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
9752,ERR3489858,ERX3511273,ERS3556001,ERP116106,PRJEB33323,Deconstructing the individual steps of vertebrate translation initiation,ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422,Other,In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.,ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03,,,Sphere 3,SAMEA5752542,Computational Biology Unit,ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752542|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:5|common name:zebrafish|dev stage:Sphere|sample name:5|scientific name:Danio rerio,,,,,,,,,NextSeq 500 sequencing,ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 10,Sphere 3 LSU,None,RCP seq,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,NextSeq 500,,ERP116106,NextSeq 500 sequencing,ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22,,,2740392724.0,36057799.0,ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 10,0:76,A:1790452280;C:354001675;G:431182140;T:164697730;N:58899,76,,,,1790452280,354001675,431182140,164697730,58899,ERX3511273,ERS3556001,ERA2100634,Computational Biology Unit|European Nucleotide Archive,Computational Biology Unit,1,0.87154,,0.5323,,0.99793,,0.02983,,76,,B,,usable mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2019-07-03,Blastula,Embryo,Undetermined,Embryo Imprecise
9753,ERR3489857,ERX3511272,ERS3556001,ERP116106,PRJEB33323,Deconstructing the individual steps of vertebrate translation initiation,ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422,Other,In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.,ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03,,,Sphere 3,SAMEA5752542,Computational Biology Unit,ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752542|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:5|common name:zebrafish|dev stage:Sphere|sample name:5|scientific name:Danio rerio,,,,,,,,,NextSeq 500 sequencing,ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 9,Sphere 3 SSU,None,RCP seq,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,NextSeq 500,,ERP116106,NextSeq 500 sequencing,ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22,,,6277242192.0,82595292.0,ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 9,0:76,A:3129446012;C:1311888416;G:1369035262;T:466745503;N:126999,76,,,,3129446012,1311888416,1369035262,466745503,126999,ERX3511272,ERS3556001,ERA2100634,Computational Biology Unit|European Nucleotide Archive,Computational Biology Unit,1,0.65637,,0.35975,,0.9936,,0.24734,,76,,B,,usable mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2019-07-03,Blastula,Embryo,Undetermined,Embryo Imprecise
9754,ERR3489856,ERX3511271,ERS3556000,ERP116106,PRJEB33323,Deconstructing the individual steps of vertebrate translation initiation,ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422,Other,In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.,ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03,,,Sphere 2,SAMEA5752541,Computational Biology Unit,ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752541|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:4|common name:zebrafish|dev stage:Sphere|sample name:4|scientific name:Danio rerio,,,,,,,,,NextSeq 500 sequencing,ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 8,Sphere 2 LSU,None,RCP seq,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,NextSeq 500,,ERP116106,NextSeq 500 sequencing,ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 24,,,6679993476.0,87894651.0,ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 8,0:76,A:3113787833;C:1255798935;G:1750515950;T:559763997;N:126761,76,,,,3113787833,1255798935,1750515950,559763997,126761,ERX3511271,ERS3556000,ERA2100634,Computational Biology Unit|European Nucleotide Archive,Computational Biology Unit,1,0.66287,,0.41208,,0.99602,,0.17083,,76,,B,,usable mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2019-07-03,Blastula,Embryo,Undetermined,Embryo Imprecise
9755,ERR3489855,ERX3511270,ERS3556000,ERP116106,PRJEB33323,Deconstructing the individual steps of vertebrate translation initiation,ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422,Other,In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.,ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03,,,Sphere 2,SAMEA5752541,Computational Biology Unit,ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752541|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:4|common name:zebrafish|dev stage:Sphere|sample name:4|scientific name:Danio rerio,,,,,,,,,NextSeq 500 sequencing,ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 7,Sphere 2 SSU,None,RCP seq,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,NextSeq 500,,ERP116106,NextSeq 500 sequencing,ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22,,,13238731764.0,174193839.0,ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 7,0:76,A:7630016769;C:1835321568;G:2775223283;T:997916159;N:253985,76,,,,7630016769,1835321568,2775223283,997916159,253985,ERX3511270,ERS3556000,ERA2100634,Computational Biology Unit|European Nucleotide Archive,Computational Biology Unit,1,0.77269,,0.45994,,0.99683,,0.04249,,76,,B,,usable mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2019-07-03,Blastula,Embryo,Undetermined,Embryo Imprecise
9756,ERR3489854,ERX3511269,ERS3555999,ERP116106,PRJEB33323,Deconstructing the individual steps of vertebrate translation initiation,ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422,Other,In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.,ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03,,,Sphere 1,SAMEA5752540,Computational Biology Unit,ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752540|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:3|common name:zebrafish|dev stage:Sphere|sample name:3|scientific name:Danio rerio,,,,,,,,,NextSeq 500 sequencing,ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 6,Sphere 1 LSU,None,RCP seq,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,NextSeq 500,,ERP116106,NextSeq 500 sequencing,ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 24,,,3311799332.0,43576307.0,ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 6,0:76,A:1182325939;C:888677953;G:922571204;T:318159754;N:64482,76,,,,1182325939,888677953,922571204,318159754,64482,ERX3511269,ERS3555999,ERA2100634,Computational Biology Unit|European Nucleotide Archive,Computational Biology Unit,1,0.57505,,0.24459,,0.99582,,0.43365,,76,,B,,usable mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2019-07-03,Blastula,Embryo,Undetermined,Embryo Imprecise
9757,ERR3489853,ERX3511268,ERS3555999,ERP116106,PRJEB33323,Deconstructing the individual steps of vertebrate translation initiation,ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422,Other,In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.,ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03,,,Sphere 1,SAMEA5752540,Computational Biology Unit,ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752540|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:3|common name:zebrafish|dev stage:Sphere|sample name:3|scientific name:Danio rerio,,,,,,,,,NextSeq 500 sequencing,ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 5,Sphere 1 SSU,None,RCP seq,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,NextSeq 500,,ERP116106,NextSeq 500 sequencing,ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22,,,7403181508.0,97410283.0,ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 5,0:76,A:4338227974;C:1233250165;G:1372229712;T:459322295;N:151362,76,,,,4338227974,1233250165,1372229712,459322295,151362,ERX3511268,ERS3555999,ERA2100634,Computational Biology Unit|European Nucleotide Archive,Computational Biology Unit,1,0.765,,0.44747,,0.99515,,0.12467,,76,,B,,usable mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2019-07-03,Blastula,Embryo,Undetermined,Embryo Imprecise
