1634176455 1344899134 1345048404 1632256963 646744 ERX190996 ERS094085 ERA182034 SC Wellcome Sanger Institute 2 0.94169 0.94387 0.09489 0.09587 0.69406 0.69869 0.51459 0.51918 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-01-07 Adult Adult Trunk Surface Structure
9172 9172 ERR216330 ERX190995 ERS094084 ERP001234 PRJEB2894 ZF adult transcriptome ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.         SAMEA1689283 SC ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689283|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355128|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355128|scientific name:Danio rerio|strain:SAT                 1 SC EXP 7896 6#4 4927106 Illumina sequencing of library 4927106 constructed from sample accession ERS094084 for study accession ERP001234. This is part of an Illumina multiplexed sequencing run 7896 6. This submission includes reads tagged with the sequence TGACCACT. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001234 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16 7896_6#4.bam bam 4130918700.0 27539458.0 SC RUN 7896 6#4 0:75 1:75 A:1129107864;C:933544249;G:934913323;T:1132901907;N:451357 75 75     1129107864 933544249 934913323 1132901907 451357 ERX190995 ERS094084 ERA182034 SC Wellcome Sanger Institute 2 0.94225 0.94433 0.09272 0.09299 0.70043 0.70534 0.51333 0.52182 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-01-07 Adult Adult Trunk Surface Structure
9173 9173 ERR216329 ERX190994 ERS094083 ERP001234 PRJEB2894 ZF adult transcriptome ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.         SAMEA1689282 SC ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689282|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:27Z 1355127|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:27Z 1355127|scientific name:Danio rerio|strain:SAT                 1 SC EXP 7896 6#3 4927105 Illumina sequencing of library 4927105 constructed from sample accession ERS094083 for study accession ERP001234. This is part of an Illumina multiplexed sequencing run 7896 6. This submission includes reads tagged with the sequence TTAGGCAT. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001234 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16 7896_6#3.bam bam 5102725800.0 34018172.0 SC RUN 7896 6#3 0:75 1:75 A:1400946711;C:1145033579;G:1143298888;T:1412890130;N:556492 75 75     1400946711 1145033579 1143298888 1412890130 556492 ERX190994 ERS094083 ERA182034 SC Wellcome Sanger Institute 2 0.93688 0.93952 0.07363 0.07321 0.69645 0.70161 0.48708 0.48926 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-01-07 Adult Adult Trunk Surface Structure
9174 9174 ERR216328 ERX190993 ERS094082 ERP001234 PRJEB2894 ZF adult transcriptome ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.         SAMEA1689281 SC ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T10:04:12Z|ENA LAST UPDATE:2018 03 08T15:36:11Z|External Id:SAMEA1689281|INSDC center name:SC|INSDC first public:2013 01 07T10:04:12Z|INSDC last update:2018 03 08T15:36:11Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:26Z 1355126|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:26Z 1355126|scientific name:Danio rerio|strain:SAT                 1 SC EXP 7896 6#2 4927104 Illumina sequencing of library 4927104 constructed from sample accession ERS094082 for study accession ERP001234. This is part of an Illumina multiplexed sequencing run 7896 6. This submission includes reads tagged with the sequence CGATGTTT. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001234 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16 7896_6#2.bam bam 4350577950.0 29003853.0 SC RUN 7896 6#2 0:75 1:75 A:1214100125;C:955724962;G:954429461;T:1225838270;N:485132 75 75     1214100125 955724962 954429461 1225838270 485132 ERX190993 ERS094082 ERA182034 SC Wellcome Sanger Institute 2 0.92911 0.93026 0.0749 0.07514 0.69418 0.69775 0.48934 0.49 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-01-07 Adult Adult Trunk Surface Structure
9175 9175 ERR216327 ERX190992 ERS094081 ERP001234 PRJEB2894 ZF adult transcriptome ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125 Transcriptome Analysis Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.         SAMEA1689284 SC ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689284|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:23Z 1355125|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:23Z 1355125|scientific name:Danio rerio|strain:SAT                 1 SC EXP 7896 6#1 4927103 Illumina sequencing of library 4927103 constructed from sample accession ERS094081 for study accession ERP001234. This is part of an Illumina multiplexed sequencing run 7896 6. This submission includes reads tagged with the sequence ATCACGTT. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001234 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16 7896_6#1.bam bam 5063629350.0 33757529.0 SC RUN 7896 6#1 0:75 1:75 A:1416301768;C:1110273098;G:1105481234;T:1431015934;N:557316 75 75     1416301768 1110273098 1105481234 1431015934 557316 ERX190992 ERS094081 ERA182034 SC Wellcome Sanger Institute 2 0.93508 0.93634 0.11212 0.11206 0.70009 0.70538 0.50126 0.49177 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-01-07 Adult Adult Trunk Surface Structure
34153 34153 SRR31377592 SRX26751157 SRS23239770 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       CCSER1 S Body R6 GSM8637009   source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing CCSER1 S Body R6 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:CCSER1 S48Y* GSM8637009 GSM8637009: CCSER1 S Body R6; Danio rerio; RNA Seq GSM8637009 r1 GSM8637009 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW041_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW041_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 3891217754.0 12884827.0 GSM8637009 r1 0:151 1:151 A:1016852836;C:927774615;G:947465133;T:998741423;N:383747 151 151     1016852836 927774615 947465133 998741423 383747 SRX26751157 SRS23239770 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34154 34154 SRR31377593 SRX26751156 SRS23239769 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       CCSER1 S Body R5 GSM8637008   source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing CCSER1 S Body R5 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:CCSER1 S48Y* GSM8637008 GSM8637008: CCSER1 S Body R5; Danio rerio; RNA Seq GSM8637008 r1 GSM8637008 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW040_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW040_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 3646264950.0 12073725.0 GSM8637008 r1 0:151 1:151 A:939260848;C:884661915;G:900614466;T:921376437;N:351284 151 151     939260848 884661915 900614466 921376437 351284 SRX26751156 SRS23239769 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34155 34155 SRR31377594 SRX26751155 SRS23239768 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       CCSER1 S Body R4 GSM8637007   source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing CCSER1 S Body R4 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:CCSER1 S48Y* GSM8637007 GSM8637007: CCSER1 S Body R4; Danio rerio; RNA Seq GSM8637007 r1 GSM8637007 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW039_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW039_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 4173716406.0 13820253.0 GSM8637007 r1 0:151 1:151 A:1101647100;C:985852757;G:1008447663;T:1077356024;N:412862 151 151     1101647100 985852757 1008447663 1077356024 412862 SRX26751155 SRS23239768 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34156 34156 SRR31377595 SRX26751154 SRS23239766 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       CCSER1 S Body R3 GSM8637006   source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing CCSER1 S Body R3 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:CCSER1 S48Y* GSM8637006 GSM8637006: CCSER1 S Body R3; Danio rerio; RNA Seq GSM8637006 r1 GSM8637006 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW038_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW038_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 4042195708.0 13384754.0 GSM8637006 r1 0:151 1:151 A:1060347597;C:961319252;G:982742171;T:1037395227;N:391461 151 151     1060347597 961319252 982742171 1037395227 391461 SRX26751154 SRS23239766 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34157 34157 SRR31377596 SRX26751153 SRS23239767 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       CCSER1 S Body R2 GSM8637005   source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing CCSER1 S Body R2 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:CCSER1 S48Y* GSM8637005 GSM8637005: CCSER1 S Body R2; Danio rerio; RNA Seq GSM8637005 r1 GSM8637005 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW037_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW037_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 4273642468.0 14151134.0 GSM8637005 r1 0:151 1:151 A:1128762921;C:1007923026;G:1029470831;T:1107066433;N:419257 151 151     1128762921 1007923026 1029470831 1107066433 419257 SRX26751153 SRS23239767 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34158 34158 SRR31377597 SRX26751152 SRS23239764 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       CCSER1 S Body R1 GSM8637004   source name:whole body|tissue:whole body|genotype:CCSER1 S48Y*|geo loc name:missing|collection date:missing CCSER1 S Body R1 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:CCSER1 S48Y* GSM8637004 GSM8637004: CCSER1 S Body R1; Danio rerio; RNA Seq GSM8637004 r1 GSM8637004 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW036_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW036_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 3653975010.0 12099255.0 GSM8637004 r1 0:151 1:151 A:955600414;C:873541559;G:890489547;T:933988860;N:354630 151 151     955600414 873541559 890489547 933988860 354630 SRX26751152 SRS23239764 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34159 34159 SRR31377598 SRX26751151 SRS23239765 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       CCSER1 M Body R6 GSM8637003   source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing CCSER1 M Body R6 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:CCSER1 P471 GSM8637003 GSM8637003: CCSER1 M Body R6; Danio rerio; RNA Seq GSM8637003 r1 GSM8637003 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW035_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW035_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 4080528266.0 13511683.0 GSM8637003 r1 0:151 1:151 A:1061173416;C:977476934;G:997386836;T:1044093823;N:397257 151 151     1061173416 977476934 997386836 1044093823 397257 SRX26751151 SRS23239765 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34160 34160 SRR31377599 SRX26751150 SRS23239762 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       CCSER1 M Body R5 GSM8637002   source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing CCSER1 M Body R5 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:CCSER1 P471 GSM8637002 GSM8637002: CCSER1 M Body R5; Danio rerio; RNA Seq GSM8637002 r1 GSM8637002 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW034_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW034_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 4337490402.0 14362551.0 GSM8637002 r1 0:151 1:151 A:1123121935;C:1047421198;G:1062576487;T:1103949606;N:421176 151 151     1123121935 1047421198 1062576487 1103949606 421176 SRX26751150 SRS23239762 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34161 34161 SRR31377600 SRX26751149 SRS23239760 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       CCSER1 M Body R4 GSM8637001   source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing CCSER1 M Body R4 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:CCSER1 P471 GSM8637001 GSM8637001: CCSER1 M Body R4; Danio rerio; RNA Seq GSM8637001 r1 GSM8637001 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW033_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW033_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 3844091862.0 12728781.0 GSM8637001 r1 0:151 1:151 A:991817790;C:930869770;G:945916630;T:975114794;N:372878 151 151     991817790 930869770 945916630 975114794 372878 SRX26751149 SRS23239760 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34162 34162 SRR31377601 SRX26751148 SRS23239763 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       CCSER1 M Body R3 GSM8637000   source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing CCSER1 M Body R3 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:CCSER1 P471 GSM8637000 GSM8637000: CCSER1 M Body R3; Danio rerio; RNA Seq GSM8637000 r1 GSM8637000 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW032_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW032_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 3561535830.0 11793165.0 GSM8637000 r1 0:151 1:151 A:925501870;C:854996726;G:868955460;T:911732180;N:349594 151 151     925501870 854996726 868955460 911732180 349594 SRX26751148 SRS23239763 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34163 34163 SRR31377602 SRX26751147 SRS23239761 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       CCSER1 M Body R2 GSM8636999   source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing CCSER1 M Body R2 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:CCSER1 P471 GSM8636999 GSM8636999: CCSER1 M Body R2; Danio rerio; RNA Seq GSM8636999 r1 GSM8636999 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW031_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW031_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 4010996088.0 13281444.0 GSM8636999 r1 0:151 1:151 A:1041141909;C:965136690;G:981220550;T:1023106736;N:390203 151 151     1041141909 965136690 981220550 1023106736 390203 SRX26751147 SRS23239761 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34164 34164 SRR31377603 SRX26751146 SRS23239759 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       CCSER1 M Body R1 GSM8636998   source name:whole body|tissue:whole body|genotype:CCSER1 