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 24546,ERR964671,ERX1041634,ERS792101,ERP011038,PRJEB9889,The Zebrafish transcriptome during early development,ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22,Other,Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.,,,,KI BN JKE DRERIO RNASEQ,SAMEA3484816,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484816|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 1cell|common name:zebrafish|dev stage:1cell|sample name:KI BN JKE DRERIO RNASEQ 2009 1cell|strain:Tuebingen,,,,,,,,,AB SOLiD System 3.0 sequencing,ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 5,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,ERP011038,AB SOLiD System 3.0 sequencing,ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-20091014-1cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-1cell_F3_QV.qual.gz,SOLiD_native SOLiD_native,2625510200.0,52510204.0,ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 5,0:50,0:677149824;1:606769571;2:761187530;3:578170290;.:2232985,50,,,,,,,,,ERX1041634,ERS792101,ERA458495,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,1,0.71662,,0.0994,,0.91644,,0.74578,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Sweden,2015-07-15,Zygote,Embryo,Undetermined,Embryo Imprecise 24547,ERR964670,ERX1041633,ERS792104,ERP011038,PRJEB9889,The Zebrafish transcriptome during early development,ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22,Other,Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.,,,,KI BN JKE DRERIO RNASEQ,SAMEA3484819,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484819|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 50epiboly|common name:zebrafish|dev stage:50% epiboly|sample name:KI BN JKE DRERIO RNASEQ 2009 50epiboly|strain:Tuebingen,,,,,,,,,AB SOLiD System 3.0 sequencing,ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 4,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,ERP011038,AB SOLiD System 3.0 sequencing,ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-20090709-50epiboly_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-50epiboly_F3_QV.qual.gz,SOLiD_native SOLiD_native,5325942150.0,106518843.0,ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 4,0:50,0:1376469323;1:1227617853;2:1499234750;3:1210700143;.:11920081,50,,,,,,,,,ERX1041633,ERS792104,ERA458495,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,1,0.7059,,0.10511,,0.91492,,0.75125,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Sweden,2015-07-15,Gastrula,Embryo,Undetermined,Embryo Imprecise 24548,ERR964669,ERX1041632,ERS792103,ERP011038,PRJEB9889,The Zebrafish transcriptome during early development,ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22,Other,Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.,,,,KI BN JKE DRERIO RNASEQ,SAMEA3484818,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484818|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 512cell|common name:zebrafish|dev stage:512 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 512cell|strain:Tuebingen,,,,,,,,,AB SOLiD System 3.0 sequencing,ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 3,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,ERP011038,AB SOLiD System 3.0 sequencing,ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-20090709-512cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-512cell_F3_QV.qual.gz,SOLiD_native SOLiD_native,5452772750.0,109055455.0,ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 3,0:50,0:1391108289;1:1312099760;2:1551659810;3:1179923010;.:17981881,50,,,,,,,,,ERX1041632,ERS792103,ERA458495,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,1,0.73133,,0.07897,,0.88057,,0.63645,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Sweden,2015-07-15,Blastula,Embryo,Undetermined,Embryo Imprecise 24549,ERR964667,ERX1041630,ERS792101,ERP011038,PRJEB9889,The Zebrafish transcriptome during early development,ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22,Other,Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.,,,,KI BN JKE DRERIO RNASEQ,SAMEA3484816,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484816|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 1cell|common name:zebrafish|dev stage:1cell|sample name:KI BN JKE DRERIO RNASEQ 2009 1cell|strain:Tuebingen,,,,,,,,,AB SOLiD System 3.0 sequencing,ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,ERP011038,AB SOLiD System 3.0 sequencing,ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-20090709-1cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-1cell_F3_QV.qual.gz,SOLiD_native SOLiD_native,5717685400.0,114353708.0,ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 1,0:50,0:1643444976;1:1261570333;2:1504304496;3:1282815913;.:25549682,50,,,,,,,,,ERX1041630,ERS792101,ERA458495,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,1,0.72274,,0.11151,,0.92348,,0.71904,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Sweden,2015-07-15,Zygote,Embryo,Undetermined,Embryo Imprecise 24550,ERR964668,ERX1041631,ERS792102,ERP011038,PRJEB9889,The Zebrafish transcriptome during early development,ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22,Other,Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.,,,,KI