9781,ERR3838748,ERX3851414,ERS4266438,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma High rep2,SAMEA6501989,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501989|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma High rep2|age:3.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma High rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma High rep2 p,Soma High rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,Fabio_High_rep2_soma_R1.fastq.gz Fabio_High_rep2_soma_R2.fastq.gz,fastq fastq,2072343523.0,13904136.0,E MTAB 8707:Fabio High rep2 soma R,0:74.52 1:74.53,A:596021076;C:439789413;G:451992691;T:583604290;N:936053,74,74,,,596021076,439789413,451992691,583604290,936053,ERX3851414,ERS4266438,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.94263,0.94098,0.04804,0.04844,0.75797,0.76039,0.50847,0.5014,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9782,ERR3838747,ERX3851413,ERS4266437,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma High rep1,SAMEA6501988,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501988|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma High rep1|age:3.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma High rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma High rep1 p,Soma High rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,Somatic_High_rep1_R1.fastq.gz Somatic_High_rep1_R2.fastq.gz,fastq fastq,6013555644.0,40662218.0,E MTAB 8707:Somatic High rep1 R,0:73.94 1:73.95,A:1821348300;C:1185534582;G:1227848010;T:1774836657;N:3988095,73,73,,,1821348300,1185534582,1227848010,1774836657,3988095,ERX3851413,ERS4266437,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93539,0.9357,0.07066,0.07028,0.76197,0.76386,0.54301,0.54343,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9783,ERR3838746,ERX3851412,ERS4266436,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma dome rep2,SAMEA6501987,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501987|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma dome rep2|age:4.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma dome rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma dome rep2 p,Soma dome rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S10_R1.fastq.gz S10_R2.fastq.gz,fastq fastq,1086124503.0,7272505.0,E MTAB 8707:S10 R,0:74.67 1:74.68,A:305920447;C:235855931;G:243442186;T:300439294;N:466645,74,74,,,305920447,235855931,243442186,300439294,466645,ERX3851412,ERS4266436,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.94089,0.94085,0.04872,0.04916,0.7419,0.74355,0.51209,0.5119,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9784,ERR3838745,ERX3851411,ERS4266435,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma dome rep1,SAMEA6501986,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501986|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma dome rep1|age:4.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma dome rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma dome rep1 p,Soma dome rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S8_R1.fastq.gz S8_R2.fastq.gz,fastq fastq,336100162.0,2240589.0,E MTAB 8707:S8 R,0:75.00 1:75.00,A:93960580;C:73499585;G:75981355;T:92580945;N:77697,75,75,,,93960580,73499585,75981355,92580945,77697,ERX3851411,ERS4266435,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93874,0.93856,0.05265,0.0517,0.74188,0.74381,0.51181,0.51086,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9785,ERR3838744,ERX3851410,ERS4266434,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma 256 cell rep2,SAMEA6501985,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501985|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 256 cell rep2|age:2.5|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 256 cell rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma 256 cell rep2 p,Soma 256 cell rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S2_R1.fastq.gz S2_R2.fastq.gz,fastq fastq,1272080863.0,8551103.0,E MTAB 8707:S2 R,0:74.38 1:74.38,A:364033393;C:268850689;G:276270908;T:362172455;N:753418,74,74,,,364033393,268850689,276270908,362172455,753418,ERX3851410,ERS4266434,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.80562,0.80436,0.23702,0.23786,0.77914,0.77991,0.51225,0.5092,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9786,ERR3838743,ERX3851409,ERS4266433,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma 256 cell rep1,SAMEA6501984,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501984|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 256 cell rep1|age:2.5|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 256 cell rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma 256 cell rep1 p,Soma 256 cell rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,Somatic_256_rep1_R1.fastq.gz Somatic_256_rep1_R2.fastq.gz,fastq fastq,2254901578.0,15144857.0,E MTAB 8707:Somatic 256 rep1 R,0:74.44 1:74.45,A:648357135;C:475813294;G:492914743;T:636658631;N:1157775,74,74,,,648357135,475813294,492914743,636658631,1157775,ERX3851409,ERS4266433,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.92992,0.92787,0.07245,0.07214,0.7599,0.76084,0.53758,0.53839,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9795,ERR3838734,ERX3851400,ERS4266424,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC High rep2,SAMEA6501975,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501975|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC High rep2|age:3.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC High rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC High rep2 p,PGC High rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,PGC_High_rep2_R1.fastq.gz PGC_High_rep2_R2.fastq.gz,fastq fastq,2491013839.0,16740632.0,E MTAB 8707:PGC High rep2 R,0:74.40 1:74.40,A:715637079;C:527451931;G:545855323;T:700774175;N:1295331,74,74,,,715637079,527451931,545855323,700774175,1295331,ERX3851400,ERS4266424,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93381,0.93556,0.06095,0.06172,0.76094,0.76364,0.52942,0.53118,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9796,ERR3838733,ERX3851399,ERS4266423,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC High rep1,SAMEA6501974,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501974|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC High rep1|age:3.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC High rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC High rep1 p,PGC High rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,PGC_High_rep1_R1.fastq.gz PGC_High_rep1_R2.fastq.gz,fastq fastq,2055218051.0,13801653.0,E MTAB 8707:PGC High rep1 R,0:74.45 1:74.46,A:594747301;C:431446277;G:445665283;T:582330624;N:1028566,74,74,,,594747301,431446277,445665283,582330624,1028566,ERX3851399,ERS4266423,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93644,0.93494,0.06937,0.07015,0.76353,0.7653,0.45909,0.44979,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9797,ERR3838732,ERX3851398,ERS4266422,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC dome rep2,SAMEA6501973,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501973|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC dome rep2|age:4.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC dome rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC dome rep2 p,PGC dome rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S9_R1.fastq.gz S9_R2.fastq.gz,fastq fastq,882858901.0,5912255.0,E MTAB 8707:S9 R,0:74.66 1:74.67,A:246639630;C:193554406;G:199940889;T:242369366;N:354610,74,74,,,246639630,193554406,199940889,242369366,354610,ERX3851398,ERS4266422,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.94045,0.9404,0.04635,0.04658,0.74582,0.74777,0.4915,0.49248,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9798,ERR3838731,ERX3851397,ERS4266421,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC dome rep1,SAMEA6501972,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501972|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC dome rep1|age:4.