P471|geo loc name:missing|collection date:missing CCSER1 M Body R1 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:CCSER1 P471 GSM8636998 GSM8636998: CCSER1 M Body R1; Danio rerio; RNA Seq GSM8636998 r1 GSM8636998 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW030_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW030_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 3897705620.0 12906310.0 GSM8636998 r1 0:151 1:151 A:1018200154;C:931829100;G:950742174;T:996554508;N:379684 151 151     1018200154 931829100 950742174 996554508 379684 SRX26751146 SRS23239759 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34165 34165 SRR31377604 SRX26751145 SRS23239758 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       WT Body R6 GSM8636997   source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing WT Body R6 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:WT GSM8636997 GSM8636997: WT Body R6; Danio rerio; RNA Seq GSM8636997 r1 GSM8636997 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW029_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW029_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 3865866666.0 12800883.0 GSM8636997 r1 0:151 1:151 A:1011251980;C:922495324;G:940649850;T:991092479;N:377033 151 151     1011251980 922495324 940649850 991092479 377033 SRX26751145 SRS23239758 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34166 34166 SRR31377605 SRX26751144 SRS23239756 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       WT Body R5 GSM8636996   source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing WT Body R5 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:WT GSM8636996 GSM8636996: WT Body R5; Danio rerio; RNA Seq GSM8636996 r1 GSM8636996 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW028_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW028_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 4063620192.0 13455696.0 GSM8636996 r1 0:151 1:151 A:1059319911;C:972296744;G:990411694;T:1041199642;N:392201 151 151     1059319911 972296744 990411694 1041199642 392201 SRX26751144 SRS23239756 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34167 34167 SRR31377606 SRX26751143 SRS23239757 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       WT Body R4 GSM8636995   source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing WT Body R4 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:WT GSM8636995 GSM8636995: WT Body R4; Danio rerio; RNA Seq GSM8636995 r1 GSM8636995 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW027_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW027_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 3813832368.0 12628584.0 GSM8636995 r1 0:151 1:151 A:1000392936;C:909932334;G:925952997;T:977190341;N:363760 151 151     1000392936 909932334 925952997 977190341 363760 SRX26751143 SRS23239757 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34168 34168 SRR31377607 SRX26751142 SRS23239754 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       WT Body R3 GSM8636994   source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing WT Body R3 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:WT GSM8636994 GSM8636994: WT Body R3; Danio rerio; RNA Seq GSM8636994 r1 GSM8636994 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW026_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW026_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 4006681716.0 13267158.0 GSM8636994 r1 0:151 1:151 A:1048048089;C:954759070;G:972606862;T:1030876175;N:391520 151 151     1048048089 954759070 972606862 1030876175 391520 SRX26751142 SRS23239754 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34169 34169 SRR31377608 SRX26751141 SRS23239755 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       WT Body R2 GSM8636993   source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing WT Body R2 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:WT GSM8636993 GSM8636993: WT Body R2; Danio rerio; RNA Seq GSM8636993 r1 GSM8636993 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW025_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW025_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 4208402314.0 13935107.0 GSM8636993 r1 0:151 1:151 A:1096841306;C:1009718849;G:1025250660;T:1076184256;N:407243 151 151     1096841306 1009718849 1025250660 1076184256 407243 SRX26751141 SRS23239755 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
34170 34170 SRR31377609 SRX26751140 SRS23239752 SRP545865 PRJNA1187491 CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. GSE282155 Transcriptome Analysis CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.       WT Body R1 GSM8636992   source name:whole body|tissue:whole body|genotype:WT|geo loc name:missing|collection date:missing WT Body R1 Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned whole body   The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   tissue:whole body|genotype:WT GSM8636992 GSM8636992: WT Body R1; Danio rerio; RNA Seq GSM8636992 r1 GSM8636992 1 The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1000   SRP545865     RZW024_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW024_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz fastq fastq 4407394644.0 14594022.0 GSM8636992 r1 0:151 1:151 A:1153185021;C:1053968670;G:1069220613;T:1130594464;N:425876 151 151     1153185021 1053968670 1069220613 1130594464 425876 SRX26751140 SRS23239752 SRA2016812 ASM Lab, Physiology, NUS ASM Lab, Physiology, NUS                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2024-11-18 Undetermined Adult Trunk Surface Structure
39615 39615 SRR1873565 SRX915245 SRS870229 SRP056014 PRJNA277780 Identification of small non coding RNAs in zebrafish GSE66718 Transcriptome Analysis MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.   pubmed:26694924   adult GSM1630509   source name:entire adult|strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:adult|age:1 year adult Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs… entire adult   100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing. Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle. strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:adult|age:1 year GSM1630509 GSM1630509: adult; Danio rerio; miRNA Seq GSM1630509   1 100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing. GEO Accession:GSM1630509 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE LS454 454 GS FLX   SRP056014         361024.0 6498.0 GSM1630509 r1 0:4 1:51.56 A:104704;C:84406;G:83224;T:87843;N:847 4 51     104704 84406 83224 87843 847 SRX915245 SRS870229 SRA246117 GEO University of Aveiro 1 0.0   0.0   1.0       51   T   under 1.2% mapping rate legacy early 3prime size_fractionation unknown bulk other_seq 454   Portugal 2015-03-09 Adult Adult Trunk Surface Structure
41421 41421 SRR4423115 SRX2245299 SRS1745859 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Adult MWB Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: Adult male whole body 94 3 94 3 Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP091534     maleRID0094BC03smallZF.fastq fastq 697814234.0 14408051.0 maleRID0094BC03smallZF.fastq 0:48.43 A:165337411;C:177790468;G:184204311;T:170482044;N:0 48       165337411 177790468 184204311 170482044 0 SRX2245299 SRS1745859 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.70426   0.16215   0.91027   0.5459   120   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Adult Adult Trunk Surface Structure
41423 41423 SRR4423113 SRX2245297 SRS1745859 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Adult MWB Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish: Adult male whole body 99 5 99 5 Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP091534     maleRID0099BC05LargeZF.fastq fastq 3606425618.0 40350582.0 maleRID0099BC05LargeZF.fastq 0:89.38 A:900873268;C:899774590;G:1079098037;T:726679723;N:0 89       900873268 899774590 1079098037 726679723 0 SRX2245297 SRS1745859 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.90069   0.21287   0.95726   0.72186   53   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Netherlands 2016-10-19 Adult Adult Trunk Surface Structure
41425 41425 SRR4423111 SRX2245295 SRS1745859 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Adult MWB Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: Adult male whole body 88 3 88 3 Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP091534     maleRID0088BC03smallZF.fastq fastq 523776538.0 11118832.0 maleRID0088BC03smallZF.fastq 0:47.11 A:123827431;C:133478804;G:138882662;T:127587641;N:0 47       123827431 133478804 138882662 127587641 0 SRX2245295 SRS1745859 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.69556   0.16368   0.9093   0.54838   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Adult Adult Trunk Surface Structure
41427 41427 SRR4423109 SRX2245293 SRS1745859 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Adult MWB Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal                 miRNA Seq of Zebrafish: Adult male whole body 93 3 93 3 Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP091534     maleRID0093BC03smallZF.fastq fastq 692750598.0 14286031.0 maleRID0093BC03smallZF.fastq 0:48.49 A:164412063;C:176380331;G:182539801;T:169418403;N:0 48       164412063 176380331 182539801 169418403 0 SRX2245293 SRS1745859 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.70738   0.16645   0.90948   0.55306   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-19 Adult Adult Trunk Surface Structure
47611 47611 SRR6671794 SRX3648486 SRS2913085 SRP132190 PRJNA432942 Zebrafish genes regulated in response to Mucor circinelloides infection PRJNA432942 Other Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi using zebrafish and the fungus Mucor circinelloides as host and pathogen model respectively. Total RNA was sequenced RNA seq from abdominal organs of infected fish.         PBS2   strain:AB|dev stage:Adult|sex:not determined|tissue:Abdomen|treatment:Control innoculated with PBS|BioSampleModel:Model organism or animal                 RNA seq of Darnio rerio: uninffected PBS2 PBS2 Total RNA isolated from uninfected abdominal tissue was used to generate the library using truseq kit     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP132190     PBS2_GCCAAT_L001_R1_001_BH8U70ADXX.filt.fastq.gz fastq 792892359.0 15546909.0 PBS2 GCCAAT L001 R1 001 BH8U70ADXX.filt.fastq.gz 0:51 A:207417646;C:188867370;G:187996499;T:208448675;N:162169 51       207417646 188867370 187996499 208448675 162169 SRX3648486 SRS2913085 SRA655550 University of Murcia|Genetics and Microbiology University of Murcia 1 0.92826   0.02642   0.72815   0.45776   51   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Spain 2018-09-28 Adult Adult Trunk Surface Structure
47612 47612 SRR6671795 SRX3648485 SRS2913084 SRP132190 PRJNA432942 Zebrafish genes regulated in response to Mucor circinelloides infection PRJNA432942 Other Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi using zebrafish and the fungus Mucor circinelloides as host and pathogen model respectively. Total RNA was sequenced RNA seq from abdominal organs of infected fish.         RDRZ   strain:AB|dev stage:Adult|sex:not determined|tissue:Abdomen|treatment:Infected with Mucor circinelloides spores|BioSampleModel:Model organism or animal                 RNA seq of Darnio rerio: infected with Mucor circinelloides RDRZ RDRZ Total RNA isolated from abdominal tissue infected with Mucor circinelloides was used to generate the library using truseq kit     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP132190     RDRZ_TGACCA_L001_R1_001_BH8U70ADXX.filt.fastq.gz fastq 741005418.0 14529518.0 RDRZ TGACCA L001 R1 001 BH8U70ADXX.filt.fastq.gz 0:51 A:192330774;C:178252917;G:175501754;T:194766886;N:153087 51       192330774 178252917 175501754 194766886 153087 SRX3648485 SRS2913084 SRA655550 University of Murcia|Genetics and Microbiology University of Murcia 1 0.91685   0.03703   0.70873   0.49947   51   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Spain 2018-09-28 Adult Adult Trunk Surface Structure