BN JKE DRERIO RNASEQ,SAMEA3484817,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484817|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 16cell|common name:zebrafish|dev stage:16 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 16cell|strain:Tuebingen,,,,,,,,,AB SOLiD System 3.0 sequencing,ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 2,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,ERP011038,AB SOLiD System 3.0 sequencing,ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-20090709-16cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-16cell_F3_QV.qual.gz,SOLiD_native SOLiD_native,5278508300.0,105570166.0,ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 2,0:50,0:1410981717;1:1203936808;2:1415708111;3:1223403795;.:24477869,50,,,,,,,,,ERX1041631,ERS792102,ERA458495,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,1,0.71371,,0.09346,,0.91539,,0.73015,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Sweden,2015-07-15,Cleavage,Embryo,Undetermined,Embryo Imprecise 24551,ERR964674,ERX1041637,ERS792104,ERP011038,PRJEB9889,The Zebrafish transcriptome during early development,ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22,Other,Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.,,,,KI BN JKE DRERIO RNASEQ,SAMEA3484819,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484819|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 50epiboly|common name:zebrafish|dev stage:50% epiboly|sample name:KI BN JKE DRERIO RNASEQ 2009 50epiboly|strain:Tuebingen,,,,,,,,,AB SOLiD System 3.0 sequencing,ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:873 8,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,ERP011038,AB SOLiD System 3.0 sequencing,ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-20091014-50epiboly_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-50epiboly_F3_QV.qual.gz,SOLiD_native SOLiD_native,2541596650.0,50831933.0,ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:873 8,0:50,0:670988333;1:585266057;2:708634642;3:574052618;.:2655000,50,,,,,,,,,ERX1041637,ERS792104,ERA458495,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,1,0.72135,,0.10529,,0.90997,,0.76049,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Sweden,2015-07-15,Gastrula,Embryo,Undetermined,Embryo Imprecise 24552,ERR964673,ERX1041636,ERS792103,ERP011038,PRJEB9889,The Zebrafish transcriptome during early development,ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22,Other,Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.,,,,KI BN JKE DRERIO RNASEQ,SAMEA3484818,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484818|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 512cell|common name:zebrafish|dev stage:512 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 512cell|strain:Tuebingen,,,,,,,,,AB SOLiD System 3.0 sequencing,ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 7,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,ERP011038,AB SOLiD System 3.0 sequencing,ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-20091014-512cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-512cell_F3_QV.qual.gz,SOLiD_native SOLiD_native,2027760000.0,40555200.0,ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 7,0:50,0:511413081;1:492642968;2:594959353;3:426692118;.:2052480,50,,,,,,,,,ERX1041636,ERS792103,ERA458495,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,1,0.77106,,0.08154,,0.85675,,0.64875,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Sweden,2015-07-15,Blastula,Embryo,Undetermined,Embryo Imprecise 24553,ERR964672,ERX1041635,ERS792102,ERP011038,PRJEB9889,The Zebrafish transcriptome during early development,ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22,Other,Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.,,,,KI BN JKE DRERIO RNASEQ,SAMEA3484817,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484817|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 16cell|common name:zebrafish|dev stage:16 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 16cell|strain:Tuebingen,,,,,,,,,AB SOLiD System 3.0 sequencing,ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 6,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,ERP011038,AB SOLiD System 3.0 sequencing,ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-20091014-16cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-16cell_F3_QV.qual.gz,SOLiD_native SOLiD_native,2719433200.0,54388664.0,ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 6,0:50,0:699731678;1:628745158;2:754903505;3:633574679;.:2478180,50,,,,,,,,,ERX1041635,ERS792102,ERA458495,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive,KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION,1,0.73214,,0.09566,,0.90836,,0.74043,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Sweden,2015-07-15,Cleavage,Embryo,Undetermined,Embryo Imprecise 58479,SRR12436783,SRX8932472,SRS7188817,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,GEO accession GSM4724702 is currently private and is scheduled to be released on Mar 17 2023.,GSM4724702,,,Ski7 FER R3 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:ski7 / |developmental stage:fertilized egg|strain:TLAB,GSM4724702,GSM4724702: Ski7 FER R3 polyA; Danio rerio; RNA Seq,GSM4724702,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724702,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,Ski7_Ooc_FER_R3_polyA.fastq,fastq,1777842000.0,17778420.0,GSM4724702 r1,0:100,A:440367983;C:434184573;G:419300944;T:483847825;N:140675,100,,,,440367983,434184573,419300944,483847825,140675,SRX8932472,SRS7188817,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96519,,0.0558,,0.79762,,0.49071,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58480,SRR12436782,SRX8932471,SRS7188816,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,GEO accession GSM4724701 is currently private and is scheduled to be released on Mar 17 2023.,GSM4724701,,,Ski7 FER R2 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:ski7 / |developmental stage:fertilized egg|strain:TLAB,GSM4724701,GSM4724701: Ski7 FER R2 polyA; Danio rerio; RNA Seq,GSM4724701,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724701,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,Ski7_Ooc_FER_R2_polyA.fastq,fastq,1580941100.0,15809411.0,GSM4724701 r1,0:100,A:393346905;C:386319994;G:375568338;T:425580399;N:125464,100,,,,393346905,386319994,375568338,425580399,125464,SRX8932471,SRS7188816,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96387,,0.06115,,0.80251,,0.48311,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58481,SRR12436781,SRX8932470,SRS7188815,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,Ski7 FER R1 polyA,GSM4724700,,tissue:zebrafish egg|genotype:ski7 / |developmental stage:fertilized egg|strain:TLAB,Ski7 FER R1 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:ski7 / |developmental stage:fertilized egg|strain:TLAB,GSM4724700,GSM4724700: Ski7 FER R1 polyA; Danio rerio; RNA Seq,GSM4724700,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724700,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,Ski7_Ooc_FER_R1_polyA.fastq,fastq,2213300600.0,22133006.0,GSM4724700 r1,0:100,A:554108128;C:532528202;G:525489897;T:601097373;N:77000,100,,,,554108128,532528202,525489897,601097373,77000,SRX8932470,SRS7188815,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96118,,0.06109,,0.8046,,0.48546,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58482,SRR12436780,SRX8932469,SRS7188814,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,Ski7 ACT R3 polyA,GSM4724699,,tissue:zebrafish egg|genotype:ski7 / |developmental stage:activated egg|strain:TLAB,Ski7 ACT R3 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:ski7 / |developmental stage:activated egg|strain:TLAB,GSM4724699,GSM4724699: Ski7 ACT R3 polyA; Danio rerio; RNA Seq,GSM4724699,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724699,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,Ski7_Ooc_ACT_R3_polyA.fastq,fastq,1922804200.0,19228042.0,GSM4724699 r1,0:100,A:480850703;C:463917366;G:452391538;T:525491911;N:152682,100,,,,480850703,463917366,452391538,525491911,152682,SRX8932469,SRS7188814,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96391,,0.0566,,0.80046,,0.48338,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58483,SRR12436779,SRX8932468,SRS7188813,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,Ski7 ACT R2 polyA,GSM4724698,,tissue:zebrafish egg|genotype:ski7 / |developmental stage:activated egg|strain:TLAB,Ski7 ACT R2 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:ski7 / |developmental stage:activated egg|strain:TLAB,GSM4724698,GSM4724698: Ski7 ACT R2 polyA; Danio rerio; RNA Seq,GSM4724698,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724698,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,Ski7_Ooc_ACT_R2_polyA.fastq,fastq,1928647900.0,19286479.0,GSM4724698 r1,0:100,A:482751186;C:469163733;G:460738816;T:515841418;N:152747,100,,,,482751186,469163733,460738816,515841418,152747,SRX8932468,SRS7188813,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96439,,0.05875,,0.80921,,0.47651,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58484,SRR12436778,SRX8932467,SRS7188812,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,Ski7 ACT R1 polyA,GSM4724697,,tissue:zebrafish egg|genotype:ski7 / |developmental stage:activated egg|strain:TLAB,Ski7 ACT R1 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:ski7 / |developmental stage:activated egg|strain:TLAB,GSM4724697,GSM4724697: Ski7 ACT R1 polyA; Danio rerio; RNA Seq,GSM4724697,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724697,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,Ski7_Ooc_ACT_R1_polyA.fastq,fastq,1459115400.0,14591154.0,GSM4724697 r1,0:100,A:361126428;C:358381337;G:346060607;T:393431535;N:115493,100,,,,361126428,358381337,346060607,393431535,115493,SRX8932467,SRS7188812,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96515,,0.06732,,0.80395,,0.48544,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58485,SRR12436777,SRX8932466,SRS7188811,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,Ski7 INA R3 polyA,GSM4724696,,tissue:zebrafish egg|genotype:ski7 / |developmental stage:inactive egg|strain:TLAB,Ski7 INA R3 