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC dome rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC dome rep1 p,PGC dome rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S7_R1.fastq.gz S7_R2.fastq.gz,fastq fastq,592299285.0,3961989.0,E MTAB 8707:S7 R,0:74.75 1:74.75,A:166664600;C:128421892;G:132787149;T:164189412;N:236232,74,74,,,166664600,128421892,132787149,164189412,236232,ERX3851397,ERS4266421,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93981,0.94032,0.04868,0.04843,0.74627,0.74722,0.49243,0.48872,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9799,ERR3838730,ERX3851396,ERS4266420,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC 256 cell rep2,SAMEA6501971,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501971|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 256 cell rep2|age:2.5|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 256 cell rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC 256 cell rep2 p,PGC 256 cell rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S1_R1.fastq.gz S1_R2.fastq.gz,fastq fastq,745277323.0,4983607.0,E MTAB 8707:S1 R,0:74.77 1:74.77,A:208352741;C:163024343;G:168234953;T:205391192;N:274094,74,74,,,208352741,163024343,168234953,205391192,274094,ERX3851396,ERS4266420,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.9393,0.9395,0.03941,0.03941,0.75473,0.75708,0.51338,0.51754,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9800,ERR3838729,ERX3851395,ERS4266419,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC 256 cell rep1,SAMEA6501970,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501970|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 256 cell rep1|age:2.5|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 256 cell rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC 256 cell rep1 p,PGC 256 cell rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,PGC_256_rep1_R1.fastq.gz PGC_256_rep1_R2.fastq.gz,fastq fastq,1876891175.0,12625794.0,E MTAB 8707:PGC 256 rep1 R,0:74.32 1:74.33,A:539140549;C:396392844;G:411568412;T:528672735;N:1116635,74,74,,,539140549,396392844,411568412,528672735,1116635,ERX3851395,ERS4266419,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.92251,0.92173,0.06705,0.06723,0.76059,0.76374,0.54467,0.54135,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
10212,ERR6511331,ERX6138167,ERS7264190,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of PolyA selected sample biological replicate 1 including 4 hpf RNA,Zebrafish PolyA 4 hpf,SAMEA9541420,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541420|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish PolyA 4 hpf|common name:zebrafish|sample name:Zebrafish PolyA 4 hpf|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,cDNA8523612,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_polya_4hpf.tar.gz,nanopore,330562220.0,233101.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,0:1418.11,A:86572446;C:74232962;G:69203462;T:100553350;N:0,1418,,,,86572446,74232962,69203462,100553350,0,ERX6138167,ERS7264190,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),1,0.0,,0.0,,1.0,,,,1536,,T,,long read,ont,ont,full_length,poly_a,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Blastula,Embryo,Undetermined,Embryo Imprecise
25296,SRR25764046,SRX21486722,SRS18719023,SRP457105,PRJNA1009809,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [Ribo Seq],GSE241753,Other,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT sphere 4 hpf Ribo seq rep1,GSM7734769,,source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|treatment:100 µg/ml CHX  100 µg/ml TIG|geo loc name:missing|collection date:missing,WT sphere 4 hpf Ribo seq rep1,We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018]  which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters  b 100   single  l 180  s 20  t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms  all RNAfold dependencies in Scikit ribo were omitted  and the index was built separately for each chromosome. To make the hg38 GTF compatible with Scikit ribo  transcript/UTR annotations were removed. For each transcript  the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates  taking into account the gene strand. To estimate codon dwell times  short 20 23 nt and long 28 33 nt ribosome footprints were analyzed separately. rRNA filtered reads were aligned to GRCz11.108 using STAR v2.6.1c [Dobin et al.  2013] the following options:   outFilterMultimapNmax 1   seedSearchStartLmax 15   outSAMtype BAM SortedByCoordinate   outFilterMismatchNmax 2   alignEndsType EndToEnd   quantMode TranscriptomeSAM   outSAMattributes NH HI AS nM NM MD We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018]  which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters  b 100   single  l 180  s 20  t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms  all RNAfold dependencies in Scikit ribo were omitted  and the index was built separately for each chromosome. To make the GRCz11 GTF compatible with Scikit ribo  transcript/UTR annotations were removed. For each transcript  the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates  taking into account the gene strand. To estimate codon dwell times  we utilised ribosome footprints with length 30 34 nt. Assembly: GRCz11 Supplementary files format and content: csv; codon dwell times from scikit ribo for all samples Supplementary files format and content: csv; transcript per million TPM counts per transcript in MANE annotation Library strategy: Ribo Seq,Blastula,unperturbed growth conditions in E3 medium for zebrafish embryos.,200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 µg/ml CHX and 100 µg/ml TIG  0.1% NP 40  10 µg/ml aprotinin  20 µM leupeptin  2.5 µM pepstatin A  0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously  triturated through a 26G gauge needle  and spun down for 7 minutes at 16 000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22°C. post incubation on ice for 5 minutes  extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4°C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose  20 mM Tris pH=8.0  140 mM KCl  5 mM MgCl2  1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4°C. Ribosome pellets were rinsed once  dissolved in 200 µl drug free polysome lysis buffer  and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22°C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia  2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection  with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their 5’ ends McGlinzy 2017 with T4 RNA Ligase 2  truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples  and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.,Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.,strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|treatment:100 µg/ml CHX  100 µg/ml TIG,GSM7734769,GSM7734769: WT sphere 4 hpf Ribo seq rep1; Danio rerio; OTHER,GSM7734769 r1,GSM7734769,1,200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 µg/ml CHX and 100 µg/ml TIG  0.1% NP 40  10 µg/ml aprotinin  20 µM leupeptin  2.5 µM pepstatin A  0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously  triturated through a 26G gauge needle  and spun down for 7 minutes at 16 000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22°C. post incubation on ice for 5 minutes  extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4°C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose  20 mM Tris pH=8.0  140 mM KCl  5 mM MgCl2  1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4°C. Ribosome pellets were rinsed once  dissolved in 200 µl drug free polysome lysis buffer  and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22°C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia  2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection  with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their five prime ends McGlinzy 2017 with T4 RNA Ligase 2  truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples  and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,NextSeq 500,,SRP457105,,,WT_ribo_sphere_1.fastq.gz,fastq,1336027898.0,47907512.0,GSM7734769 r1,0:27.89,A:229038284;C:439455963;G:429428292;T:238088512;N:16847,27,,,,229038284,439455963,429428292,238088512,16847,SRX21486722,SRS18719023,SRA1700409,"Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry",Max Planck Institute of Biochemistry,1,0.85867,,0.20418,,0.8776,,0.79481,,24,,B,,usable mapping rate,illumina,nextseq,5prime,rrna_depletion,ribozero,bulk,unknown,unknown,,Germany,2023-08-28,Blastula,Embryo,Whole Organism,All anatomical structures