52281 52281 SRR9077085 SRX5852372 SRS4776365 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body2 mock s11   breed:zebrafish|dev stage:adult|sex:NA|tissue:body6|BioSampleModel:Model organism or animal                 body2 mock WC TC 060 WC TC 060 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_060_S11.R2.fastq.gz WC_TC_060_S11.R1.fastq.gz fastq fastq 6570204104.0 43225027.0 WC TC 060 S11.R1.fastq.gz 0:101 1:51 A:1688920476;C:1591936403;G:1547543861;T:1736945913;N:4857451 101 51     1688920476 1591936403 1547543861 1736945913 4857451 SRX5852372 SRS4776365 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96893 0.96531 0.06012 0.06428 0.74002 0.74308 0.44405 0.45056 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52282 52282 SRR9077086 SRX5852371 SRS4776364 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body2 control s12   breed:zebrafish|dev stage:adult|sex:NA|tissue:body7|BioSampleModel:Model organism or animal                 body2 control WC TC 061 WC TC 061 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_061_S12.R1.fastq.gz WC_TC_061_S12.R2.fastq.gz fastq fastq 5298115192.0 34856021.0 WC TC 061 S12.R1.fastq.gz 0:101 1:51 A:1365002199;C:1284749208;G:1236476294;T:1407970678;N:3916813 101 51     1365002199 1284749208 1236476294 1407970678 3916813 SRX5852371 SRS4776364 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96855 0.96437 0.06631 0.06978 0.72819 0.73158 0.43805 0.4516 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52283 52283 SRR9077087 SRX5852370 SRS4776363 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body2 kd s13   breed:zebrafish|dev stage:adult|sex:NA|tissue:body8|BioSampleModel:Model organism or animal                 body2 kd WC TC 062 WC TC 062 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_062_S13.R1.fastq.gz WC_TC_062_S13.R2.fastq.gz fastq fastq 6381036304.0 41980502.0 WC TC 062 S13.R1.fastq.gz 0:101 1:51 A:1647560028;C:1537878827;G:1499984084;T:1690940053;N:4673312 101 51     1647560028 1537878827 1499984084 1690940053 4673312 SRX5852370 SRS4776363 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96684 0.96194 0.06383 0.06747 0.73608 0.74052 0.45347 0.4621 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52284 52284 SRR9077088 SRX5852369 SRS4776362 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body2 kd+wt s14   breed:zebrafish|dev stage:adult|sex:NA|tissue:body9|BioSampleModel:Model organism or animal                 body2 kd+wt WC TC 063 WC TC 063 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_063_S14.R1.fastq.gz WC_TC_063_S14.R2.fastq.gz fastq fastq 5465511120.0 35957310.0 WC TC 063 S14.R1.fastq.gz 0:101 1:51 A:1414511882;C:1316966059;G:1276815442;T:1453177754;N:4039983 101 51     1414511882 1316966059 1276815442 1453177754 4039983 SRX5852369 SRS4776362 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96743 0.96269 0.06264 0.06717 0.73768 0.74002 0.43946 0.44951 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52289 52289 SRR9077093 SRX5852364 SRS4776357 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body1 mock s6   breed:zebrafish|dev stage:adult|sex:NA|tissue:body1|BioSampleModel:Model organism or animal                 body1 mock WC TC 055 WC TC 055 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_055_S6.R1.fastq.gz WC_TC_055_S6.R2.fastq.gz fastq fastq 5140707792.0 33820446.0 WC TC 055 S6.R1.fastq.gz 0:101 1:51 A:1316539385;C:1252228375;G:1214956681;T:1353162802;N:3820549 101 51     1316539385 1252228375 1214956681 1353162802 3820549 SRX5852364 SRS4776357 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.97114 0.96587 0.05961 0.06293 0.73596 0.73979 0.43233 0.4586 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52290 52290 SRR9077094 SRX5852363 SRS4776356 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body1 control s7   breed:zebrafish|dev stage:adult|sex:NA|tissue:body2|BioSampleModel:Model organism or animal                 body1 control WC TC 056 WC TC 056 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_056_S7.R1.fastq.gz WC_TC_056_S7.R2.fastq.gz fastq fastq 5020859136.0 33031968.0 WC TC 056 S7.R1.fastq.gz 0:101 1:51 A:1291539287;C:1214422587;G:1184146239;T:1327013927;N:3737096 101 51     1291539287 1214422587 1184146239 1327013927 3737096 SRX5852363 SRS4776356 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96884 0.96505 0.0623 0.06643 0.73572 0.73904 0.44643 0.45988 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52291 52291 SRR9077095 SRX5852362 SRS4776355 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body1 kd+wt s9   breed:zebrafish|dev stage:adult|sex:NA|tissue:body4|BioSampleModel:Model organism or animal                 body1 kd+wt WC TC 058 WC TC 058 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_058_S9.R1.fastq.gz WC_TC_058_S9.R2.fastq.gz fastq fastq 6018676056.0 39596553.0 WC TC 058 S9.R1.fastq.gz 0:101 1:51 A:1548315021;C:1452922375;G:1413529417;T:1599423213;N:4486030 101 51     1548315021 1452922375 1413529417 1599423213 4486030 SRX5852362 SRS4776355 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96912 0.96439 0.06373 0.06781 0.73612 0.73988 0.44769 0.46236 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52293 52293 SRR9077097 SRX5852360 SRS4776353 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body1 kd+mt s10   breed:zebrafish|dev stage:adult|sex:NA|tissue:body5|BioSampleModel:Model organism or animal                 body1 kd+mt WC TC 059 WC TC 059 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_059_S10.R2.fastq.gz WC_TC_059_S10.R1.fastq.gz fastq fastq 6271465432.0 41259641.0 WC TC 059 S10.R1.fastq.gz 0:101 1:51 A:1629820249;C:1502782160;G:1459060597;T:1675172643;N:4629783 101 51     1629820249 1502782160 1459060597 1675172643 4629783 SRX5852360 SRS4776353 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96576 0.96033 0.06782 0.07173 0.73547 0.74014 0.45453 0.45359 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52294 52294 SRR9077098 SRX5852359 SRS4776352 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body1 kd s8   breed:zebrafish|dev stage:adult|sex:NA|tissue:body3|BioSampleModel:Model organism or animal                 body1 kd WC TC 057 WC TC 057 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_057_S8.R1.fastq.gz WC_TC_057_S8.R2.fastq.gz fastq fastq 4742849768.0 31202959.0 WC TC 057 S8.R1.fastq.gz 0:101 1:51 A:1229413754;C:1139873278;G:1110810068;T:1259324043;N:3428625 101 51     1229413754 1139873278 1110810068 1259324043 3428625 SRX5852359 SRS4776352 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96593 0.96237 0.06455 0.06966 0.73618 0.74126 0.45216 0.4641 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52295 52295 SRR9077099 SRX5852358 SRS4776351 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body2 kd+mt s15   breed:zebrafish|dev stage:adult|sex:NA|tissue:body|BioSampleModel:Model organism or animal                 body2 kd+mt WC TC 064 WC TC 064 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_064_S15.R2.fastq.gz WC_TC_064_S15.R1.fastq.gz fastq fastq 5256312456.0 34581003.0 WC TC 064 S15.R1.fastq.gz 0:101 1:51 A:1366908192;C:1258394092;G:1221379603;T:1405741204;N:3889365 101 51     1366908192 1258394092 1221379603 1405741204 3889365 SRX5852358 SRS4776351 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96533 0.96121 0.06858 0.07356 0.73547 0.7387 0.46254 0.46106 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
53490 53490 SRR9945454 SRX6694025 SRS5251307 SRP218026 PRJNA557895 The origin and evolution of RNA editing in Metazoan PRJNA557895 Other We shed light on the origin and evolution of RNA editing in Metazoan by selected representative 22 species 18 of which were sequenced by ourselves.         Replicate 2 for D.rerio   isolate:Drer 2|age:not collected|dev stage:not collected|sex:not collected|tissue:whole body|BioSampleModel:Model organism or animal                 Strand specific RNA seq of Danio rerio rep2: whole body DrerWHANIddyEAAORAAPEI 218 DrerWHANIddyEAAORAAPEI 218 Both genomic DNA and total RNA were extracted from the whole body of an adult. The strand specific RNA seq library was prepared using the TruSeq Stranded mRNA LT Sample Prep RS 122 2101 Illumina and sequenced on the Illumina HiSeq 4000 platform according to the manufacturer's instructions. The DNA library was prepared using the MGIEasy DNA Library Prep Kit V1.1 MGI Tech and sequenced on the BGISEQ 500RS platform according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP218026     170403_I133_FCHGL72BBXX_L7_WHANIddyEAAORAAPEI-218_1.fq.gz 170403_I133_FCHGL72BBXX_L7_WHANIddyEAAORAAPEI-218_2.fq.gz 170403_I133_FCHGL72BBXX_L8_WHANIddyEAAORAAPEI-218_1.fq.gz 170403_I133_FCHGL72BBXX_L8_WHANIddyEAAORAAPEI-218_2.fq.gz fastq fastq fastq fastq 36897471600.0 184487358.0 170403 I133 FCHGL72BBXX L7 WHANIddyEAAORAAPEI 218 1.fq.gz 0:100 1:100 A:9529576187;C:8838331599;G:9026934437;T:9496422810;N:6206567 100 100     9529576187 8838331599 9026934437 9496422810 6206567 SRX6694025 SRS5251307 SRA937931 Kunming Institute of Zoology, Chinese Academy of Sciences|State Key Laboratory of Genetic Resources and Evol Kunming Institute of Zoology, Chinese Academy of Sciences 2 0.95202 0.95483 0.0516 0.0503 0.70853 0.71224 0.50665 0.50669 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   China 2019-08-11 Adult Adult Trunk Surface Structure
53491 53491 SRR9945455 SRX6694024 SRS5251306 SRP218026 PRJNA557895 The origin and evolution of RNA editing in Metazoan PRJNA557895 Other We shed light on the origin and evolution of RNA editing in Metazoan by selected representative 22 species 18 of which were sequenced by ourselves.         Replicate 1 for D.rerio   isolate:Drer 1|age:not collected|dev stage:not collected|sex:not collected|tissue:whole body|BioSampleModel:Model organism or animal                 Strand specific RNA seq of Danio rerio rep1: whole body DrerWHINSpmnpBABRAAPEI 219 DrerWHINSpmnpBABRAAPEI 219 Both genomic DNA and total RNA were extracted from the whole body of an adult. The strand specific RNA seq library was prepared using the TruSeq Stranded mRNA LT Sample Prep RS 122 2101 Illumina and the DNA library was constructed according to the standard protocol provided by Illumina San Diego CA USA. Paired end sequencing was performed for the two libraries on the HiSeq 4000 platform according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP218026     160415_I136_FCH7MJKBBXX_L4_WHINSpmnpBABRAAPEI-219_1.fq.gz 160415_I136_FCH7MJKBBXX_L4_WHINSpmnpBABRAAPEI-219_2.fq.gz fastq fastq 23885022200.0 119425111.0 160415 I136 FCH7MJKBBXX L4 WHINSpmnpBABRAAPEI 219 1.fq.gz 0:100 1:100 A:6260820125;C:5693318287;G:5662248033;T:6264079999;N:4555756 100 100     6260820125 5693318287 5662248033 6264079999 4555756 SRX6694024 SRS5251306 SRA937931 Kunming Institute of Zoology, Chinese Academy of Sciences|State Key Laboratory of Genetic Resources and Evol Kunming Institute of Zoology, Chinese Academy of Sciences 2 0.9539 0.95672 0.05875 0.05826 0.70782 0.70885 0.50825 0.51884 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   China 2019-08-11 Adult Adult Trunk Surface Structure
53492 53492 SRR9945460 SRX6694019 SRS5251305 SRP218026 PRJNA557895 The origin and evolution of RNA editing in Metazoan PRJNA557895 Other We shed light on the origin and evolution of RNA editing in Metazoan by selected representative 22 species 18 of which were sequenced by ourselves.         Replicate 3 for D.rerio   isolate:Drer 3|age:not collected|dev stage:not collected|sex:not collected|tissue:whole body|BioSampleModel:Model organism or animal                 Strand specific RNA seq of Danio rerio rep3: whole body DrerWHANIddyEAAPRAAPEI 219 DrerWHANIddyEAAPRAAPEI 219 Both genomic DNA and total RNA were extracted from the whole body of an adult. The strand specific RNA seq library was prepared using the TruSeq Stranded mRNA LT Sample Prep RS 122 2101 Illumina and sequenced on the Illumina HiSeq 4000 platform according to the manufacturer's instructions. The DNA library was prepared using the MGIEasy DNA Library Prep Kit V1.1 MGI Tech and sequenced on the BGISEQ 500RS platform according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP218026     170403_I133_FCHGL72BBXX_L6_WHANIddyEAAPRAAPEI-219_1.fq.gz 170403_I133_FCHGL72BBXX_L6_WHANIddyEAAPRAAPEI-219_2.fq.gz fastq fastq 28065364200.0 140326821.0 170403 I133 FCHGL72BBXX L6 WHANIddyEAAPRAAPEI 219 1.fq.gz 0:100 1:100 A:7411372143;C:6577171300;G:6693925569;T:7377537100;N:5358088 100 100     7411372143 6577171300 6693925569 7377537100 5358088 SRX6694019 SRS5251305 SRA937931 Kunming Institute of Zoology, Chinese Academy of Sciences|State Key Laboratory of Genetic Resources and Evol Kunming Institute of Zoology, Chinese Academy of Sciences 2 0.94764 0.95274 0.06893 0.06709 0.68966 0.69154 0.49095 0.52264 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   China 2019-08-11 Adult Adult Trunk Surface Structure
61775 61775 SRR13015641 SRX9466595 SRS7678751 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       body tissue of parents from cross 2 male cross 2 adult body transcriptome   strain:AB wildtype|dev stage:adult|sex:male|tissue:body|embryos derived by cross:single cross 2|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq body zebrafish male from single cross 2 lane2 PJ KH 036 2 PJ KH 036 2 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_036_S36_L004_R1_001.fastq.gz PJ_KH_036_S36_L004_R2_001.fastq.gz fastq fastq 6478281728.0 21451264.0 PJ KH 036 S36 L004 R1 001.fastq.gz 0:151 1:151 A:1648862369;C:1591549903;G:1631652727;T:1605015568;N:1201161 151 151     1648862369 1591549903 1631652727 1605015568 1201161 SRX9466595 SRS7678751 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.9608 0.96246 0.02387 0.02325 0.78386 0.78608 0.5048 0.50714 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Adult Adult Trunk Surface Structure
61776 61776 SRR13015642 SRX9466594 SRS7678751 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       body tissue of parents from cross 2 male cross 2 adult body transcriptome   strain:AB wildtype|dev stage:adult|sex:male|tissue:body|embryos derived by cross:single cross 2|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq body zebrafish male from single cross 2 lane1 PJ KH 036 1 PJ KH 036 1 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_036_S36_L003_R1_001.fastq.gz PJ_KH_036_S36_L003_R2_001.fastq.gz fastq fastq 6439955814.0 21324357.0 PJ KH 036 S36 L003 R1 001.fastq.gz 0:151 1:151 A:1639459063;C:1581604775;G:1623817049;T:1594197994;N:876933 151 151     1639459063 1581604775 1623817049 1594197994 876933 SRX9466594 SRS7678751 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.96081 0.96284 0.02389 0.02312 0.78393 0.78713 0.50411 0.50535 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Adult Adult Trunk Surface Structure
61777 61777 SRR13015643 SRX9466593 SRS7678749 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       body tissue of parents from cross 2 female cross 2 adult body transcriptome   strain:AB wildtype|dev stage:adult|sex:female|tissue:body|embryos derived by cross:single cross 2|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq body zebrafish female from single cross 2 lane2 PJ KH 035 2 PJ KH 035 2 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_035_S35_L004_R1_001.fastq.gz PJ_KH_035_S35_L004_R2_001.fastq.gz fastq fastq 9422957190.0 31201845.0 PJ KH 035 S35 L004 R1 001.fastq.gz 0:151 1:151 A:2404649667;C:2302545232;G:2348124627;T:2365889998;N:1747666 151 151     2404649667 2302545232 2348124627 2365889998 1747666 SRX9466593 SRS7678749 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.94329 0.9456 0.02717 0.02634 0.71029 0.71451 0.46936 0.47075 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Adult Adult Trunk Surface Structure
61779 61779 SRR13015645 SRX9466591 SRS7678749 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       body tissue of parents from cross 2 female cross 2 adult body transcriptome   strain:AB wildtype|dev stage:adult|sex:female|tissue:body|embryos derived by cross:single cross 2|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq body zebrafish female from single cross 2 lane1 PJ KH 035 1 PJ KH 035 1 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_035_S35_L003_R1_001.fastq.gz PJ_KH_035_S35_L003_R2_001.fastq.gz fastq fastq 9366027774.0 31013337.0 PJ KH 035 S35 L003 R1 001.fastq.gz 0:151 1:151 A:2391627126;C:2287177887;G:2335767866;T:2350185771;N:1269124 151 151     2391627126 2287177887 2335767866 2350185771 1269124 SRX9466591 SRS7678749 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.94406 0.94614 0.02757 0.02656 0.70968 0.71366 0.468 0.46571 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Adult Adult Trunk Surface Structure