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:ski7 / |developmental stage:inactive egg|strain:TLAB,GSM4724696,GSM4724696: Ski7 INA R3 polyA; Danio rerio; RNA Seq,GSM4724696,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724696,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,Ski7_Ooc_SQU_R3_polyA.fastq,fastq,1063954100.0,10639541.0,GSM4724696 r1,0:100,A:265551085;C:258698639;G:249117151;T:290502423;N:84802,100,,,,265551085,258698639,249117151,290502423,84802,SRX8932466,SRS7188811,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96171,,0.05846,,0.77346,,0.49713,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58486,SRR12436776,SRX8932465,SRS7188810,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,Ski7 INA R2 polyA,GSM4724695,,tissue:zebrafish egg|genotype:ski7 / |developmental stage:inactive egg|strain:TLAB,Ski7 INA R2 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:ski7 / |developmental stage:inactive egg|strain:TLAB,GSM4724695,GSM4724695: Ski7 INA R2 polyA; Danio rerio; RNA Seq,GSM4724695,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724695,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,Ski7_Ooc_SQU_R2_polyA.fastq,fastq,12041609400.0,120416094.0,GSM4724695 r1,0:100,A:3032420667;C:2912793806;G:2864619397;T:3231646175;N:129355,100,,,,3032420667,2912793806,2864619397,3231646175,129355,SRX8932465,SRS7188810,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.9612,,0.0577,,0.81091,,0.48028,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58487,SRR12436775,SRX8932464,SRS7188809,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,Ski7 INA R1 polyA,GSM4724694,,tissue:zebrafish egg|genotype:ski7 / |developmental stage:inactive egg|strain:TLAB,Ski7 INA R1 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:ski7 / |developmental stage:inactive egg|strain:TLAB,GSM4724694,GSM4724694: Ski7 INA R1 polyA; Danio rerio; RNA Seq,GSM4724694,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724694,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,Ski7_Ooc_SQU_R1_polyA.fastq,fastq,1017000600.0,10170006.0,GSM4724694 r1,0:100,A:250669909;C:250298820;G:241072052;T:274878959;N:80860,100,,,,250669909,250298820,241072052,274878959,80860,SRX8932464,SRS7188809,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96496,,0.05463,,0.80592,,0.47885,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58512,SRR12436750,SRX8932439,SRS7188784,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,WT FER R3 polyA,GSM4724669,,tissue:zebrafish egg|genotype:wild type|developmental stage:fertilized egg|strain:TLAB,WT FER R3 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|developmental stage:fertilized egg|strain:TLAB,GSM4724669,GSM4724669: WT FER R3 polyA; Danio rerio; RNA Seq,GSM4724669,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724669,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,WT_Ooc_FER_R3_polyA.fastq,fastq,6771381900.0,67713819.0,GSM4724669 r1,0:100,A:1749508781;C:1638169429;G:1570468624;T:1813188646;N:46420,100,,,,1749508781,1638169429,1570468624,1813188646,46420,SRX8932439,SRS7188784,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96178,,0.0557,,0.8254,,0.49638,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58513,SRR12436749,SRX8932438,SRS7188783,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,WT FER R2 polyA,GSM4724668,,tissue:zebrafish egg|genotype:wild type|developmental stage:fertilized egg|strain:TLAB,WT FER R2 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|developmental stage:fertilized egg|strain:TLAB,GSM4724668,GSM4724668: WT FER R2 polyA; Danio rerio; RNA Seq,GSM4724668,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724668,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,WT_Ooc_FER_R2_polyA.fastq,fastq,1061307000.0,10613070.0,GSM4724668 r1,0:100,A:257645591;C:262618152;G:256246632;T:284713098;N:83527,100,,,,257645591,262618152,256246632,284713098,83527,SRX8932438,SRS7188783,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.97035,,0.03791,,0.81769,,0.49181,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58514,SRR12436748,SRX8932437,SRS7188782,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,WT FER R1 polyA,GSM4724667,,tissue:zebrafish egg|genotype:wild type|developmental stage:fertilized egg|strain:TLAB,WT FER R1 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|developmental stage:fertilized egg|strain:TLAB,GSM4724667,GSM4724667: WT FER R1 polyA; Danio rerio; RNA Seq,GSM4724667,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724667,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,WT_Ooc_FER_R1_polyA.fastq,fastq,1139600300.0,11396003.0,GSM4724667 r1,0:100,A:278063418;C:281065192;G:275555423;T:304826973;N:89294,100,,,,278063418,281065192,275555423,304826973,89294,SRX8932437,SRS7188782,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96734,,0.06497,,0.81515,,0.49598,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58515,SRR12436747,SRX8932436,SRS7188781,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,WT ACT R3 polyA,GSM4724666,,tissue:zebrafish egg|genotype:wild type|developmental stage:activated egg|strain:TLAB,WT ACT R3 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|developmental