29212,SRR27489728,SRX23160981,SRS20111138,SRP483112,PRJNA1056276,five prime UTR MPRA during early zebrafish embryogenesis,PRJNA1056276,Other,The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.,,,polysome fraction,HMW fraction 4hpf replica A,MPRA repA fractions 8 9 4hpf,,strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:8|replicate:replicate A|BioSampleModel:Model organism or animal,,,,,,,,,HMW fraction 4hpf replica A,Library 8,Library 8,Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.,,,OTHER,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483112,,,BSSE_QGF_206643_HGWLYDSX3_3_MPRA_repA_fractions_8_9_4hpf_GACCTGAA_TTGGTGAG_S8_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206643_HGWLYDSX3_3_MPRA_repA_fractions_8_9_4hpf_GACCTGAA_TTGGTGAG_S8_L003_R1_001_MM_1.fastq.gz,fastq fastq,12066108000.0,39954000.0,BSSE QGF 206643 HGWLYDSX3 3 MPRA repA fractions 8 9 4hpf GACCTGAA TTGGTGAG S8 L003 R1 001 MM 1.fastq.gz,0:151 1:151,A:3060316371;C:3136678983;G:2965588104;T:2902920606;N:603936,151,151,,,3060316371,3136678983,2965588104,2902920606,603936,SRX23160981,SRS20111138,SRA1775336,University of Basel|Biozentrum Basel,University of Basel,2,0.01336,5e-05,0.00027,0.0,0.99143,0.99983,0.40418,0.125,151,151,T,T,mates < 9% mapping rate,illumina,novaseq_era,5prime,other,unknown,bulk,unknown,unknown,,Switzerland,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29213,SRR27489729,SRX23160980,SRS20111142,SRP483112,PRJNA1056276,five prime UTR MPRA during early zebrafish embryogenesis,PRJNA1056276,Other,The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.,,,polysome fraction,LMW fraction 4hpf replica A,MPRA repA fractions 6 7 4hpf,,strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:7|replicate:replicate A|BioSampleModel:Model organism or animal,,,,,,,,,LMW fraction 4hpf replica A,Library 7,Library 7,Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.,,,OTHER,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483112,,,BSSE_QGF_206642_HGWLYDSX3_3_MPRA_repA_fractions_6_7_4hpf_AGTTCAGG_CCAACAGA_S7_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206642_HGWLYDSX3_3_MPRA_repA_fractions_6_7_4hpf_AGTTCAGG_CCAACAGA_S7_L003_R1_001_MM_1.fastq.gz,fastq fastq,11998643314.0,39730607.0,BSSE QGF 206642 HGWLYDSX3 3 MPRA repA fractions 6 7 4hpf AGTTCAGG CCAACAGA S7 L003 R1 001 MM 1.fastq.gz,0:151 1:151,A:3044270548;C:3145201016;G:2907229129;T:2901344613;N:598008,151,151,,,3044270548,3145201016,2907229129,2901344613,598008,SRX23160980,SRS20111142,SRA1775336,University of Basel|Biozentrum Basel,University of Basel,2,0.01631,0.00013,0.00035,1e-05,0.99101,0.99965,0.40542,0.33333,151,151,T,T,mates < 9% mapping rate,illumina,novaseq_era,5prime,other,unknown,bulk,unknown,unknown,,Switzerland,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29214,SRR27489730,SRX23160979,SRS20111137,SRP483112,PRJNA1056276,five prime UTR MPRA during early zebrafish embryogenesis,PRJNA1056276,Other,The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.,,,polysome fraction,80S fraction 4hpf replica A,MPRA repA fractions 4 5 4hpf,,strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:6|replicate:replicate A|BioSampleModel:Model organism or animal,,,,,,,,,80S fraction 4hpf replica A,Library 6,Library 6,Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.,,,OTHER,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483112,,,BSSE_QGF_206641_HGWLYDSX3_3_MPRA_repA_fractions_4_5_4hpf_TGGATCGA_GTGCGATA_S6_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206641_HGWLYDSX3_3_MPRA_repA_fractions_4_5_4hpf_TGGATCGA_GTGCGATA_S6_L003_R2_001_MM_1.fastq.gz,fastq fastq,12838157410.0,42510455.0,BSSE QGF 206641 HGWLYDSX3 3 MPRA repA fractions 4 5 4hpf TGGATCGA GTGCGATA S6 L003 R1 001 MM 1.fastq.gz,0:151 1:151,A:3238698530;C:3377705608;G:3143460419;T:3077655243;N:637610,151,151,,,3238698530,3377705608,3143460419,3077655243,637610,SRX23160979,SRS20111137,SRA1775336,University of Basel|Biozentrum Basel,University of Basel,2,0.01549,3e-05,0.00042,1e-05,0.99097,0.99995,0.42138,0.5,151,151,T,T,mates < 9% mapping rate,illumina,novaseq_era,5prime,other,unknown,bulk,unknown,unknown,,Switzerland,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29224,SRR27489741,SRX23160968,SRS20111133,SRP483112,PRJNA1056276,five prime UTR MPRA during early zebrafish embryogenesis,PRJNA1056276,Other,The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.,,,input sample,Total 4hpf replica A,MPRA repA input 4hpf,,strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:5|replicate:replicate A|BioSampleModel:Model organism or animal,,,,,,,,,Total 4hpf replica A,Library 5,Library 5,Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.,,,OTHER,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483112,,,BSSE_QGF_206640_HGWLYDSX3_3_MPRA_repA_input_4hpf_CAAGCTAG_ACATAGCG_S5_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206640_HGWLYDSX3_3_MPRA_repA_input_4hpf_CAAGCTAG_ACATAGCG_S5_L003_R2_001_MM_1.fastq.gz,fastq fastq,13631534966.0,45137533.0,BSSE QGF 206640 HGWLYDSX3 3 MPRA repA input 4hpf CAAGCTAG ACATAGCG S5 L003 R1 001 MM 1.fastq.gz,0:151 1:151,A:3486253250;C:3611078376;G:3219396920;T:3314128840;N:677580,151,151,,,3486253250,3611078376,3219396920,3314128840,677580,SRX23160968,SRS20111133,SRA1775336,University of Basel|Biozentrum Basel,University of Basel,2,0.02225,2e-05,0.00066,0.0,0.98975,0.99993,0.40257,0.33333,151,151,T,T,mates < 9% mapping rate,illumina,novaseq_era,5prime,other,unknown,bulk,unknown,unknown,,Switzerland,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29225,SRR27489742,SRX23160967,SRS20111126,SRP483112,PRJNA1056276,five prime UTR MPRA during early zebrafish embryogenesis,PRJNA1056276,Other,The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.,,,polysome fraction,HMW fraction 4hpf replica C,MPRA repC fractions 8 9 4hpf,,strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:40|replicate:replicate C|BioSampleModel:Model organism or animal,,,,,,,,,HMW fraction 4hpf replica C,Library 40,Library 40,Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.,,,OTHER,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483112,,,BSSE_QGF_206675_HGWLYDSX3_3_MPRA_repC_fractions_8_9_4hpf_ATGGCATG_AAGGTACC_S40_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206675_HGWLYDSX3_3_MPRA_repC_fractions_8_9_4hpf_ATGGCATG_AAGGTACC_S40_L003_R2_001_MM_1.fastq.gz,fastq fastq,16854209582.0,55808641.0,BSSE QGF 206675 HGWLYDSX3 3 MPRA repC fractions 8 9 4hpf ATGGCATG AAGGTACC S40 L003 R1 001 MM 1.fastq.gz,0:151 1:151,A:4270727222;C:4383022813;G:4143081915;T:4056541855;N:835777,151,151,,,4270727222,4383022813,4143081915,4056541855,835777,SRX23160967,SRS20111126,SRA1775336,University of Basel|Biozentrum Basel,University of Basel,2,0.01329,0.00015,0.00029,2e-05,0.99141,0.99953,0.4263,0.47826,151,151,T,T,mates < 9% mapping rate,illumina,novaseq_era,5prime,other,unknown,bulk,unknown,unknown,,Switzerland,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29226,SRR27489743,SRX23160966,SRS20111124,SRP483112,PRJNA1056276,five prime UTR MPRA during early zebrafish embryogenesis,PRJNA1056276,Other,The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.,,,polysome fraction,LMW fraction 4hpf replica C,MPRA repC fractions 6 7 4hpf,,strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:39|replicate:replicate C|BioSampleModel:Model organism or animal,,,,,,,,,LMW fraction 4hpf replica C,Library 39,Library 39,Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.,,,OTHER,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483112,,,BSSE_QGF_206674_HGWLYDSX3_3_MPRA_repC_fractions_6_7_4hpf_GGAGCGTC_GTCCGTGC_S39_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206674_HGWLYDSX3_3_MPRA_repC_fractions_6_7_4hpf_GGAGCGTC_GTCCGTGC_S39_L003_R2_001_MM_1.fastq.gz,fastq fastq,12146174844.0,40219122.0,BSSE QGF 206674 HGWLYDSX3 3 MPRA repC fractions 6 7 4hpf GGAGCGTC GTCCGTGC S39 L003 R1 001 MM 1.fastq.gz,0:151 1:151,A:3060215849;C:3176615755;G:3002666854;T:2906066243;N:610143,151,151,,,3060215849,3176615755,3002666854,2906066243,610143,SRX23160966,SRS20111124,SRA1775336,University of Basel|Biozentrum Basel,University of Basel,2,0.01309,0.0002,0.00031,0.0,0.99164,0.99939,0.40018,0.57142,151,151,T,T,mates < 9% mapping rate,illumina,novaseq_era,5prime,other,unknown,bulk,unknown,unknown,,Switzerland,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29227,SRR27489744,SRX23160965,SRS20111123,SRP483112,PRJNA1056276,five prime UTR MPRA during early zebrafish embryogenesis,PRJNA1056276,Other,The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.,,,polysome fraction,80S fraction 4hpf replica C,MPRA repC fractions 4 5 4hpf,,strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:38|replicate:replicate C|BioSampleModel:Model organism or animal,,,,,,,,,80S fraction 4hpf replica C,Library 38,Library 