61780 61780 SRR13015646 SRX9466590 SRS7678748 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       body tissue of parents from cross 1 male cross 1 adult body transcriptome   strain:AB wildtype|dev stage:adult|sex:male|tissue:body|embryos derived by cross:single cross 1|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq body zebrafish male from single cross 1 lane2 PJ KH 034 2 PJ KH 034 2 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_034_S34_L004_R1_001.fastq.gz PJ_KH_034_S34_L004_R2_001.fastq.gz fastq fastq 7735112712.0 25612956.0 PJ KH 034 S34 L004 R1 001.fastq.gz 0:151 1:151 A:1974870696;C:1890581361;G:1943734005;T:1924490964;N:1435686 151 151     1974870696 1890581361 1943734005 1924490964 1435686 SRX9466590 SRS7678748 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.96448 0.966 0.03488 0.03342 0.72594 0.72985 0.49998 0.49893 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Adult Adult Trunk Surface Structure
61781 61781 SRR13015647 SRX9466589 SRS7678748 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       body tissue of parents from cross 1 male cross 1 adult body transcriptome   strain:AB wildtype|dev stage:adult|sex:male|tissue:body|embryos derived by cross:single cross 1|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq body zebrafish male from single cross 1 lane1 PJ KH 034 1 PJ KH 034 1 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_034_S34_L003_R1_001.fastq.gz PJ_KH_034_S34_L003_R2_001.fastq.gz fastq fastq 7674468092.0 25412146.0 PJ KH 034 S34 L003 R1 001.fastq.gz 0:151 1:151 A:1959722716;C:1874876878;G:1930984650;T:1907843658;N:1040190 151 151     1959722716 1874876878 1930984650 1907843658 1040190 SRX9466589 SRS7678748 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.96342 0.9657 0.03463 0.03334 0.72638 0.73196 0.49758 0.50234 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Adult Adult Trunk Surface Structure
61782 61782 SRR13015648 SRX9466588 SRS7678747 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       body tissue of parents from cross 1 female cross 1 adult body transcriptome   strain:AB wildtype|dev stage:adult|sex:female|tissue:body|embryos derived by cross:single cross 1|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq body zebrafish female from single cross 1 lane2 PJ KH 033 2 PJ KH 033 2 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_033_S33_L004_R1_001.fastq.gz PJ_KH_033_S33_L004_R2_001.fastq.gz fastq fastq 6190583240.0 20498620.0 PJ KH 033 S33 L004 R1 001.fastq.gz 0:151 1:151 A:1564701976;C:1533323455;G:1577799625;T:1513606117;N:1152067 151 151     1564701976 1533323455 1577799625 1513606117 1152067 SRX9466588 SRS7678747 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.95429 0.95588 0.02079 0.01982 0.75779 0.76065 0.44557 0.45493 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Adult Adult Trunk Surface Structure
61783 61783 SRR13015649 SRX9466587 SRS7678747 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       body tissue of parents from cross 1 female cross 1 adult body transcriptome   strain:AB wildtype|dev stage:adult|sex:female|tissue:body|embryos derived by cross:single cross 1|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq body zebrafish female from single cross 1 lane1 PJ KH 033 1 PJ KH 033 1 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_033_S33_L003_R1_001.fastq.gz PJ_KH_033_S33_L003_R2_001.fastq.gz fastq fastq 6121465406.0 20269753.0 PJ KH 033 S33 L003 R1 001.fastq.gz 0:151 1:151 A:1547607194;C:1515704901;G:1561793302;T:1495528175;N:831834 151 151     1547607194 1515704901 1561793302 1495528175 831834 SRX9466587 SRS7678747 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.9549 0.95671 0.02143 0.02065 0.75844 0.76138 0.49503 0.50077 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Adult Adult Trunk Surface Structure
65593 65593 SRR15390207 SRX11692437 SRS9724034 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XBN GSM5510265   source name:Zebrafish body skin|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP XBN Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish body skin   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP GSM5510265 GSM5510265: XBN; Danio rerio; RNA Seq GSM5510265   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510265 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2387_XBN_IGO_11718_6_S6_L001_R1_001.fastq.gz 2387_XBN_IGO_11718_6_S6_L001_R2_001.fastq.gz fastq fastq 19425231072.0 166027616.0 GSM5510265 r1 0:29 1:88 A:5317276529;C:4456617510;G:4523328168;T:5127353259;N:655606 29 88     5317276529 4456617510 4523328168 5127353259 655606 SRX11692437 SRS9724034 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00419 0.81051 0.00138 0.0994 0.9936 0.81523 0.4397 0.5459 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Trunk Surface Structure
65594 65594 SRR15390208 SRX11692437 SRS9724034 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XBN GSM5510265   source name:Zebrafish body skin|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP XBN Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish body skin   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP GSM5510265 GSM5510265: XBN; Danio rerio; RNA Seq GSM5510265   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510265 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2387_XBN_IGO_11718_6_S6_L002_R1_001.fastq.gz 2387_XBN_IGO_11718_6_S6_L002_R2_001.fastq.gz fastq fastq 19057747059.0 162886727.0 GSM5510265 r2 0:29 1:88 A:5220986791;C:4370566015;G:4433233229;T:5032336069;N:624955 29 88     5220986791 4370566015 4433233229 5032336069 624955 SRX11692437 SRS9724034 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00434 0.81103 0.00156 0.09907 0.99417 0.81274 0.44052 0.54695 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Trunk Surface Structure
65595 65595 SRR15390205 SRX11692435 SRS9724032 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XBG GSM5510264   source name:Zebrafish body skin|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP+ XBG Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish body skin   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP+ GSM5510264 GSM5510264: XBG; Danio rerio; RNA Seq GSM5510264   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510264 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2386_XBG_IGO_11718_5_S5_L001_R1_001.fastq.gz 2386_XBG_IGO_11718_5_S5_L001_R2_001.fastq.gz fastq fastq 21756379320.0 185951960.0 GSM5510264 r1 0:29 1:88 A:6175271825;C:4793640120;G:4981225446;T:5805505185;N:736744 29 88     6175271825 4793640120 4981225446 5805505185 736744 SRX11692435 SRS9724032 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00899 0.8935 0.00261 0.14469 0.99056 0.79849 0.434 0.5426 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Trunk Surface Structure
65596 65596 SRR15390206 SRX11692435 SRS9724032 SRP331755 PRJNA753151 scRNA seq of fin and body zebrafish melanocytes GSE181748 Transcriptome Analysis Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body whereas the acral subtype arises on the palms of the hands soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes compared to body melanocytes revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma which was generated by injecting Casper fish with MniCoopR GFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total GFP+ body cells GFP body cells GFP+ fin cells GFP fin cells. Data was then analyzed and pooled together …   pubmed:35355015   XBG GSM5510264   source name:Zebrafish body skin|model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP+ XBG Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao Hao et al. 2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija 2019. Principal component analysis Joliffe 1986 and UMAP dimensionality reduction McInnes 2018 were performed using default parameters with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al. 2020; Hunter Moncada et al. 2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output Zebrafish body skin   Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics   model:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Body|cell type:GFP+ GSM5510264 GSM5510264: XBG; Danio rerio; RNA Seq GSM5510264   1 Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles i5 10 cycles i7 10 cycles Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics GEO Accession:GSM5510264 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP331755     2386_XBG_IGO_11718_5_S5_L002_R1_001.fastq.gz 2386_XBG_IGO_11718_5_S5_L002_R2_001.fastq.gz fastq fastq 21271780062.0 181810086.0 GSM5510264 r2 0:29 1:88 A:6043225103;C:4683532253;G:4864212050;T:5680108261;N:702395 29 88     6043225103 4683532253 4864212050 5680108261 702395 SRX11692435 SRS9724032 SRA1274997 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.00858 0.89419 0.00266 0.14661 0.99034 0.79622 0.39545 0.56688 29 88 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-09 Undetermined Adult Trunk Surface Structure
70846 70846 SRR20822767 SRX16842343 SRS14446856 SRP389580 PRJNA865512 TCR alpha and beta repseq PRJNA865512 Other TCR Repertoire sequencing raw reads TCR alpha and beta for several species   pubmed:37344590     ZF 6   strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 6|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire ZF 39 ZF 39 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP389580     ZF_Tu2_10_R1.fastq.gz ZF_Tu2_10_R2.fastq.gz ZF_Tu2_11_R1.fastq.gz ZF_Tu2_11_R2.fastq.gz ZF_Tu2_12_R1.fastq.gz ZF_Tu2_12_R2.fastq.gz ZF_Tu2_13_R1.fastq.gz ZF_Tu2_13_R2.fastq.gz ZF_Tu2_14_R1.fastq.gz ZF_Tu2_14_R2.fastq.gz ZF_Tu2_15_R1.fastq.gz ZF_Tu2_15_R2.fastq.gz ZF_Tu2_16_R1.fastq.gz ZF_Tu2_16_R2.fastq.gz ZF_Tu2_1_R1.fastq.gz ZF_Tu2_1_R2.fastq.gz ZF_Tu2_2_R1.fastq.gz ZF_Tu2_2_R2.fastq.gz ZF_Tu2_3_R1.fastq.gz ZF_Tu2_3_R2.fastq.gz ZF_Tu2_4_R1.fastq.gz ZF_Tu2_4_R2.fastq.gz ZF_Tu2_5_R1.fastq.gz ZF_Tu2_5_R2.fastq.gz ZF_Tu2_6_R1.fastq.gz ZF_Tu2_6_R2.fastq.gz ZF_Tu2_7_R1.fastq.gz ZF_Tu2_7_R2.fastq.gz ZF_Tu2_8_R1.fastq.gz ZF_Tu2_8_R2.fastq.gz ZF_Tu2_9_R1.fastq.gz ZF_Tu2_9_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 19600815900.0 39045450.0 ZF Tu2 10 R1.fastq.gz 0:251 1:251 A:5586816283;C:3957164453;G:4183919538;T:5872635753;N:279873 251 251     5586816283 3957164453 4183919538 5872635753 279873 SRX16842343 SRS14446856 SRA1468938 Max Planck Institut|Boehm Max Planck Institut 2 0.23669 0.0002 0.00499 0.00015 0.98908 0.99993 0.27742 0.8 251 251 B T mate2 technical by mapping diff illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70847 70847 SRR20822058 SRX16841660 SRS14446856 SRP389580 PRJNA865512 TCR alpha and beta repseq PRJNA865512 Other TCR Repertoire sequencing raw reads TCR alpha and beta for several species   pubmed:37344590     ZF 6   strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 6|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire ZF 37 ZF 37 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP389580     ZF_Tu2_10_R1.fastq.gz ZF_Tu2_10_R2.fastq.gz ZF_Tu2_11_R1.fastq.gz ZF_Tu2_11_R2.fastq.gz ZF_Tu2_12_R1.fastq.gz ZF_Tu2_12_R2.fastq.gz ZF_Tu2_13_R1.fastq.gz ZF_Tu2_13_R2.fastq.gz ZF_Tu2_14_R1.fastq.gz ZF_Tu2_14_R2.fastq.gz ZF_Tu2_15_R1.fastq.gz ZF_Tu2_15_R2.fastq.gz ZF_Tu2_16_R1.fastq.gz ZF_Tu2_16_R2.fastq.gz ZF_Tu2_1_R1.fastq.gz ZF_Tu2_1_R2.fastq.gz ZF_Tu2_2_R1.fastq.gz ZF_Tu2_2_R2.fastq.gz ZF_Tu2_3_R1.fastq.gz ZF_Tu2_3_R2.fastq.gz ZF_Tu2_4_R1.fastq.gz ZF_Tu2_4_R2.fastq.gz ZF_Tu2_5_R1.fastq.gz ZF_Tu2_5_R2.fastq.gz ZF_Tu2_6_R1.fastq.gz ZF_Tu2_6_R2.fastq.gz ZF_Tu2_7_R1.fastq.gz ZF_Tu2_7_R2.fastq.gz ZF_Tu2_8_R1.fastq.gz ZF_Tu2_8_R2.fastq.gz ZF_Tu2_9_R1.fastq.gz ZF_Tu2_9_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 28345644856.0 56465428.0 ZF Tu2 10 R1.fastq.gz 0:251 1:251 A:8023828983;C:5867289387;G:5956780834;T:8497336426;N:409226 251 251     8023828983 5867289387 5956780834 8497336426 409226 SRX16841660 SRS14446856 SRA1468916 Max Planck Institut|Boehm Max Planck Institut 2 0.24302 0.00391 0.0049 0.0036 0.98766 0.99965 0.25169 0.2619 251 251 B T mate2 technical by mapping diff illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70848 70848 SRR20821267 SRX16840871 SRS14445862 SRP389580 PRJNA865512 TCR alpha and beta repseq PRJNA865512 Other TCR Repertoire sequencing raw reads TCR alpha and beta for several species   pubmed:37344590     ZF 5   strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 5|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire ZF 15 5 ZF 15 5 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP389580     ZF_5_01_R1.fastq.gz ZF_5_01_R2.fastq.gz ZF_5_02_R1.fastq.gz ZF_5_02_R2.fastq.gz ZF_5_03_R1.fastq.gz ZF_5_03_R2.fastq.gz ZF_5_04_R1.fastq.gz ZF_5_04_R2.fastq.gz ZF_5_05_R1.fastq.gz ZF_5_05_R2.fastq.gz ZF_5_06_R1.fastq.gz ZF_5_06_R2.fastq.gz ZF_5_07_R1.fastq.gz ZF_5_07_R2.fastq.gz ZF_5_08_R1.fastq.gz ZF_5_08_R2.fastq.gz ZF_5_09_R1.fastq.gz ZF_5_09_R2.fastq.gz ZF_5_10_R1.fastq.gz ZF_5_10_R2.fastq.gz ZF_5_11_R1.fastq.gz ZF_5_11_R2.fastq.gz ZF_5_12_R1.fastq.gz ZF_5_12_R2.fastq.gz ZF_5_13_R1.fastq.gz ZF_5_13_R2.fastq.gz ZF_5_14_R1.fastq.gz ZF_5_14_R2.fastq.gz ZF_5_15_R1.fastq.gz ZF_5_15_R2.fastq.gz ZF_5_16_R1.fastq.gz ZF_5_16_R2.fastq.gz ZF_5_17_R1.fastq.gz ZF_5_17_R2.fastq.gz ZF_5_18_R1.fastq.gz ZF_5_18_R2.fastq.gz ZF_5_19_R1.fastq.gz ZF_5_19_R2.fastq.gz ZF_5_20_R1.fastq.gz ZF_5_20_R2.fastq.gz ZF_5_21_R1.fastq.gz ZF_5_21_R2.fastq.gz ZF_5_22_R1.fastq.gz ZF_5_22_R2.fastq.gz ZF_5_23_R1.fastq.gz ZF_5_23_R2.fastq.gz ZF_5_24_R1.fastq.gz ZF_5_24_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 20320004000.0 40640008.0 ZF 5 01 R1.fastq.gz 0:250 1:250 A:5513136568;C:4158821282;G:4255839821;T:6389137086;N:3069243 250 250     5513136568 4158821282 4255839821 6389137086 3069243 SRX16840871 SRS14445862 SRA1468898 Max Planck