stage:activated egg|strain:TLAB,GSM4724666,GSM4724666: WT ACT R3 polyA; Danio rerio; RNA Seq,GSM4724666,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724666,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,WT_Ooc_ACT_R3_polyA.fastq,fastq,8285065900.0,82850659.0,GSM4724666 r1,0:100,A:2144352935;C:1997916723;G:1922332681;T:2220387512;N:76049,100,,,,2144352935,1997916723,1922332681,2220387512,76049,SRX8932436,SRS7188781,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96318,,0.06182,,0.82511,,0.49104,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58516,SRR12436746,SRX8932435,SRS7188780,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,WT ACT R2 polyA,GSM4724665,,tissue:zebrafish egg|genotype:wild type|developmental stage:activated egg|strain:TLAB,WT ACT R2 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|developmental stage:activated egg|strain:TLAB,GSM4724665,GSM4724665: WT ACT R2 polyA; Danio rerio; RNA Seq,GSM4724665,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724665,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,WT_Ooc_ACT_R2_polyA.fastq,fastq,1209882800.0,12098828.0,GSM4724665 r1,0:100,A:302800050;C:293974175;G:286616960;T:326395031;N:96584,100,,,,302800050,293974175,286616960,326395031,96584,SRX8932435,SRS7188780,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96659,,0.054,,0.81694,,0.49155,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58517,SRR12436745,SRX8932434,SRS7188779,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,WT ACT R1 polyA,GSM4724664,,tissue:zebrafish egg|genotype:wild type|developmental stage:activated egg|strain:TLAB,WT ACT R1 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|developmental stage:activated egg|strain:TLAB,GSM4724664,GSM4724664: WT ACT R1 polyA; Danio rerio; RNA Seq,GSM4724664,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724664,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,WT_Ooc_ACT_R1_polyA.fastq,fastq,1664829900.0,16648299.0,GSM4724664 r1,0:100,A:407654756;C:407749206;G:401595821;T:447697470;N:132647,100,,,,407654756,407749206,401595821,447697470,132647,SRX8932434,SRS7188779,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96622,,0.06206,,0.81477,,0.49247,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58518,SRR12436744,SRX8932433,SRS7188778,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,WT INA R3 polyA,GSM4724663,,tissue:zebrafish egg|genotype:wild type|developmental stage:inactive egg|strain:TLAB,WT INA R3 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|developmental stage:inactive egg|strain:TLAB,GSM4724663,GSM4724663: WT INA R3 polyA; Danio rerio; RNA Seq,GSM4724663,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724663,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,WT_Ooc_SQU_R3_polyA.fastq,fastq,7170278200.0,71702782.0,GSM4724663 r1,0:100,A:1852022154;C:1727198429;G:1664295627;T:1926714520;N:47470,100,,,,1852022154,1727198429,1664295627,1926714520,47470,SRX8932433,SRS7188778,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96163,,0.06005,,0.81686,,0.48888,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58519,SRR12436743,SRX8932432,SRS7188777,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,WT INA R2 polyA,GSM4724662,,tissue:zebrafish egg|genotype:wild type|developmental stage:inactive egg|strain:TLAB,WT INA R2 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|developmental stage:inactive egg|strain:TLAB,GSM4724662,GSM4724662: WT INA R2 polyA; Danio rerio; RNA Seq,GSM4724662,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724662,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,WT_Ooc_SQU_R2_polyA.fastq,fastq,3912697500.0,39126975.0,GSM4724662 r1,0:100,A:975441132;C:951912258;G:931850781;T:1053181584;N:311745,100,,,,975441132,951912258,931850781,1053181584,311745,SRX8932432,SRS7188777,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96632,,0.05261,,0.80685,,0.49154,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise 58520,SRR12436742,SRX8932431,SRS7188776,SRP253077,PRJNA613025,Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition,GSE147112,Transcriptome Analysis,Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.,,pubmed:33600438;pubmed:34556579,,WT INA R1 polyA,GSM4724661,,tissue:zebrafish egg|genotype:wild type|developmental stage:inactive egg|strain:TLAB,WT INA R1 polyA,Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM,zebrafish egg,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|developmental stage:inactive egg|strain:TLAB,GSM4724661,GSM4724661: WT INA R1 polyA; Danio rerio; RNA Seq,GSM4724661,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM4724661,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253077,,,WT_Ooc_SQU_R1_polyA.fastq,fastq,1688458000.0,16884580.0,GSM4724661 r1,0:100,A:417912368;C:413739954;G:398861614;T:457809401;N:134663,100,,,,417912368,413739954,398861614,457809401,134663,SRX8932431,SRS7188776,SRA1055855,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.96554,,0.06045,,0.81972,,0.48378,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2020-08-12,Undetermined,Embryo,Undetermined,Embryo Imprecise