38,Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.,,,OTHER,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483112,,,BSSE_QGF_206673_HGWLYDSX3_3_MPRA_repC_fractions_4_5_4hpf_AAGATACT_ACTTACAT_S38_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206673_HGWLYDSX3_3_MPRA_repC_fractions_4_5_4hpf_AAGATACT_ACTTACAT_S38_L003_R1_001_MM_1.fastq.gz,fastq fastq,14100203330.0,46689415.0,BSSE QGF 206673 HGWLYDSX3 3 MPRA repC fractions 4 5 4hpf AAGATACT ACTTACAT S38 L003 R1 001 MM 1.fastq.gz,0:151 1:151,A:3544539088;C:3702795841;G:3493240125;T:3358929671;N:698605,151,151,,,3544539088,3702795841,3493240125,3358929671,698605,SRX23160965,SRS20111123,SRA1775336,University of Basel|Biozentrum Basel,University of Basel,2,0.01368,0.00016,0.00037,0.0,0.99107,0.99951,0.40864,0.5,151,151,T,T,mates < 9% mapping rate,illumina,novaseq_era,5prime,other,unknown,bulk,unknown,unknown,,Switzerland,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29228,SRR27489745,SRX23160964,SRS20111120,SRP483112,PRJNA1056276,five prime UTR MPRA during early zebrafish embryogenesis,PRJNA1056276,Other,The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.,,,input sample,Total 4hpf replica C,MPRA repC input 4hpf,,strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:37|replicate:replicate C|BioSampleModel:Model organism or animal,,,,,,,,,Total 4hpf replica C,Library 37,Library 37,Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.,,,OTHER,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483112,,,BSSE_QGF_206672_HGWLYDSX3_3_MPRA_repC_input_4hpf_GCGCAAGC_TCACGCCG_S37_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206672_HGWLYDSX3_3_MPRA_repC_input_4hpf_GCGCAAGC_TCACGCCG_S37_L003_R2_001_MM_1.fastq.gz,fastq fastq,10925301792.0,36176496.0,BSSE QGF 206672 HGWLYDSX3 3 MPRA repC input 4hpf GCGCAAGC TCACGCCG S37 L003 R1 001 MM 1.fastq.gz,0:151 1:151,A:2802490901;C:2878602103;G:2592316062;T:2651349641;N:543085,151,151,,,2802490901,2878602103,2592316062,2651349641,543085,SRX23160964,SRS20111120,SRA1775336,University of Basel|Biozentrum Basel,University of Basel,2,0.02108,3e-05,0.0006,0.0,0.98981,0.99991,0.42181,0.0,151,151,T,T,mates < 9% mapping rate,illumina,novaseq_era,5prime,other,unknown,bulk,unknown,unknown,,Switzerland,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29242,SRR27489759,SRX23160950,SRS20111107,SRP483112,PRJNA1056276,five prime UTR MPRA during early zebrafish embryogenesis,PRJNA1056276,Other,The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.,,,polysome fraction,HMW fraction 4hpf replica B,MPRA repB fractions 8 9 4hpf,,strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:24|replicate:replicate B|BioSampleModel:Model organism or animal,,,,,,,,,HMW fraction 4hpf replica B,Library 24,Library 24,Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.,,,OTHER,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483112,,,BSSE_QGF_206659_HGWLYDSX3_3_MPRA_repB_fractions_8_9_4hpf_CCGTGAAG_CAGTGGAT_S24_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206659_HGWLYDSX3_3_MPRA_repB_fractions_8_9_4hpf_CCGTGAAG_CAGTGGAT_S24_L003_R2_001_MM_1.fastq.gz,fastq fastq,11600767978.0,38413139.0,BSSE QGF 206659 HGWLYDSX3 3 MPRA repB fractions 8 9 4hpf CCGTGAAG CAGTGGAT S24 L003 R1 001 MM 1.fastq.gz,0:151 1:151,A:2943303855;C:3024500200;G:2833306086;T:2799077405;N:580432,151,151,,,2943303855,3024500200,2833306086,2799077405,580432,SRX23160950,SRS20111107,SRA1775336,University of Basel|Biozentrum Basel,University of Basel,2,0.01371,0.00013,0.00031,1e-05,0.99143,0.99955,0.41912,0.5909,151,151,T,T,mates < 9% mapping rate,illumina,novaseq_era,5prime,other,unknown,bulk,unknown,unknown,,Switzerland,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29243,SRR27489760,SRX23160949,SRS20111106,SRP483112,PRJNA1056276,five prime UTR MPRA during early zebrafish embryogenesis,PRJNA1056276,Other,The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.,,,polysome fraction,LMW fraction 4hpf replica B,MPRA repB fractions 6 7 4hpf,,strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:23|replicate:replicate B|BioSampleModel:Model organism or animal,,,,,,,,,LMW fraction 4hpf replica B,Library 23,Library 23,Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.,,,OTHER,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483112,,,BSSE_QGF_206658_HGWLYDSX3_3_MPRA_repB_fractions_6_7_4hpf_CTTGGTAT_CCAAGTCC_S23_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206658_HGWLYDSX3_3_MPRA_repB_fractions_6_7_4hpf_CTTGGTAT_CCAAGTCC_S23_L003_R2_001_MM_1.fastq.gz,fastq fastq,13216553444.0,43763422.0,BSSE QGF 206658 HGWLYDSX3 3 MPRA repB fractions 6 7 4hpf CTTGGTAT CCAAGTCC S23 L003 R1 001 MM 1.fastq.gz,0:151 1:151,A:3339016083;C:3457419680;G:3233764657;T:3185687490;N:665534,151,151,,,3339016083,3457419680,3233764657,3185687490,665534,SRX23160949,SRS20111106,SRA1775336,University of Basel|Biozentrum Basel,University of Basel,2,0.01431,0.00024,0.00034,1e-05,0.99135,0.99924,0.41915,0.45238,151,151,T,T,mates < 9% mapping rate,illumina,novaseq_era,5prime,other,unknown,bulk,unknown,unknown,,Switzerland,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29244,SRR27489761,SRX23160948,SRS20111105,SRP483112,PRJNA1056276,five prime UTR MPRA during early zebrafish embryogenesis,PRJNA1056276,Other,The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.,,,polysome fraction,80S fraction 4hpf replica B,MPRA repB fractions 4 5 4hpf,,strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:22|replicate:replicate B|BioSampleModel:Model organism or animal,,,,,,,,,80S fraction 4hpf replica B,Library 22,Library 22,Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.,,,OTHER,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483112,,,BSSE_QGF_206657_HGWLYDSX3_3_MPRA_repB_fractions_4_5_4hpf_ATGAGGCC_GTTAATTG_S22_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206657_HGWLYDSX3_3_MPRA_repB_fractions_4_5_4hpf_ATGAGGCC_GTTAATTG_S22_L003_R2_001_MM_1.fastq.gz,fastq fastq,11938250562.0,39530631.0,BSSE QGF 206657 HGWLYDSX3 3 MPRA repB fractions 4 5 4hpf ATGAGGCC GTTAATTG S22 L003 R1 001 MM 1.fastq.gz,0:151 1:151,A:3040684418;C:3144238599;G:2873359599;T:2879374531;N:593415,151,151,,,3040684418,3144238599,2873359599,2879374531,593415,SRX23160948,SRS20111105,SRA1775336,University of Basel|Biozentrum Basel,University of Basel,2,0.0185,8e-05,0.00056,0.0,0.9903,0.99969,0.4376,0.4,151,151,T,T,mates < 9% mapping rate,illumina,novaseq_era,5prime,other,unknown,bulk,unknown,unknown,,Switzerland,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29245,SRR27489762,SRX23160947,SRS20111104,SRP483112,PRJNA1056276,five prime UTR MPRA during early zebrafish embryogenesis,PRJNA1056276,Other,The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.,,,input sample,Total 4hpf replica B,MPRA repB input 4hpf,,strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:21|replicate:replicate B|BioSampleModel:Model organism or animal,,,,,,,,,Total 4hpf replica B,Library 21,Library 21,Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.,,,OTHER,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483112,,,BSSE_QGF_206656_HGWLYDSX3_3_MPRA_repB_input_4hpf_GCAGAATT_ACCGGCCA_S21_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206656_HGWLYDSX3_3_MPRA_repB_input_4hpf_GCAGAATT_ACCGGCCA_S21_L003_R1_001_MM_1.fastq.gz,fastq fastq,14482326346.0,47954723.0,BSSE QGF 206656 HGWLYDSX3 3 MPRA repB input 4hpf GCAGAATT ACCGGCCA S21 L003 R1 001 MM 1.fastq.gz,0:151 1:151,A:3697691325;C:3838972714;G:3432418300;T:3512522230;N:721777,151,151,,,3697691325,3838972714,3432418300,3512522230,721777,SRX23160947,SRS20111104,SRA1775336,University of Basel|Biozentrum Basel,University of Basel,2,0.0211,2e-05,0.00055,0.0,0.9903,0.99993,0.42543,0.0,151,151,T,T,mates < 9% mapping rate,illumina,novaseq_era,5prime,other,unknown,bulk,unknown,unknown,,Switzerland,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures
29739,SRR27467672,SRX23139234,SRS20090275,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome mock R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  mock  rep2,EV04009,EV04009,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04009.R1.fastq.gz,fastq,609590940.0,4354221.0,EV04009.R1.fastq.gz,0:140,A:155062144;C:147628702;G:168099121;T:138772205;N:28768,140,,,,155062144,147628702,168099121,138772205,28768,SRX23139234,SRS20090275,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Blastula,Embryo,Whole Organism,All anatomical structures