Institut|Boehm Max Planck Institut 2 0.48427 3e-05 0.0017 1e-05 0.99663 0.99997 0.55487 1.0 250 250 B T mate2 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70849 70849 SRR20821266 SRX16840870 SRS14445861 SRP389580 PRJNA865512 TCR alpha and beta repseq PRJNA865512 Other TCR Repertoire sequencing raw reads TCR alpha and beta for several species   pubmed:37344590     ZF 4   strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 4|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire ZF 15 4 ZF 15 4 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP389580     ZF_4_01_R1.fastq.gz ZF_4_01_R2.fastq.gz ZF_4_02_R1.fastq.gz ZF_4_02_R2.fastq.gz ZF_4_03_R1.fastq.gz ZF_4_03_R2.fastq.gz ZF_4_04_R1.fastq.gz ZF_4_04_R2.fastq.gz ZF_4_05_R1.fastq.gz ZF_4_05_R2.fastq.gz ZF_4_06_R1.fastq.gz ZF_4_06_R2.fastq.gz ZF_4_07_R1.fastq.gz ZF_4_07_R2.fastq.gz ZF_4_08_R1.fastq.gz ZF_4_08_R2.fastq.gz ZF_4_09_R1.fastq.gz ZF_4_09_R2.fastq.gz ZF_4_10_R1.fastq.gz ZF_4_10_R2.fastq.gz ZF_4_11_R1.fastq.gz ZF_4_11_R2.fastq.gz ZF_4_12_R1.fastq.gz ZF_4_12_R2.fastq.gz ZF_4_13_R1.fastq.gz ZF_4_13_R2.fastq.gz ZF_4_14_R1.fastq.gz ZF_4_14_R2.fastq.gz ZF_4_15_R1.fastq.gz ZF_4_15_R2.fastq.gz ZF_4_16_R1.fastq.gz ZF_4_16_R2.fastq.gz ZF_4_17_R1.fastq.gz ZF_4_17_R2.fastq.gz ZF_4_18_R1.fastq.gz ZF_4_18_R2.fastq.gz ZF_4_19_R1.fastq.gz ZF_4_19_R2.fastq.gz ZF_4_20_R1.fastq.gz ZF_4_20_R2.fastq.gz ZF_4_21_R1.fastq.gz ZF_4_21_R2.fastq.gz ZF_4_22_R1.fastq.gz ZF_4_22_R2.fastq.gz ZF_4_23_R1.fastq.gz ZF_4_23_R2.fastq.gz ZF_4_24_R1.fastq.gz ZF_4_24_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 26480052500.0 52960105.0 ZF 4 01 R1.fastq.gz 0:250 1:250 A:7438425276;C:5364918772;G:5496497801;T:8176167902;N:4042749 250 250     7438425276 5364918772 5496497801 8176167902 4042749 SRX16840870 SRS14445861 SRA1468898 Max Planck Institut|Boehm Max Planck Institut 2 0.21859 0.00094 0.00058 0.00078 0.99734 0.99989 0.24747 0.38095 250 250 B T mate2 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70850 70850 SRR20821265 SRX16840869 SRS14445860 SRP389580 PRJNA865512 TCR alpha and beta repseq PRJNA865512 Other TCR Repertoire sequencing raw reads TCR alpha and beta for several species   pubmed:37344590     ZF 3   strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 3|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire ZF 15 3 ZF 15 3 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP389580     ZF_3_01_R1.fastq.gz ZF_3_04_R1.fastq.gz ZF_3_04_R2.fastq.gz ZF_3_05_R1.fastq.gz ZF_3_05_R2.fastq.gz ZF_3_06_R1.fastq.gz ZF_3_06_R2.fastq.gz ZF_3_07_R1.fastq.gz ZF_3_07_R2.fastq.gz ZF_3_08_R1.fastq.gz ZF_3_08_R2.fastq.gz ZF_3_09_R1.fastq.gz ZF_3_09_R2.fastq.gz ZF_3_10_R1.fastq.gz ZF_3_10_R2.fastq.gz ZF_3_11_R1.fastq.gz ZF_3_11_R2.fastq.gz ZF_3_12_R1.fastq.gz ZF_3_12_R2.fastq.gz ZF_3_13_R1.fastq.gz ZF_3_13_R2.fastq.gz ZF_3_14_R1.fastq.gz ZF_3_14_R2.fastq.gz ZF_3_15_R1.fastq.gz ZF_3_15_R2.fastq.gz ZF_3_16_R1.fastq.gz ZF_3_16_R2.fastq.gz ZF_3_17_R1.fastq.gz ZF_3_17_R2.fastq.gz ZF_3_18_R1.fastq.gz ZF_3_18_R2.fastq.gz ZF_3_19_R1.fastq.gz ZF_3_19_R2.fastq.gz ZF_3_03_R2.fastq.gz ZF_3_03_R1.fastq.gz ZF_3_02_R2.fastq.gz ZF_3_02_R1.fastq.gz ZF_3_01_R2.fastq.gz ZF_3_20_R1.fastq.gz ZF_3_20_R2.fastq.gz ZF_3_21_R1.fastq.gz ZF_3_21_R2.fastq.gz ZF_3_22_R1.fastq.gz ZF_3_22_R2.fastq.gz ZF_3_23_R1.fastq.gz ZF_3_23_R2.fastq.gz ZF_3_24_R1.fastq.gz ZF_3_24_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 29081958500.0 58163917.0 ZF 3 01 R1.fastq.gz 0:250 1:250 A:7805451909;C:6022172769;G:6087748826;T:9162169304;N:4415692 250 250     7805451909 6022172769 6087748826 9162169304 4415692 SRX16840869 SRS14445860 SRA1468898 Max Planck Institut|Boehm Max Planck Institut 2 0.62325 0.00106 0.0032 0.00082 0.98957 0.99979 0.66228 0.16 250 250 B T mate2 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70851 70851 SRR20821268 SRX16840868 SRS14446084 SRP389580 PRJNA865512 TCR alpha and beta repseq PRJNA865512 Other TCR Repertoire sequencing raw reads TCR alpha and beta for several species   pubmed:37344590     ZF 2   strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 2|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire ZF 15 2 ZF 15 2 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP389580     ZF_2_01_R1.fastq.gz ZF_2_01_R2.fastq.gz ZF_2_02_R1.fastq.gz ZF_2_02_R2.fastq.gz ZF_2_03_R1.fastq.gz ZF_2_03_R2.fastq.gz ZF_2_04_R1.fastq.gz ZF_2_04_R2.fastq.gz ZF_2_05_R1.fastq.gz ZF_2_05_R2.fastq.gz ZF_2_06_R1.fastq.gz ZF_2_06_R2.fastq.gz ZF_2_07_R1.fastq.gz ZF_2_07_R2.fastq.gz ZF_2_08_R1.fastq.gz ZF_2_08_R2.fastq.gz ZF_2_09_R1.fastq.gz ZF_2_09_R2.fastq.gz ZF_2_10_R1.fastq.gz ZF_2_10_R2.fastq.gz ZF_2_11_R1.fastq.gz ZF_2_11_R2.fastq.gz ZF_2_12_R1.fastq.gz ZF_2_12_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 11339660500.0 22679321.0 ZF 2 01 R1.fastq.gz 0:250 1:250 A:3182635402;C:2291052382;G:2349897358;T:3514348167;N:1727191 250 250     3182635402 2291052382 2349897358 3514348167 1727191 SRX16840868 SRS14446084 SRA1468898 Max Planck Institut|Boehm Max Planck Institut 2 0.27918 0.0001 0.00045 9e-05 0.99701 1.0 0.09245   250 250 B T mate2 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70852 70852 SRR20821269 SRX16840867 SRS14416088 SRP389580 PRJNA865512 TCR alpha and beta repseq PRJNA865512 Other TCR Repertoire sequencing raw reads TCR alpha and beta for several species   pubmed:37344590     ZF 1   strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire ZF 15 1 ZF 15 1 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP389580     ZF_1_01_R1.fastq.gz ZF_1_01_R2.fastq.gz ZF_1_02_R1.fastq.gz ZF_1_02_R2.fastq.gz ZF_1_03_R1.fastq.gz ZF_1_03_R2.fastq.gz ZF_1_04_R1.fastq.gz ZF_1_04_R2.fastq.gz ZF_1_05_R1.fastq.gz ZF_1_05_R2.fastq.gz ZF_1_06_R1.fastq.gz ZF_1_06_R2.fastq.gz ZF_1_07_R1.fastq.gz ZF_1_07_R2.fastq.gz ZF_1_08_R1.fastq.gz ZF_1_08_R2.fastq.gz ZF_1_09_R1.fastq.gz ZF_1_09_R2.fastq.gz ZF_1_10_R1.fastq.gz ZF_1_10_R2.fastq.gz ZF_1_11_R1.fastq.gz ZF_1_11_R2.fastq.gz ZF_1_12_R1.fastq.gz ZF_1_12_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 11128555000.0 22257110.0 ZF 1 01 R1.fastq.gz 0:250 1:250 A:3130611303;C:2262908040;G:2314518134;T:3418822646;N:1694877 250 250     3130611303 2262908040 2314518134 3418822646 1694877 SRX16840867 SRS14416088 SRA1468898 Max Planck Institut|Boehm Max Planck Institut 2 0.26276 0.0002 0.00063 0.00019 0.99669 1.0 0.16038   250 250 B T mate2 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70853 70853 SRR20821016 SRX16840621 SRS14445862 SRP389580 PRJNA865512 TCR alpha and beta repseq PRJNA865512 Other TCR Repertoire sequencing raw reads TCR alpha and beta for several species   pubmed:37344590     ZF 5   strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 5|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire ZF 15 5 ZF 15 5 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP389580     Fish_5_s1_R1.fastq.gz Fish_5_s1_R2.fastq.gz Fish_5_s2_R1.fastq.gz Fish_5_s2_R2.fastq.gz Fish_5_s3_R1.fastq.gz Fish_5_s3_R2.fastq.gz Fish_5_s4_R1.fastq.gz Fish_5_s4_R2.fastq.gz Fish_5_s5_R1.fastq.gz Fish_5_s5_R2.fastq.gz Fish_5_s6_R1.fastq.gz Fish_5_s6_R2.fastq.gz Fish_5_s7_R1.fastq.gz Fish_5_s7_R2.fastq.gz Fish_5_s8_R1.fastq.gz Fish_5_s8_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 12404050000.0 24808100.0 Fish 5 s1 R1.fastq.gz 0:250 1:250 A:3320455167;C:2599567608;G:2616971343;T:3833147517;N:33908365 250 250     3320455167 2599567608 2616971343 3833147517 33908365 SRX16840621 SRS14445862 SRA1468889 Max Planck Institut|Boehm Max Planck Institut 2 0.46656 1e-05 0.00102 0.0 0.99715 1.0 0.67642   250 250 B T mate2 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70854 70854 SRR20821017 SRX16840620 SRS14445861 SRP389580 PRJNA865512 TCR alpha and beta repseq PRJNA865512 Other TCR Repertoire sequencing raw reads TCR alpha and beta for several species   pubmed:37344590     ZF 4   strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 4|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire ZF 15 4 ZF 15 4 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP389580     Fish_4_s1_R1.fastq.gz Fish_4_s1_R2.fastq.gz Fish_4_s2_R1.fastq.gz Fish_4_s2_R2.fastq.gz Fish_4_s3_R1.fastq.gz Fish_4_s3_R2.fastq.gz Fish_4_s4_R1.fastq.gz Fish_4_s4_R2.fastq.gz Fish_4_s5_R1.fastq.gz Fish_4_s5_R2.fastq.gz Fish_4_s6_R1.fastq.gz Fish_4_s6_R2.fastq.gz Fish_4_s7_R1.fastq.gz Fish_4_s7_R2.fastq.gz Fish_4_s8_R1.fastq.gz Fish_4_s8_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 14690229000.0 29380458.0 Fish 4 s1 R1.fastq.gz 0:250 1:250 A:4100988732;C:3028728956;G:3105063955;T:4415320433;N:40126924 250 250     4100988732 3028728956 3105063955 4415320433 40126924 SRX16840620 SRS14445861 SRA1468889 Max Planck Institut|Boehm Max Planck Institut 2 0.20173 4e-05 9e-05 3e-05 0.99886 0.99997 0.02749 0.0 250 250 B T mate2 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70855 70855 SRR20821018 SRX16840619 SRS14445860 SRP389580 PRJNA865512 TCR alpha and beta repseq PRJNA865512 Other TCR Repertoire sequencing raw reads TCR alpha and beta for several species   pubmed:37344590     ZF 3   strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 3|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire ZF 15 3 ZF 15 3 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP389580     Fish_3_s1_R1.fastq.gz Fish_3_s1_R2.fastq.gz Fish_3_s2_R1.fastq.gz Fish_3_s2_R2.fastq.gz Fish_3_s3_R1.fastq.gz Fish_3_s3_R2.fastq.gz Fish_3_s4_R1.fastq.gz Fish_3_s4_R2.fastq.gz Fish_3_s5_R1.fastq.gz Fish_3_s5_R2.fastq.gz Fish_3_s6_R1.fastq.gz Fish_3_s6_R2.fastq.gz Fish_3_s7_R1.fastq.gz Fish_3_s7_R2.fastq.gz Fish_3_s8_R1.fastq.gz Fish_3_s8_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 11142784000.0 22285568.0 Fish 3 s1 R1.fastq.gz 0:250 1:250 A:2958284498;C:2329155931;G:2358380909;T:3466617016;N:30345646 250 250     2958284498 2329155931 2358380909 3466617016 30345646 SRX16840619 SRS14445860 SRA1468889 Max Planck Institut|Boehm Max Planck Institut 2 0.56406 2e-05 0.00159 1e-05 0.99868 1.0 0.67877   250 250 B T mate2 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70856 70856 SRR20821019 SRX16840618 SRS14416088 SRP389580 PRJNA865512 TCR alpha and beta repseq PRJNA865512 Other TCR Repertoire sequencing raw reads TCR alpha and beta for several species   pubmed:37344590     ZF 1   strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire ZF 15 1 ZF 15 1 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP389580     Fish_1_s1_R1.fastq.gz Fish_1_s1_R2.fastq.gz Fish_1_s2_R1.fastq.gz Fish_1_s2_R2.fastq.gz Fish_1_s3_R1.fastq.gz Fish_1_s3_R2.fastq.gz Fish_1_s4_R1.fastq.gz Fish_1_s4_R2.fastq.gz Fish_1_s5_R1.fastq.gz Fish_1_s5_R2.fastq.gz Fish_1_s6_R1.fastq.gz Fish_1_s6_R2.fastq.gz Fish_1_s7_R1.fastq.gz Fish_1_s7_R2.fastq.gz Fish_1_s8_R1.fastq.gz Fish_1_s8_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 23425111500.0 46850223.0 Fish 1 s1 R1.fastq.gz 0:250 1:250 A:6539165809;C:4856848776;G:4965848496;T:6999397120;N:63851299 250 250     6539165809 4856848776 4965848496 6999397120 63851299 SRX16840618 SRS14416088 SRA1468889 Max Planck Institut|Boehm Max Planck Institut 2 0.22816 3e-05 3e-05 2e-05 0.99931 1.0 0.01795   250 250 B T mate2 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70857 70857 SRR20774919 SRX16794795 SRS14416088 SRP389580 PRJNA865512 TCR alpha and beta repseq PRJNA865512 Other TCR Repertoire sequencing raw reads TCR alpha and beta for several species   pubmed:37344590     ZF 1   strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire ZF 14 ZF 14 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389580     ZF_1_R1.fastq.gz ZF_1_R2.fastq.gz ZF_2_R1.fastq.gz ZF_2_R2.fastq.gz ZF_3_R1.fastq.gz ZF_3_R2.fastq.gz ZF_4_R1.fastq.gz ZF_4_R2.fastq.gz ZF_5_R1.fastq.gz ZF_5_R2.fastq.gz ZF_6_R1.fastq.gz ZF_6_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 2060446800.0 3434078.0 ZF 1 R1.fastq.gz 0:300 1:300 A:583057434;C:430231786;G:436041334;T:600779904;N:10336342 300 300     583057434 430231786 436041334 600779904 10336342 SRX16794795 SRS14416088 SRA1467929 Max Planck Institut|Boehm Max Planck Institut 2 0.22937 0.00332 0.00094 0.00296 0.99853 0.99977 0.07993 0.34426 300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-03 Adult Adult Trunk Surface Structure
70858 70858 SRR20770403 SRX16790285 SRS14416088 SRP389580 PRJNA865512 TCR alpha and beta repseq PRJNA865512 Other TCR Repertoire sequencing raw reads TCR alpha and beta for several species   pubmed:37344590     ZF 1   strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire ZF 13 ZF 13 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389580     ZF_1_R1.fastq.gz ZF_1_R2.fastq.gz ZF_2_R1.fastq.gz ZF_2_R2.fastq.gz ZF_3_R1.fastq.gz ZF_3_R2.fastq.gz ZF_4_R1.fastq.gz ZF_4_R2.fastq.gz ZF_5_R1.fastq.gz ZF_5_R2.fastq.gz ZF_6_R1.fastq.gz ZF_6_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 404958600.0 674931.0 ZF 1 R1.fastq.gz 0:300 1:300 A:115477181;C:85168234;G:86149957;T:118163222;N:6 300 300     115477181 85168234 86149957 118163222 6 SRX16790285 SRS14416088 SRA1467850 Max Planck Institut|Boehm Max Planck Institut 2 0.22832 0.00294 0.00097 0.00267 0.9987 0.99981 0.06408 0.06382 300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-03 Adult Adult Trunk Surface Structure
70865 70865 SRR21025648 SRX17041895 SRS14626477 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590   Cb mutant ZF ZF B1   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Cb mutant fish 1|BioSampleModel:Model organism or animal                 TCR Cbeta mutant zebrafish repertoire ZF B1 39 ZF B1 39 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     ZF_B_1_R1.fastq.gz ZF_B_1_R2.fastq.gz fastq fastq 542089800.0 903483.0 ZF B 1 R1.fastq.gz 0:300 1:300 A:135658810;C:102336162;G:99078828;T:137378936;N:67637064 300 300     135658810 102336162 99078828 137378936 67637064 SRX17041895 SRS14626477 SRA1474283 Max Planck Institut|Boehm Max Planck Institut 2 0.12189 0.0 0.00343 0.0 0.99504 1.0 0.39007   300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-12 Adult Adult Trunk Surface Structure