29740,SRR27467673,SRX23139233,SRS20090278,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell BS R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  BS  rep2,EV04008,EV04008,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04008.R1.fastq.gz,fastq,675505180.0,4825037.0,EV04008.R1.fastq.gz,0:140,A:178823976;C:121648962;G:198428643;T:176572292;N:31307,140,,,,178823976,121648962,198428643,176572292,31307,SRX23139233,SRS20090278,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Blastula,Embryo,Whole Organism,All anatomical structures
29741,SRR27467674,SRX23139232,SRS20090272,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell DM R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  DM  rep2,EV04007,EV04007,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04007.R1.fastq.gz,fastq,702064440.0,5014746.0,EV04007.R1.fastq.gz,0:140,A:176719694;C:166467163;G:207893965;T:150951950;N:31668,140,,,,176719694,166467163,207893965,150951950,31668,SRX23139232,SRS20090272,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,2e-05,,0.0,,0.99997,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Blastula,Embryo,Whole Organism,All anatomical structures
29742,SRR27467675,SRX23139231,SRS20090271,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell mock R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  mock  rep2,EV04006,EV04006,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04006.R1.fastq.gz,fastq,664790700.0,4748505.0,EV04006.R1.fastq.gz,0:140,A:172014219;C:146545691;G:200358431;T:145840649;N:31710,140,,,,172014219,146545691,200358431,145840649,31710,SRX23139231,SRS20090271,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,3e-05,,0.0,,0.99993,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Blastula,Embryo,Whole Organism,All anatomical structures
29753,SRR27467686,SRX23139220,SRS20090263,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome BS R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  BS  rep2,EV04011,EV04011,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04011.R1.fastq.gz,fastq,720913200.0,5149380.0,EV04011.R1.fastq.gz,0:140,A:185414155;C:126110104;G:238649631;T:170706590;N:32720,140,,,,185414155,126110104,238649631,170706590,32720,SRX23139220,SRS20090263,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Blastula,Embryo,Whole Organism,All anatomical structures
29754,SRR27467687,SRX23139219,SRS20090259,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome DM R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  DM  rep2,EV04010,EV04010,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04010.R1.fastq.gz,fastq,443650200.0,3168930.0,EV04010.R1.fastq.gz,0:140,A:114663509;C:102512276;G:135709753;T:90744641;N:20021,140,,,,114663509,102512276,135709753,90744641,20021,SRX23139219,SRS20090259,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,1e-05,,0.0,,0.99997,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Blastula,Embryo,Whole Organism,All anatomical structures
29757,SRR27437477,SRX23109820,SRS20064574,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell mock R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  mock  rep3,EV07007,EV07007,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07007.R1.fastq.gz,fastq,479994620.0,3428533.0,EV07007.R1.fastq.gz,0:140,A:124628886;C:116843590;G:123136721;T:115372734;N:12689,140,,,,124628886,116843590,123136721,115372734,12689,SRX23109820,SRS20064574,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,6e-05,,1e-05,,0.99989,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Blastula,Embryo,Whole Organism,All anatomical structures
29771,SRR27437491,SRX23109806,SRS20064560,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome BS R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  BS  rep3,EV07011,EV07011,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07011.R1.fastq.gz,fastq,893528580.0,6382347.0,EV07011.R1.fastq.gz,0:140,A:240101890;C:155985797;G:262065322;T:235351334;N:24237,140,,,,240101890,155985797,262065322,235351334,24237,SRX23109806,SRS20064560,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Blastula,Embryo,Whole Organism,All anatomical structures
29772,SRR27437492,SRX23109805,SRS20064559,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome DM R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  DM  rep3,EV07012,EV07012,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07012.R1.fastq.gz,fastq,797662600.0,5697590.0,EV07012.R1.fastq.gz,0:140,A:201908589;C:182656132;G:249672167;T:163404182;N:21530,140,,,,201908589,182656132,249672167,163404182,21530,SRX23109805,SRS20064559,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,3e-05,,0.0,,0.99991,,0.75,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Blastula,Embryo,Whole Organism,All anatomical structures
29773,SRR27437493,SRX23109804,SRS20064558,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome mock R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  mock  rep3,EV07010,EV07010,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07010.R1.fastq.gz,fastq,467593280.0,3339952.0,EV07010.R1.fastq.gz,0:140,A:122604957;C:118747514;G:124074466;T:102153374;N:12969,140,,,,122604957,118747514,124074466,102153374,12969,SRX23109804,SRS20064558,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,4e-05,,0.0,,0.99993,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Blastula,Embryo,Whole Organism,All anatomical structures
29774,SRR27437494,SRX23109803,SRS20064557,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell BS R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  BS  rep3,EV07008,EV07008,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07008.R1.fastq.gz,fastq,705682040.0,5040586.0,EV07008.R1.fastq.gz,0:140,A:194506527;C:127442743;G:192893716;T:190818958;N:20096,140,,,,194506527,127442743,192893716,190818958,20096,SRX23109803,SRS20064557,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Blastula,Embryo,Whole Organism,All anatomical structures
29775,SRR27437495,SRX23109802,SRS20064556,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell DM R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  DM  rep3,EV07009,EV07009,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07009.R1.fastq.gz,fastq,380716280.0,2719402.0,EV07009.R1.fastq.gz,0:140,A:95351632;C:89558330;G:115625953;T:80169603;N:10762,140,,,,95351632,89558330,115625953,80169603,10762,SRX23109802,SRS20064556,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,6e-05,,1e-05,,0.99991,,0.75,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Blastula,Embryo,Whole Organism,All anatomical structures
29778,SRR27435863,SRX23108233,SRS20063070,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell mock R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  mock  rep4,EV08010,EV08010,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08010.R1.fastq.gz,fastq,678729520.0,4848068.0,EV08010.R1.fastq.gz,0:140,A:170672553;C:182320916;G:171865707;T:153824163;N:46181,140,,,,170672553,182320916,171865707,153824163,46181,SRX23108233,SRS20063070,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0006,,4e-05,,0.99878,,0.79069,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Blastula,Embryo,Whole Organism,All anatomical structures
29792,SRR27435877,SRX23108219,SRS20063056,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome BS R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  BS  rep4,EV08015,EV08015,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08015.R1.fastq.gz,fastq,804598200.0,5747130.0,EV08015.R1.fastq.gz,0:140,A:215467427;C:134937180;G:189531758;T:264604493;N:57342,140,,,,215467427,134937180,189531758,264604493,57342,SRX23108219,SRS20063056,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,2e-05,,0.0,,0.99995,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Blastula,Embryo,Whole Organism,All anatomical structures
29793,SRR27435878,SRX23108218,SRS20063055,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome DM R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  DM  rep4,EV08014,EV08014,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08014.R1.fastq.gz,fastq,662443740.0,4731741.0,EV08014.R1.fastq.gz,0:140,A:164941700;C:167025964;G:177255084;T:153175163;N:45829,140,,,,164941700,167025964,177255084,153175163,45829,SRX23108218,SRS20063055,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00069,,0.0001,,0.9992,,0.83076,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Blastula,Embryo,Whole Organism,All anatomical structures