70866 70866 SRR21025649 SRX17041894 SRS14626476 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590   Ca mutant ZF ZF A3   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Ca mutant fish 3|BioSampleModel:Model organism or animal                 TCR Calpha mutant zebrafish repertoire ZF A3 39 ZF A3 39 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     ZF_A_3_R1.fastq.gz ZF_A_3_R2.fastq.gz fastq fastq 308308200.0 513847.0 ZF A 3 R1.fastq.gz 0:300 1:300 A:78000370;C:58841499;G:57272527;T:75682806;N:38510998 300 300     78000370 58841499 57272527 75682806 38510998 SRX17041894 SRS14626476 SRA1474283 Max Planck Institut|Boehm Max Planck Institut 2 0.12647 0.0 0.00605 0.0 0.99492 1.0 0.53455   300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-12 Adult Adult Trunk Surface Structure
70867 70867 SRR21025650 SRX17041893 SRS14626475 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590   Ca mutant ZF ZF A2   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Ca mutant fish 2|BioSampleModel:Model organism or animal                 TCR Calpha mutant zebrafish repertoire ZF A2 39 ZF A2 39 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     ZF_A_2_R1.fastq.gz ZF_A_2_R2.fastq.gz fastq fastq 478462200.0 797437.0 ZF A 2 R1.fastq.gz 0:300 1:300 A:121169167;C:89660025;G:88748678;T:119119069;N:59765261 300 300     121169167 89660025 88748678 119119069 59765261 SRX17041893 SRS14626475 SRA1474283 Max Planck Institut|Boehm Max Planck Institut 2 0.14904 0.0 0.00506 0.0 0.995 1.0 0.41067   300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-12 Adult Adult Trunk Surface Structure
70868 70868 SRR21025651 SRX17041892 SRS14626474 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590   Ca mutant ZF ZF A1   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Ca mutant fish 1|BioSampleModel:Model organism or animal                 TCR Calpha mutant zebrafish repertoire ZF A1 39 ZF A1 39 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     ZF_A_1_R1.fastq.gz ZF_A_1_R2.fastq.gz fastq fastq 678536400.0 1130894.0 ZF A 1 R1.fastq.gz 0:300 1:300 A:171085705;C:127441930;G:123964513;T:171506152;N:84538100 300 300     171085705 127441930 123964513 171506152 84538100 SRX17041892 SRS14626474 SRA1474283 Max Planck Institut|Boehm Max Planck Institut 2 0.15972 0.0 0.00626 0.0 0.99358 1.0 0.41112   300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-12 Adult Adult Trunk Surface Structure
70869 70869 SRR21025647 SRX17041891 SRS14626540 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590   Ca mutant ZF ZF e7   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal                 TCR Calpha mutant zebrafish repertoire ZF e7 39 ZF e7 39 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP389887     ZF_E7_1_R1.fastq.gz ZF_E7_1_R2.fastq.gz ZF_E7_2_R1.fastq.gz ZF_E7_2_R2.fastq.gz ZF_E7_3_R1.fastq.gz ZF_E7_3_R2.fastq.gz ZF_E7_4_R1.fastq.gz ZF_E7_4_R2.fastq.gz ZF_E7_5_R1.fastq.gz ZF_E7_5_R2.fastq.gz ZF_E7_6_R1.fastq.gz ZF_E7_6_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 3743030974.0 7456237.0 ZF E7 1 R1.fastq.gz 0:251 1:251 A:1059538576;C:756862432;G:800743054;T:1125844134;N:42778 251 251     1059538576 756862432 800743054 1125844134 42778 SRX17041891 SRS14626540 SRA1474280 Max Planck Institut|Boehm Max Planck Institut 2 0.17475 4e-05 0.00048 3e-05 0.99606 1.0 0.06216   251 251 B T mate2 technical by mapping diff illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Germany 2022-08-12 Adult Adult Trunk Surface Structure
70870 70870 SRR21025625 SRX17041869 SRS14626540 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590   Ca mutant ZF ZF e7   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal                 TCR Calpha mutant zebrafish repertoire ZF e7 37 ZF e7 37 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP389887     ZF_E7_1_R1.fastq.gz ZF_E7_1_R2.fastq.gz ZF_E7_2_R1.fastq.gz ZF_E7_2_R2.fastq.gz ZF_E7_3_R1.fastq.gz ZF_E7_3_R2.fastq.gz ZF_E7_4_R1.fastq.gz ZF_E7_4_R2.fastq.gz ZF_E7_5_R1.fastq.gz ZF_E7_5_R2.fastq.gz ZF_E7_6_R1.fastq.gz ZF_E7_6_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 6358841530.0 12667015.0 ZF E7 1 R1.fastq.gz 0:251 1:251 A:1780832978;C:1325459337;G:1324964858;T:1927430147;N:154210 251 251     1780832978 1325459337 1324964858 1927430147 154210 SRX17041869 SRS14626540 SRA1474264 Max Planck Institut|Boehm Max Planck Institut 2 0.17062 0.00202 0.00036 0.00201 0.9961 1.0 0.45331   251 251 B T mate2 technical by mapping diff illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Germany 2022-08-12 Adult Adult Trunk Surface Structure
70871 70871 SRR21025558 SRX17041805 SRS14626477 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590   Cb mutant ZF ZF B1   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Cb mutant fish 1|BioSampleModel:Model organism or animal                 TCR Cbeta mutant zebrafish repertoire ZF B1 37 ZF B1 37 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     ZF_B_1_R1.fastq.gz ZF_B_1_R2.fastq.gz fastq fastq 690565200.0 1150942.0 ZF B 1 R1.fastq.gz 0:300 1:300 A:190561034;C:142350146;G:136690824;T:190637972;N:30325224 300 300     190561034 142350146 136690824 190637972 30325224 SRX17041805 SRS14626477 SRA1474258 Max Planck Institut|Boehm Max Planck Institut 2 0.11811 9e-05 0.00424 4e-05 0.99472 0.99995 0.43275 0.5 300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-12 Adult Adult Trunk Surface Structure
70872 70872 SRR21025559 SRX17041804 SRS14626476 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590   Ca mutant ZF ZF A3   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Ca mutant fish 3|BioSampleModel:Model organism or animal                 TCR Calpha mutant zebrafish repertoire ZF A3 37 ZF A3 37 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     ZF_A_3_R1.fastq.gz ZF_A_3_R2.fastq.gz fastq fastq 460708800.0 767848.0 ZF A 3 R1.fastq.gz 0:300 1:300 A:128444122;C:96066218;G:93502400;T:122577077;N:20118983 300 300     128444122 96066218 93502400 122577077 20118983 SRX17041804 SRS14626476 SRA1474258 Max Planck Institut|Boehm Max Planck Institut 2 0.12334 8e-05 0.00785 5e-05 0.99486 0.99997 0.57556 1.0 300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-12 Adult Adult Trunk Surface Structure
70873 70873 SRR21025560 SRX17041803 SRS14626475 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590   Ca mutant ZF ZF A2   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Ca mutant fish 2|BioSampleModel:Model organism or animal                 TCR Calpha mutant zebrafish repertoire ZF A2 37 ZF A2 37 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     ZF_A_2_R1.fastq.gz ZF_A_2_R2.fastq.gz fastq fastq 665948400.0 1109914.0 ZF A 2 R1.fastq.gz 0:300 1:300 A:185901193;C:135612243;G:135145305;T:180035490;N:29254169 300 300     185901193 135612243 135145305 180035490 29254169 SRX17041803 SRS14626475 SRA1474258 Max Planck Institut|Boehm Max Planck Institut 2 0.14435 0.0 0.00709 0.0 0.99429 1.0 0.46577   300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-12 Adult Adult Trunk Surface Structure
70874 70874 SRR21025561 SRX17041802 SRS14626474 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590   Ca mutant ZF ZF A1   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Ca mutant fish 1|BioSampleModel:Model organism or animal                 TCR Calpha mutant zebrafish repertoire ZF A1 37 ZF A1 37 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     ZF_A_1_R1.fastq.gz ZF_A_1_R2.fastq.gz fastq fastq 988403400.0 1647339.0 ZF A 1 R1.fastq.gz 0:300 1:300 A:274811390;C:202503190;G:195476681;T:272202966;N:43409173 300 300     274811390 202503190 195476681 272202966 43409173 SRX17041802 SRS14626474 SRA1474258 Max Planck Institut|Boehm Max Planck Institut 2 0.15605 0.0001 0.0075 6e-05 0.99304 0.99997 0.44452 0.0 300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-12 Adult Adult Trunk Surface Structure
70875 70875 SRR20823554 SRX16843129 SRS14446944 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 8   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 8|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 25 8 CF 25 8 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_8i_1_R1.fastq.gz CF_8i_1_R2.fastq.gz CF_8i_2_R1.fastq.gz CF_8i_2_R2.fastq.gz CF_8i_3_R1.fastq.gz CF_8i_3_R2.fastq.gz CF_8i_4_R1.fastq.gz CF_8i_4_R2.fastq.gz CF_8ii_1_R1.fastq.gz CF_8ii_1_R2.fastq.gz CF_8ii_2_R1.fastq.gz CF_8ii_2_R2.fastq.gz CF_8ii_3_R1.fastq.gz CF_8ii_3_R2.fastq.gz CF_8ii_4_R1.fastq.gz CF_8ii_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 353982600.0 589971.0 CF 8i 1 R1.fastq.gz 0:300 1:300 A:95337236;C:72187591;G:66351347;T:119978210;N:128216 300 300     95337236 72187591 66351347 119978210 128216 SRX16843129 SRS14446944 SRA1468943 Max Planck Institut|Boehm Max Planck Institut 2 0.15841 0.00021 0.00079 0.00015 0.99961 0.99995 0.44832 0.0 300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70876 70876 SRR20823555 SRX16843128 SRS14446943 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 7   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 7|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 25 7 CF 25 7 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_7i_1_R1.fastq.gz CF_7i_1_R2.fastq.gz CF_7i_2_R1.fastq.gz CF_7i_2_R2.fastq.gz CF_7i_3_R1.fastq.gz CF_7i_3_R2.fastq.gz CF_7i_4_R1.fastq.gz CF_7i_4_R2.fastq.gz CF_7ii_1_R1.fastq.gz CF_7ii_1_R2.fastq.gz CF_7ii_2_R1.fastq.gz CF_7ii_2_R2.fastq.gz CF_7ii_3_R1.fastq.gz CF_7ii_3_R2.fastq.gz CF_7ii_4_R1.fastq.gz CF_7ii_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 1747909200.0 2913182.0 CF 7i 1 R1.fastq.gz 0:300 1:300 A:483225545;C:364529202;G:366375323;T:532231673;N:1547457 300 300     483225545 364529202 366375323 532231673 1547457 SRX16843128 SRS14446943 SRA1468943 Max Planck Institut|Boehm Max Planck Institut 2 0.11826 4e-05 0.00019 3e-05 0.99939 1.0 0.0663   300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70877 70877 SRR20823556 SRX16843127 SRS14446942 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 6   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 6|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 25 6 CF 25 6 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_6i_1_R1.fastq.gz CF_6i_1_R2.fastq.gz CF_6i_2_R1.fastq.gz CF_6i_2_R2.fastq.gz CF_6i_3_R1.fastq.gz CF_6i_3_R2.fastq.gz CF_6i_4_R1.fastq.gz CF_6i_4_R2.fastq.gz CF_6ii_1_R1.fastq.gz CF_6ii_1_R2.fastq.gz CF_6ii_2_R1.fastq.gz CF_6ii_2_R2.fastq.gz CF_6ii_3_R1.fastq.gz CF_6ii_3_R2.fastq.gz CF_6ii_4_R1.fastq.gz CF_6ii_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 2113688400.0 3522814.0 CF 6i 1 R1.fastq.gz 0:300 1:300 A:584272199;C:441403541;G:441691655;T:644543652;N:1777353 300 300     584272199 441403541 441691655 644543652 1777353 SRX16843127 SRS14446942 SRA1468943 Max Planck Institut|Boehm Max Planck Institut 2 0.11642 4e-05 0.00012 1e-05 0.99955 0.99997 0.05908 0.0 300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70878 70878 SRR20823557 SRX16843126 SRS14446941 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 5   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 5|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 25 5 CF 25 5 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_5i_1_R1.fastq.gz CF_5i_1_R2.fastq.gz CF_5i_2_R1.fastq.gz CF_5i_2_R2.fastq.gz CF_5i_3_R1.fastq.gz CF_5i_3_R2.fastq.gz CF_5i_4_R1.fastq.gz CF_5i_4_R2.fastq.gz CF_5ii_1_R1.fastq.gz CF_5ii_1_R2.fastq.gz CF_5ii_2_R1.fastq.gz CF_5ii_2_R2.fastq.gz CF_5ii_3_R1.fastq.gz CF_5ii_3_R2.fastq.gz CF_5ii_4_R1.fastq.gz CF_5ii_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 1563231600.0 2605386.0 CF 5i 1 R1.fastq.gz 0:300 1:300 A:431285088;C:326876454;G:326380744;T:477247162;N:1442152 300 300     431285088 326876454 326380744 477247162 1442152 SRX16843126 SRS14446941 SRA1468943 Max Planck Institut|Boehm Max Planck Institut 2 0.11826 4e-05 0.00024 2e-05 0.99928 0.99997 0.20833 0.0 300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70879 70879 SRR20823558 SRX16843125 SRS14446939 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 4   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 4|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 25 4 CF 25 4 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_4i_1_R1.fastq.gz CF_4i_1_R2.fastq.gz CF_4i_2_R1.fastq.gz CF_4i_2_R2.fastq.gz CF_4i_3_R1.fastq.gz CF_4i_3_R2.fastq.gz CF_4i_4_R1.fastq.gz CF_4i_4_R2.fastq.gz CF_4ii_1_R1.fastq.gz CF_4ii_1_R2.fastq.gz CF_4ii_2_R1.fastq.gz CF_4ii_2_R2.fastq.gz CF_4ii_3_R1.fastq.gz CF_4ii_3_R2.fastq.gz CF_4ii_4_R1.fastq.gz CF_4ii_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 2110654800.0 3517758.0 CF 4i 1 R1.fastq.gz 0:300 1:300 A:583907147;C:441977681;G:442168609;T:640843429;N:1757934 300 300     583907147 441977681 442168609 640843429 1757934 SRX16843125 SRS14446939 SRA1468943 Max Planck Institut|Boehm Max Planck Institut 2 0.09992 3e-05 0.00029 2e-05 0.99922 1.0 0.06198   300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70880 70880 SRR20823559 SRX16843124 SRS14446940 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 3   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 3|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 25 3 CF 25 3 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_3i_1_R1.fastq.gz CF_3i_1_R2.fastq.gz CF_3i_2_R1.fastq.gz CF_3i_2_R2.fastq.gz CF_3i_3_R1.fastq.gz CF_3i_3_R2.fastq.gz CF_3i_4_R1.fastq.gz CF_3i_4_R2.fastq.gz CF_3ii_1_R1.fastq.gz CF_3ii_1_R2.fastq.gz CF_3ii_2_R1.fastq.gz CF_3ii_2_R2.fastq.gz CF_3ii_3_R1.fastq.gz CF_3ii_3_R2.fastq.gz CF_3ii_4_R1.fastq.gz CF_3ii_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 1358656200.0 2264427.0 CF 3i 1 R1.fastq.gz 0:300 1:300 A:373530868;C:285820823;G:282903019;T:415201895;N:1199595 300 300     373530868 285820823 282903019 415201895 1199595 SRX16843124 SRS14446940 SRA1468943 Max Planck Institut|Boehm Max Planck Institut 2 0.13469 7e-05 0.00024 4e-05 0.9992 0.99997 0.09944 0.0 300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70881 70881 SRR20823560 SRX16843123 SRS14446938 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 2   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 2|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 25 2 CF 25 2 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_1_2ii_5_R1.fastq.gz CF_1_2ii_5_R2.fastq.gz CF_1_2ii_6_R1.fastq.gz CF_1_2ii_6_R2.fastq.gz CF_1_2ii_7_R1.fastq.gz CF_1_2ii_7_R2.fastq.gz CF_1_2ii_8_R1.fastq.gz CF_1_2ii_8_R2.fastq.gz CF_2i_1_R1.fastq.gz CF_2i_1_R2.fastq.gz CF_2i_2_R1.fastq.gz