29794,SRR27435879,SRX23108217,SRS20063052,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome mock R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  mock  rep4,EV08013,EV08013,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08013.R1.fastq.gz,fastq,794760540.0,5676861.0,EV08013.R1.fastq.gz,0:140,A:197361776;C:210230329;G:205734036;T:181380205;N:54194,140,,,,197361776,210230329,205734036,181380205,54194,SRX23108217,SRS20063052,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00066,,9e-05,,0.99894,,0.78378,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Blastula,Embryo,Whole Organism,All anatomical structures
29795,SRR27435880,SRX23108216,SRS20063054,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell BS R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  BS  rep4,EV08012,EV08012,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08012.R1.fastq.gz,fastq,722593200.0,5161380.0,EV08012.R1.fastq.gz,0:140,A:188475497;C:119550806;G:173208825;T:241306038;N:52034,140,,,,188475497,119550806,173208825,241306038,52034,SRX23108216,SRS20063054,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Blastula,Embryo,Whole Organism,All anatomical structures
29796,SRR27435881,SRX23108215,SRS20063053,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell DM R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  DM  rep4,EV08011,EV08011,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08011.R1.fastq.gz,fastq,753783380.0,5384167.0,EV08011.R1.fastq.gz,0:140,A:190029713;C:193734250;G:194752855;T:175212145;N:54417,140,,,,190029713,193734250,194752855,175212145,54417,SRX23108215,SRS20063053,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00076,,5e-05,,0.99859,,0.70873,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Blastula,Embryo,Whole Organism,All anatomical structures
36416,SRR516554,SRX156349,SRS347209,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo dome/zfs:0000015 stage,D. rerio dome/zfs:0000015 embryo,D. rerio dome/zfs:0000015 embryo,,,,,,,,,,,CAGE   D. rerio dome/zfs:0000015 embryo,CAGE   D. rerio dome/zfs:0000015 embryo,D. rerio dome/zfs:0000015 embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_30p_dome.fastq,fastq,165690819.0,6136697.0,CAGE   D. rerio dome/zfs:0000015 embryo,0:27,A:42721293;C:36492232;G:46154926;T:40322368;N:0,27,,,,42721293,36492232,46154926,40322368,0,SRX156349,SRS347209,SRA055273,University of Bergen,ZEPROME consortium,1,0.50236,,0.0905,,0.81824,,0.8156,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36417,SRR516552,SRX156347,SRS347208,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo sphere/dome stage,D. rerio sphere/dome embryo,D. rerio sphere/dome embryo,,,,,,,,,,,CAGE   D. rerio sphere/dome embryo,CAGE   D. rerio sphere/dome embryo run2,D. rerio sphere/dome embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_sphere_dome_run1.fastq,fastq,78937740.0,2923620.0,CAGE   D. rerio sphere/dome embryo run1,0:27,A:20705496;C:17020957;G:22237043;T:18974244;N:0,27,,,,20705496,17020957,22237043,18974244,0,SRX156347,SRS347208,SRA055273,University of Bergen,ZEPROME consortium,1,0.50917,,0.09193,,0.81523,,0.8084,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36418,SRR516553,SRX156347,SRS347208,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo sphere/dome stage,D. rerio sphere/dome embryo,D. rerio sphere/dome embryo,,,,,,,,,,,CAGE   D. rerio sphere/dome embryo,CAGE   D. rerio sphere/dome embryo run2,D. rerio sphere/dome embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_sphere_dome_run2.fastq,fastq,82071009.0,3039667.0,CAGE   D. rerio sphere/dome embryo run2,0:27,A:20823133;C:17914934;G:22973465;T:20359477;N:0,27,,,,20823133,17914934,22973465,20359477,0,SRX156347,SRS347208,SRA055273,University of Bergen,ZEPROME consortium,1,0.47213,,0.07583,,0.82384,,0.8313,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36419,SRR516551,SRX156338,SRS347207,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo oblong stage,D. rerio oblong embryo,D. rerio oblong embryo,,,,,,,,,,,CAGE   D. rerio oblong embryo,CAGE   D. rerio oblong embryo,D. rerio oblong embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,,,135892080.0,5033040.0,CAGE   D. rerio oblong embryo,0:27,A:34565898;C:30442218;G:38967845;T:31916119;N:0,27,,,,34565898,30442218,38967845,31916119,0,SRX156338,SRS347207,SRA055273,University of Bergen,ZEPROME consortium,1,0.56265,,0.09335,,0.80068,,0.70759,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36421,SRR516549,SRX156336,SRS347204,SRP013950,PRJNA169500,Danio rerio embryonic promoterome,PRJNA169500,Transcriptome Analysis,Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.,,pubmed:24531765,Zebrafish wild type AB strain   embryo 512 cells stage,D. rerio 512 cells embryo,D. rerio 512 cells embyo,,,,,,,,,,,CAGE   D. rerio 512 cells embryo,CAGE   D. rerio 512 cells embryo,D. rerio 512 cells embryo,1,,,OTHER,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013950,,,CAGE_512cells.fastq,fastq,150228810.0,5564030.0,CAGE   D. rerio 512 cells embryo,0:27,A:37826960;C:33838922;G:43403014;T:35159914;N:0,27,,,,37826960,33838922,43403014,35159914,0,SRX156336,SRS347204,SRA055273,University of Bergen,ZEPROME consortium,1,0.57925,,0.08753,,0.79933,,0.72579,,27,,B,,usable mapping rate,illumina,early_illumina,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2012-06-28,Blastula,Embryo,Embryo Imprecise,All anatomical structures
37185,SRR1010334,SRX363385,SRS490049,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL7F transgenic line,,strain:AB strain MUTL7F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL7F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,D. rerio MUTL7F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL7F_transgene_R1.fastq MUTL7F_transgene_R2.fastq,fastq fastq,30678849.0,444621.0,D. rerio MUTL7F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,0:34 1:35,A:5994534;C:7452275;G:9596502;T:7623459;N:12079,34,35,,,5994534,7452275,9596502,7623459,12079,SRX363385,SRS490049,SRA104816,University of Bergen,ZEPROME consortium,2,0.38487,0.37445,0.0013,9e-05,0.99841,0.99991,0.00309,0.00012,34,35,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37186,SRR1010333,SRX363384,SRS490049,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL7F transgenic line,,strain:AB strain MUTL7F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL7F transgenic line   single locus CAGE endogeneous sf3a2,D. rerio MUTL7F transgenic line   single locus CAGE endogeneous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL7F_endogenous_R2.fastq MUTL7F_endogenous_R1.fastq,fastq fastq,78367233.0,1135757.0,D. rerio MUTL7F transgenic line   single locus CAGE endogeneous sf3a2,0:34 1:35,A:21010895;C:20506800;G:21883789;T:14935556;N:30193,34,35,,,21010895,20506800,21883789,14935556,30193,SRX363384,SRS490049,SRA104816,University of Bergen,ZEPROME consortium,2,0.56643,0.02972,6e-05,0.00056,0.99965,0.99995,0.00017,0.05769,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37187,SRR1010332,SRX363383,SRS490048,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL6F transgenic line,,strain:AB strain MUTL6F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL6F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,D. rerio MUTL6F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL6F_transgene_R2.fastq MUTL6F_transgene_R1.fastq,fastq fastq,36838272.0,533888.0,D. rerio MUTL6F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,0:34 1:35,A:7267891;C:8939911;G:11513757;T:9101861;N:14852,34,35,,,7267891,8939911,11513757,9101861,14852,SRX363383,SRS490048,SRA104816,University of Bergen,ZEPROME consortium,2,0.35237,0.20738,0.00196,4e-05,0.9991,0.99987,0.00131,0.00022,34,35,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37188,SRR1010331,SRX363382,SRS490048,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL6F transgenic line,,strain:AB strain MUTL6F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL6F transgenic line   single locus CAGE endogeneous sf3a2,D. rerio MUTL6F transgenic line   single locus CAGE endogeneous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL6F_endogenous_R1.fastq MUTL6F_endogenous_R2.fastq,fastq fastq,67887582.0,983878.0,D. rerio MUTL6F transgenic