CF_2i_2_R2.fastq.gz CF_2i_3_R1.fastq.gz CF_2i_3_R2.fastq.gz CF_2i_4_R1.fastq.gz CF_2i_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 1017871200.0 1696452.0 CF 1 2ii 5 R1.fastq.gz 0:300 1:300 A:281361148;C:213220413;G:212347028;T:310111745;N:830866 300 300     281361148 213220413 212347028 310111745 830866 SRX16843123 SRS14446938 SRA1468943 Max Planck Institut|Boehm Max Planck Institut 2 0.13088 5e-05 0.00029 3e-05 0.99949 0.99997 0.11499 0.0 300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70882 70882 SRR20823561 SRX16843122 SRS14446937 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 1   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 25 1 CF 25 1 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_1_2ii_1_R1.fastq.gz CF_1_2ii_1_R2.fastq.gz CF_1_2ii_2_R1.fastq.gz CF_1_2ii_2_R2.fastq.gz CF_1_2ii_3_R1.fastq.gz CF_1_2ii_3_R2.fastq.gz CF_1_2ii_4_R1.fastq.gz CF_1_2ii_4_R2.fastq.gz CF_1i_1_R1.fastq.gz CF_1i_1_R2.fastq.gz CF_1i_2_R1.fastq.gz CF_1i_2_R2.fastq.gz CF_1i_3_R1.fastq.gz CF_1i_3_R2.fastq.gz CF_1i_4_R1.fastq.gz CF_1i_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 725888400.0 1209814.0 CF 1 2ii 1 R1.fastq.gz 0:300 1:300 A:200725177;C:151940953;G:151616803;T:220966635;N:638832 300 300     200725177 151940953 151616803 220966635 638832 SRX16843122 SRS14446937 SRA1468943 Max Planck Institut|Boehm Max Planck Institut 2 0.12857 4e-05 0.0002 2e-05 0.99937 0.99995 0.05962 0.0 300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70883 70883 SRR20822140 SRX16841749 SRS14446944 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 8   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 8|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 23 8 CF 23 8 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_8i_1_R1.fastq.gz CF_8i_1_R2.fastq.gz CF_8i_2_R1.fastq.gz CF_8i_2_R2.fastq.gz CF_8i_3_R1.fastq.gz CF_8i_3_R2.fastq.gz CF_8i_4_R1.fastq.gz CF_8i_4_R2.fastq.gz CF_8ii_1_R1.fastq.gz CF_8ii_1_R2.fastq.gz CF_8ii_2_R1.fastq.gz CF_8ii_2_R2.fastq.gz CF_8ii_3_R1.fastq.gz CF_8ii_3_R2.fastq.gz CF_8ii_4_R1.fastq.gz CF_8ii_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 992400.0 1654.0 CF 8i 1 R1.fastq.gz 0:300 1:300 A:268792;C:212596;G:195943;T:315027;N:42 300 300     268792 212596 195943 315027 42 SRX16841749 SRS14446944 SRA1468924 Max Planck Institut|Boehm Max Planck Institut 2 0.15462 0.04181 0.0 0.03858 0.99995 0.99997 0.62809 0.0 300 300 B T mate2 technical by mapping diff illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70884 70884 SRR20822141 SRX16841748 SRS14446943 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 7   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 7|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 23 7 CF 23 7 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_7i_1_R1.fastq.gz CF_7i_1_R2.fastq.gz CF_7i_2_R1.fastq.gz CF_7i_2_R2.fastq.gz CF_7i_3_R1.fastq.gz CF_7i_3_R2.fastq.gz CF_7i_4_R1.fastq.gz CF_7i_4_R2.fastq.gz CF_7ii_1_R1.fastq.gz CF_7ii_1_R2.fastq.gz CF_7ii_2_R1.fastq.gz CF_7ii_2_R2.fastq.gz CF_7ii_3_R1.fastq.gz CF_7ii_3_R2.fastq.gz CF_7ii_4_R1.fastq.gz CF_7ii_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 90294000.0 150490.0 CF 7i 1 R1.fastq.gz 0:300 1:300 A:24528989;C:19392684;G:18743775;T:27623730;N:4822 300 300     24528989 19392684 18743775 27623730 4822 SRX16841748 SRS14446943 SRA1468924 Max Planck Institut|Boehm Max Planck Institut 2 0.07466 2e-05 0.00014 1e-05 0.99979 1.0 0.07443   300 300 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70885 70885 SRR20822142 SRX16841747 SRS14446942 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 6   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 6|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 23 6 CF 23 6 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_6i_1_R1.fastq.gz CF_6i_1_R2.fastq.gz CF_6i_2_R1.fastq.gz CF_6i_2_R2.fastq.gz CF_6i_3_R1.fastq.gz CF_6i_3_R2.fastq.gz CF_6i_4_R1.fastq.gz CF_6i_4_R2.fastq.gz CF_6ii_1_R1.fastq.gz CF_6ii_1_R2.fastq.gz CF_6ii_2_R1.fastq.gz CF_6ii_2_R2.fastq.gz CF_6ii_3_R1.fastq.gz CF_6ii_3_R2.fastq.gz CF_6ii_4_R1.fastq.gz CF_6ii_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 88349400.0 147249.0 CF 6i 1 R1.fastq.gz 0:300 1:300 A:23979442;C:18990541;G:18286837;T:27088540;N:4040 300 300     23979442 18990541 18286837 27088540 4040 SRX16841747 SRS14446942 SRA1468924 Max Planck Institut|Boehm Max Planck Institut 2 0.07 1e-05 0.00013 0.0 0.99967 1.0 0.08186   300 300 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70886 70886 SRR20822143 SRX16841746 SRS14446941 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 5   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 5|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 23 5 CF 23 5 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_5i_1_R1.fastq.gz CF_5i_1_R2.fastq.gz CF_5i_2_R1.fastq.gz CF_5i_2_R2.fastq.gz CF_5i_3_R1.fastq.gz CF_5i_3_R2.fastq.gz CF_5i_4_R1.fastq.gz CF_5i_4_R2.fastq.gz CF_5ii_1_R1.fastq.gz CF_5ii_1_R2.fastq.gz CF_5ii_2_R1.fastq.gz CF_5ii_2_R2.fastq.gz CF_5ii_3_R1.fastq.gz CF_5ii_3_R2.fastq.gz CF_5ii_4_R1.fastq.gz CF_5ii_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 64482600.0 107471.0 CF 5i 1 R1.fastq.gz 0:300 1:300 A:17454099;C:13879333;G:13325003;T:19821371;N:2794 300 300     17454099 13879333 13325003 19821371 2794 SRX16841746 SRS14446941 SRA1468924 Max Planck Institut|Boehm Max Planck Institut 2 0.06999 4e-05 0.00066 3e-05 0.99971 1.0 0.34418   300 300 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70887 70887 SRR20822144 SRX16841745 SRS14446939 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 4   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 4|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 23 4 CF 23 4 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_4i_1_R1.fastq.gz CF_4i_1_R2.fastq.gz CF_4i_2_R1.fastq.gz CF_4i_2_R2.fastq.gz CF_4i_3_R1.fastq.gz CF_4i_3_R2.fastq.gz CF_4i_4_R1.fastq.gz CF_4i_4_R2.fastq.gz CF_4ii_1_R1.fastq.gz CF_4ii_1_R2.fastq.gz CF_4ii_2_R1.fastq.gz CF_4ii_2_R2.fastq.gz CF_4ii_3_R1.fastq.gz CF_4ii_3_R2.fastq.gz CF_4ii_4_R1.fastq.gz CF_4ii_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 89868600.0 149781.0 CF 4i 1 R1.fastq.gz 0:300 1:300 A:24387218;C:19355528;G:18593888;T:27527119;N:4847 300 300     24387218 19355528 18593888 27527119 4847 SRX16841745 SRS14446939 SRA1468924 Max Planck Institut|Boehm Max Planck Institut 2 0.04754 1e-05 0.00033 0.0 0.99939 1.0 0.10674   300 300 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70888 70888 SRR20822145 SRX16841744 SRS14446940 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 3   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 3|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 23 3 CF 23 3 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_3i_1_R1.fastq.gz CF_3i_1_R2.fastq.gz CF_3i_2_R1.fastq.gz CF_3i_2_R2.fastq.gz CF_3i_3_R1.fastq.gz CF_3i_3_R2.fastq.gz CF_3i_4_R1.fastq.gz CF_3i_4_R2.fastq.gz CF_3ii_1_R1.fastq.gz CF_3ii_1_R2.fastq.gz CF_3ii_2_R1.fastq.gz CF_3ii_2_R2.fastq.gz CF_3ii_3_R1.fastq.gz CF_3ii_3_R2.fastq.gz CF_3ii_4_R1.fastq.gz CF_3ii_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 57636000.0 96060.0 CF 3i 1 R1.fastq.gz 0:300 1:300 A:15535821;C:12511228;G:11909225;T:17677153;N:2573 300 300     15535821 12511228 11909225 17677153 2573 SRX16841744 SRS14446940 SRA1468924 Max Planck Institut|Boehm Max Planck Institut 2 0.08313 3e-05 0.00034 1e-05 0.99979 0.99997 0.14815 0.0 300 300 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70889 70889 SRR20822146 SRX16841743 SRS14446938 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 2   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 2|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 23 2 CF 23 2 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_1_2ii_5_R1.fastq.gz CF_1_2ii_5_R2.fastq.gz CF_1_2ii_6_R1.fastq.gz CF_1_2ii_6_R2.fastq.gz CF_1_2ii_7_R1.fastq.gz CF_1_2ii_7_R2.fastq.gz CF_1_2ii_8_R1.fastq.gz CF_1_2ii_8_R2.fastq.gz CF_2i_1_R1.fastq.gz CF_2i_1_R2.fastq.gz CF_2i_2_R1.fastq.gz CF_2i_2_R2.fastq.gz CF_2i_3_R1.fastq.gz CF_2i_3_R2.fastq.gz CF_2i_4_R1.fastq.gz CF_2i_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 45198000.0 75330.0 CF 1 2ii 5 R1.fastq.gz 0:300 1:300 A:12248161;C:9753570;G:9327745;T:13866741;N:1783 300 300     12248161 9753570 9327745 13866741 1783 SRX16841743 SRS14446938 SRA1468924 Max Planck Institut|Boehm Max Planck Institut 2 0.07225 0.0 0.00046 0.0 0.99981 1.0 0.19253   300 300 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
70890 70890 SRR20822147 SRX16841742 SRS14446937 SRP389887 PRJNA865921 Zebrafish mutant TCR alpha and beta lines PRJNA865921 Other Cas9 generated TCR alpha or beta Zebrafish lines   pubmed:37344590     CF 1   strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal                 TCRab zebrafish repertoire CF 23 1 CF 23 1 Repertoire amplification from cDNA with C specific primers for TCRa and TCRb     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP389887     CF_1_2ii_1_R1.fastq.gz CF_1_2ii_1_R2.fastq.gz CF_1_2ii_2_R1.fastq.gz CF_1_2ii_2_R2.fastq.gz CF_1_2ii_3_R1.fastq.gz CF_1_2ii_3_R2.fastq.gz CF_1_2ii_4_R1.fastq.gz CF_1_2ii_4_R2.fastq.gz CF_1i_1_R1.fastq.gz CF_1i_1_R2.fastq.gz CF_1i_2_R1.fastq.gz CF_1i_2_R2.fastq.gz CF_1i_3_R1.fastq.gz CF_1i_3_R2.fastq.gz CF_1i_4_R1.fastq.gz CF_1i_4_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 33274200.0 55457.0 CF 1 2ii 1 R1.fastq.gz 0:300 1:300 A:9021097;C:7171844;G:6860950;T:10218627;N:1682 300 300     9021097 7171844 6860950 10218627 1682 SRX16841742 SRS14446937 SRA1468924 Max Planck Institut|Boehm Max Planck Institut 2 0.06705 3e-05 0.00012 2e-05 0.99987 1.0 0.11281   300 300 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   Germany 2022-08-04 Adult Adult Trunk Surface Structure
76317 76317 SRR24827620 SRX20592547 SRS17893040 SRP441132 PRJNA980117 Sex blind: bridging the gap between drug exposure and sex related gene expression in Danio rerio using next generation sequencing NGS data and a literature review to find the missing links in pharmaceutical and environmental toxicology studies GSE234104 Transcriptome Analysis Abstract: The sex of both humans and Danio rerio has previously been shown to affect the way individuals respond to drug exposure. Genes which allow identification of sex in juvenile zebrafish show potential to reveal these confounding variables between sex in toxicological and preclinical trials but the link between these is so far missing. These sex specific early expressed genes where expression is not altered by drug exposure must be carefully selected for this purpose. We aimed to discover genes which can be used in pharmaceutical trials and environmental toxicology studies to uncover sex related variations in gene expression with drug application using the model organism Danio rerio. Previously published early sex determining genes from King et al. were evaluated as well as additional genes selected from our zebrafish Next generation sequencing NGS data which are known from previously published works not to be susceptible to changes in expression with drug exposure. NGS revealed a further ten female specific genes vtg1 cyp17a1 cyp19a1a igf3 ftz f1 gdf9 foxl2a Nr0b1 ipo4 lhcgr and five male related candidate genes FKBP5 apobb1 hbaa1 dmrt1 spata6 which are also expressed in juvenile zebrafish 28 dpf dpf. Following this a literature review was performed to classify which of these early expressed sex specific genes are already known to be affected by drug exposure in order to determine candidate genes to be used in pharmaceutical trials or environmental toxicology testing studies. Discovery of these early sex determining genes in Danio rerio will allow identification of sex related responses to drug testing to improve sex specific healthcare and the medical treatment of human patients. Overall design: NGS RNA sequences were produced from two 28 dpf zebrafish which we classified as juvenile in this paper two adult male and two adult female zebrafish using whole body tissue samples. Juveniles were tested to indicate whether sex was genetically visible at this stage of development. RNA quality tes…   pubmed:37398910   Adult female Danio rerio 1 GSM7445820   source name:Whole body|tissue:Whole body|cell type:female|developmental stage:Adult|treatment:N/A|geo loc name:missing|collection date:missing Adult female Danio rerio 1 All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al. 2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al. 2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al. 2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2 the NGS data was normalised and differential gene expression analysis of juvenile male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al. 2014; King et al. 2020. Normalisation was based on the ‘median of ratios’ the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Assembly: StringTie Galaxy Version 1.3.4 Pertea et al. 2015. Supplementary files format and content: Tables of gene expression Whole body No experiments were carried out with live adult nor subadult fish before euthanasia. Accordingly animal welfare guidelines were followed while zebrafish were kept by the breeder. RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF Basel according to Illumina’s standard protocol for RNA sequencing Illumina Inc. San Diego USA Cat. # RS 100 0801. Galaxy server usegalaxy.org NGS data was collected from 28 dpf and adult zebrafish which had already been euthanised with Tricaine by the breeder. tissue:Whole body|cell type:female|developmental stage:Adult|treatment:N/A GSM7445820 GSM7445820: Adult female Danio rerio 1; Danio rerio; RNA Seq GSM7445820 r1 GSM7445820 1 RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF Basel according to Illumina's standard protocol for RNA sequencing Illumina Inc. San Diego USA Cat. # RS 100 0801. Galaxy server usegalaxy.org   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP441132   loader:fastq load.py adult_female1.trim.fastq.gz fastq 6960942447.0 92399725.0 GSM7445820 r1 0:75.34 A:1696472126;C:1707300560;G:1688891841;T:1868259357;N:18563 75       1696472126 1707300560 1688891841 1868259357 18563 SRX20592547 SRS17893040 SRA1649389 Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland 1 0.96065   0.03687   0.70378   0.4269   76   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Switzerland 2023-06-05 Adult Adult Trunk Surface Structure
76318 76318 SRR24827621 SRX20592546 SRS17893038 SRP441132 PRJNA980117 Sex blind: bridging the gap between drug exposure and sex related gene expression in Danio rerio using next generation sequencing NGS data and a literature review to find the missing links in pharmaceutical and environmental toxicology studies GSE234104 Transcriptome Analysis Abstract: The sex of both humans and Danio rerio has previously been shown to affect the way individuals respond to drug exposure. Genes which allow identification of sex in juvenile zebrafish show potential to reveal these confounding variables between sex in toxicological and preclinical trials but the link between these is so far missing. These sex specific early expressed genes where expression is not altered by drug exposure must be carefully selected for this purpose. We aimed to discover genes which can be used in pharmaceutical trials and environmental toxicology studies to uncover sex related variations in gene expression with drug application using the model organism Danio rerio. Previously published early sex determining genes from King et al. were evaluated as well as additional genes selected from our zebrafish Next generation sequencing NGS data which are known from previously published works not to be susceptible to changes in expression with drug exposure. NGS revealed a further ten female specific genes vtg1 cyp17a1 cyp19a1a igf3 ftz f1 gdf9 foxl2a Nr0b1 ipo4 lhcgr and five male related candidate genes FKBP5 apobb1 hbaa1 dmrt1 spata6 which are also expressed in juvenile zebrafish 28 dpf dpf. Following this a literature review was performed to classify which of these early expressed sex specific genes are already known to be affected by drug exposure in order to determine candidate genes to be used in pharmaceutical trials or environmental toxicology testing studies. Discovery of these early sex determining genes in Danio rerio will allow identification of sex related responses to drug testing to improve sex specific healthcare and the medical treatment of human patients. Overall design: NGS RNA sequences were produced from two 28 dpf zebrafish which we classified as juvenile in this paper two adult male and two adult female zebrafish using whole body tissue samples. Juveniles were tested to indicate whether sex was genetically visible at this stage of development. RNA quality tes…   pubmed:37398910   Adult male Danio rerio 2 GSM7445819   source name:Whole body|tissue:Whole body|cell type:male|developmental stage:Adult|treatment:N/A|geo loc name:missing|collection date:missing Adult male Danio rerio 2 All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al. 2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al. 2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al. 2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2 the NGS data was normalised and differential gene expression analysis of juvenile male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al. 2014; King et al. 2020. Normalisation was based on the ‘median of ratios’ the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Assembly: StringTie Galaxy Version 1.3.4 Pertea et al. 2015. Supplementary files format and content: Tables of gene expression Whole body No experiments were carried out with live adult nor subadult fish before euthanasia. Accordingly animal welfare guidelines were followed while zebrafish were kept by the breeder. RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF Basel according to Illumina’s standard protocol for RNA sequencing Illumina Inc. San Diego USA Cat. # RS 100 0801. Galaxy server usegalaxy.org NGS data was collected from 28 dpf and adult zebrafish which had already been euthanised with Tricaine by the breeder. tissue:Whole body|cell type:male|developmental stage:Adult|treatment:N/A GSM7445819 GSM7445819: Adult male Danio rerio 2; Danio rerio; RNA Seq GSM7445819 r1 GSM7445819 1 RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF Basel according to Illumina's standard protocol for RNA sequencing Illumina Inc. San Diego USA Cat. # RS 100 0801. Galaxy server usegalaxy.org   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP441132   loader:fastq load.py adult_male2.fastq.gz fastq 6427348500.0 84570375.0 GSM7445819 r1 0:76 A:1545286842;C:1577518751;G:1546293475;T:1758222296;N:27136 76       1545286842 1577518751 1546293475 1758222296 27136 SRX20592546 SRS17893038 SRA1649389 Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland 1 0.96097   0.05997   0.67892   0.50309   76   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Switzerland 2023-06-05 Adult Adult Trunk Surface Structure
76319 76319 SRR24827622 SRX20592545 SRS17893037 SRP441132 PRJNA980117 Sex blind: bridging the gap between drug exposure and sex related gene expression in Danio rerio using next generation sequencing NGS data and a literature review to find the missing links in pharmaceutical and environmental toxicology studies GSE234104 Transcriptome Analysis Abstract: The sex of both humans and Danio rerio has previously been shown to affect the way individuals respond to drug exposure. Genes which allow identification of sex in juvenile zebrafish show potential to reveal these confounding variables between sex in toxicological and preclinical trials but the link between these is so far missing. These sex specific early expressed genes where expression is not altered by drug exposure must be carefully selected for this purpose. We aimed to discover genes which can be used in pharmaceutical trials and environmental toxicology studies to uncover sex related variations in gene expression with drug application using the model organism Danio rerio. Previously published early sex determining genes from King et al. were evaluated as well as additional genes selected from our zebrafish Next generation sequencing NGS data which are known from previously published works not to be susceptible to changes in expression with drug exposure. NGS revealed a further ten female specific genes vtg1 cyp17a1 cyp19a1a igf3 ftz f1 gdf9 foxl2a Nr0b1 ipo4 lhcgr and five male related candidate genes FKBP5 apobb1 hbaa1 dmrt1 spata6 which are also expressed in juvenile zebrafish 28 dpf dpf. Following this a literature review was performed to classify which of these early expressed sex specific genes are already known to be affected by drug exposure in order to determine candidate genes to be used in pharmaceutical trials or environmental toxicology testing studies. Discovery of these early sex determining genes in Danio rerio will allow identification of sex related responses to drug testing to improve sex specific healthcare and the medical treatment of human patients. Overall design: NGS RNA sequences were produced from two 28 dpf zebrafish which we classified as juvenile in this paper two adult male and two adult female zebrafish using whole body tissue samples. Juveniles were tested to indicate whether sex was genetically visible at this stage of development. RNA quality tes…   pubmed:37398910   Adult male Danio rerio 1 GSM7445818   source name:Whole body|tissue:Whole body|cell type:male|developmental stage:Adult|treatment:N/A|geo loc name:missing|collection date:missing Adult male Danio rerio 1 All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al. 2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al. 2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al. 2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2 the NGS data was normalised and differential gene expression analysis of juvenile male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al. 2014; King et al. 2020. Normalisation was based on the ‘median of ratios’ the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Assembly: StringTie Galaxy Version 1.3.4 Pertea et al. 2015. Supplementary files format and content: Tables of gene expression Whole body No experiments were carried out with live adult nor subadult fish before euthanasia. Accordingly animal welfare guidelines were followed while zebrafish were kept by the breeder. RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF Basel according to Illumina’s standard protocol for RNA sequencing Illumina Inc. San Diego USA Cat. # RS 100 0801. Galaxy server usegalaxy.org NGS data was collected from 28 dpf and adult zebrafish which had already been euthanised with Tricaine by the breeder. tissue:Whole body|cell type:male|developmental stage:Adult|treatment:N/A GSM7445818 GSM7445818: Adult male Danio rerio 1; Danio rerio; RNA Seq GSM7445818 r1 GSM7445818 1 RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF Basel according to Illumina's standard protocol for RNA sequencing Illumina Inc. San Diego USA Cat. # RS 100 0801. Galaxy server usegalaxy.org   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP441132   loader:fastq load.py adult_male1.fastq.gz fastq 5805719116.0 76391041.0 GSM7445818 r1 0:76 A:1411248618;C:1411955007;G:1394119941;T:1588372207;N:23343 76       1411248618 1411955007 1394119941 1588372207 23343 SRX20592545 SRS17893037 SRA1649389 Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland 1 0.95916   0.06495   0.67744   0.50406   76   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Switzerland 2023-06-05 Adult Adult Trunk Surface Structure
76322 76322 SRR24827625 SRX20592542 SRS17893034 SRP441132 PRJNA980117 Sex blind: bridging the gap between drug exposure and sex related gene expression in Danio rerio using next generation sequencing NGS data and a literature review to find the missing links in pharmaceutical and environmental toxicology studies GSE234104 Transcriptome Analysis Abstract: The sex of both humans and Danio rerio has previously been shown to affect the way individuals respond to drug exposure. Genes which allow identification of sex in juvenile zebrafish show potential to reveal these confounding variables between sex in toxicological and preclinical trials but the link between these is so far missing. These sex specific early expressed genes where expression is not altered by drug exposure must be carefully selected for this purpose. We aimed to discover genes which can be used in pharmaceutical trials and environmental toxicology studies to uncover sex related variations in gene expression with drug application using the model organism Danio rerio. Previously published early sex determining genes from King et al. were evaluated as well as additional genes selected from our zebrafish Next generation sequencing NGS data which are known from previously published works not to be susceptible to changes in expression with drug exposure. NGS revealed a further ten female specific genes vtg1 cyp17a1 cyp19a1a igf3 ftz f1 gdf9 foxl2a Nr0b1 ipo4 lhcgr and five male related candidate genes FKBP5 apobb1 hbaa1 dmrt1 spata6 which are also expressed in juvenile zebrafish 28 dpf dpf. Following this a literature review was performed to classify which of these early expressed sex specific genes are already known to be affected by drug exposure in order to determine candidate genes to be used in pharmaceutical trials or environmental toxicology testing studies. Discovery of these early sex determining genes in Danio rerio will allow identification of sex related responses to drug testing to improve sex specific healthcare and the medical treatment of human patients. Overall design: NGS RNA sequences were produced from two 28 dpf zebrafish which we classified as juvenile in this paper two adult male and two adult female zebrafish using whole body tissue samples. Juveniles were tested to indicate whether sex was genetically visible at this stage of development. RNA quality tes…   pubmed:37398910   Adult female Danio rerio 2 GSM7445821   source name:Whole body|tissue:Whole body|cell type:female|developmental stage:Adult|treatment:N/A|geo loc name:missing|collection date:missing Adult female Danio rerio 2 All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al. 2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al. 2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al. 2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2 the NGS data was normalised and differential gene expression analysis of juvenile male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al. 2014; King et al. 2020. Normalisation was based on the ‘median of ratios’ the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Assembly: StringTie Galaxy Version 1.3.4 Pertea et al. 2015. Supplementary files format and content: Tables of gene expression Whole body No experiments were carried out with live adult nor subadult fish before euthanasia. Accordingly animal welfare guidelines were followed while zebrafish were kept by the breeder. RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF Basel according to Illumina’s standard protocol for RNA sequencing Illumina Inc. San Diego USA Cat. # RS 100 0801. Galaxy server usegalaxy.org NGS data was collected from 28 dpf and adult zebrafish which had already been euthanised with Tricaine by the breeder. tissue:Whole body|cell type:female|developmental stage:Adult|treatment:N/A GSM7445821 GSM7445821: Adult female Danio rerio 2; Danio rerio; RNA Seq GSM7445821 r1 GSM7445821 1 RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF Basel according to Illumina's standard protocol for RNA sequencing Illumina Inc. San Diego USA Cat. # RS 100 0801. Galaxy server usegalaxy.org   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP441132   loader:fastq load.py adult_female2.fastq.gz fastq 6198618444.0 81560769.0 GSM7445821 r1 0:76 A:1511391857;C:1515880388;G:1511198416;T:1660122547;N:25236 76       1511391857 1515880388 1511198416 1660122547 25236 SRX20592542 SRS17893034 SRA1649389 Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland 1 0.95993   0.0372   0.71242   0.42265   76   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Switzerland 2023-06-05 Adult Adult Trunk Surface Structure

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;