line   single locus CAGE endogeneous sf3a2,0:34 1:35,A:18224546;C:17687428;G:19119778;T:12829091;N:26739,34,35,,,18224546,17687428,19119778,12829091,26739,SRX363382,SRS490048,SRA104816,University of Bergen,ZEPROME consortium,2,0.57761,0.02201,0.0001,0.00048,0.99975,0.99991,0.00011,0.02247,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37189,SRR1010330,SRX363381,SRS490047,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL5F transgenic line,,strain:AB strain MUTL5F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL5F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,D. rerio MUTL5F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL5F_transgene_R1.fastq MUTL5F_transgene_R2.fastq,fastq fastq,48750708.0,706532.0,D. rerio MUTL5F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,0:34 1:35,A:9468865;C:11866504;G:15193605;T:12203213;N:18521,34,35,,,9468865,11866504,15193605,12203213,18521,SRX363381,SRS490047,SRA104816,University of Bergen,ZEPROME consortium,2,0.37677,0.39423,0.0018,0.00013,0.99801,0.99989,0.00295,0.00011,34,35,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37190,SRR1010329,SRX363380,SRS490047,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL5F transgenic line,,strain:AB strain MUTL5F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL5F transgenic line   single locus CAGE endogeneous sf3a2,D. rerio MUTL5F transgenic line   single locus CAGE endogeneous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL5F_endogenous_R1.fastq MUTL5F_endogenous_R2.fastq,fastq fastq,85325883.0,1236607.0,D. rerio MUTL5F transgenic line   single locus CAGE endogeneous sf3a2,0:34 1:35,A:22831000;C:22316529;G:23804395;T:16340044;N:33915,34,35,,,22831000,22316529,23804395,16340044,33915,SRX363380,SRS490047,SRA104816,University of Bergen,ZEPROME consortium,2,0.59785,0.01902,0.00632,0.00081,0.99941,0.99993,0.00056,0.11235,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37191,SRR1010328,SRX363379,SRS490046,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL2F transgenic line,,strain:AB strain MUTL2F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL2F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,D. rerio MUTL2F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL2F_transgene_R1.fastq MUTL2F_transgene_R2.fastq,fastq fastq,68247900.0,989100.0,D. rerio MUTL2F transgenic line   single locus CAGE mutated sf3a2:mCherry transgene,0:34 1:35,A:13037092;C:16853304;G:21557175;T:16772703;N:27626,34,35,,,13037092,16853304,21557175,16772703,27626,SRX363379,SRS490046,SRA104816,University of Bergen,ZEPROME consortium,2,0.37746,0.14836,0.00135,0.00215,0.99912,0.99995,0.00128,0.0,34,35,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37192,SRR1010327,SRX363378,SRS490046,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio MUTL2F transgenic line,,strain:AB strain MUTL2F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio MUTL2F transgenic line   single locus CAGE endogeneous sf3a2,D. rerio MUTL2F transgenic line   single locus CAGE endogeneous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,MUTL2F_endogenous_R1.fastq MUTL2F_endogenous_R2.fastq,fastq fastq,85300215.0,1236235.0,D. rerio MUTL2F transgenic line   single locus CAGE endogeneous sf3a2,0:34 1:35,A:22860161;C:22364533;G:24027064;T:16015109;N:33348,34,35,,,22860161,22364533,24027064,16015109,33348,SRX363378,SRS490046,SRA104816,University of Bergen,ZEPROME consortium,2,0.57324,0.0117,0.01138,0.00049,0.99943,0.99993,0.00087,0.02941,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37193,SRR1010326,SRX363377,SRS490045,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio WTL3F transgenic line,,strain:AB strain WTL3F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio WTL3F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,D. rerio WTL3F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,WTL3F_transgene_R1.fastq WTL3F_transgene_R2.fastq,fastq fastq,36051879.0,522491.0,D. rerio WTL3F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,0:34 1:35,A:6990071;C:8680451;G:10883119;T:9484027;N:14211,34,35,,,6990071,8680451,10883119,9484027,14211,SRX363377,SRS490045,SRA104816,University of Bergen,ZEPROME consortium,2,0.43354,0.14606,0.00247,9e-05,0.99896,0.99991,0.00217,0.00032,34,35,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37194,SRR1010325,SRX363376,SRS490045,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio WTL3F transgenic line,,strain:AB strain WTL3F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio WTL3F transgenic line   single locus CAGE endogenous sf3a2,D. rerio WTL3F transgenic line   single locus CAGE endogenous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,WTL3F_endogenous_R1.fastq WTL3F_endogenous_R2.fastq,fastq fastq,78469284.0,1137236.0,D. rerio WTL3F transgenic line   single locus CAGE endogenous sf3a2,0:34 1:35,A:21059562;C:20597989;G:21976657;T:14804744;N:30332,34,35,,,21059562,20597989,21976657,14804744,30332,SRX363376,SRS490045,SRA104816,University of Bergen,ZEPROME consortium,2,0.54772,0.02239,3e-05,0.0,0.99979,0.99993,0.00012,0.06756,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37195,SRR1010324,SRX363375,SRS490044,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio WTL2F transgenic line,,strain:AB strain WTL2F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio WTL2F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,D. rerio WTL2F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,WTL2F_transgene_R1.fastq WTL2F_transgene_R2.fastq,fastq fastq,67052544.0,971776.0,D. rerio WTL2F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,0:34 1:35,A:12413417;C:16491074;G:20506887;T:17614500;N:26666,34,35,,,12413417,16491074,20506887,17614500,26666,SRX363375,SRS490044,SRA104816,University of Bergen,ZEPROME consortium,2,0.47234,0.16966,0.00033,0.00039,0.99918,0.99993,0.00051,0.0,34,35,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37196,SRR1010323,SRX363374,SRS490044,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio WTL2F transgenic line,,strain:AB strain WTL2F line|development stage:high 3.3 hpf,,,,,,,,,D. rerio WTL2F transgenic line   single locus CAGE endogenous sf3a2,D. rerio WTL2F transgenic line   single locus CAGE endogenous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,WTL2F_endogenous_R1.fastq WTL2F_endogenous_R2.fastq,fastq fastq,71493591.0,1036139.0,D. rerio WTL2F transgenic line   single locus CAGE endogenous sf3a2,0:34 1:35,A:19123161;C:18705556;G:20092193;T:13545180;N:27501,34,35,,,19123161,18705556,20092193,13545180,27501,SRX363374,SRS490044,SRA104816,University of Bergen,ZEPROME consortium,2,0.56581,0.02161,0.00279,0.00056,0.99949,0.99991,0.00025,0.09333,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37197,SRR1010322,SRX363361,SRS490033,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio WTL1F transgenic line,,strain:AB strain WTL1F line|dev stage:high 3.3 hpf,,,,,,,,,D. rerio WTL1F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,D. rerio WTL1F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,WTL1F_transgene_R1.fastq WTL1F_transgene_R2.fastq,fastq fastq,95222070.0,1380030.0,D. rerio WTL1F transgenic line   single locus CAGE wild type sf3a2:mCherry transgene,0:34 1:35,A:17371572;C:23537350;G:29495884;T:24779827;N:37437,34,35,,,17371572,23537350,29495884,24779827,37437,SRX363361,SRS490033,SRA104816,University of Bergen,ZEPROME consortium,2,0.44573,0.30978,0.00036,0.00019,0.99943,0.99991,0.00023,0.00124,34,35,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
37198,SRR1010321,SRX363360,SRS490033,SRP030770,PRJNA222234,Danio rerio Targeted Locus Loci,PRJNA222234,Transcriptome Analysis,Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter  which guide transcription start site selection for that promoter in the zebrafish oocyte.,,pubmed:24531765,stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry,Generic sample from Danio rerio,D. rerio WTL1F transgenic line,,strain:AB strain WTL1F line|dev stage:high 3.3 hpf,,,,,,,,,D. rerio WTL1F transgenic line   single locus CAGE endogenous sf3a2,D. rerio WTL1F transgenic line   single locus CAGE endogeneous sf3a2,1,1,,,OTHER,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP030770,,,WTL1F_endogenous_R1.fastq WTL1F_endogenous_R2.fastq,fastq fastq,64955082.0,941378.0,D. rerio WTL1F transgenic line   single locus CAGE endogeneous sf3a2,0:34 1:35,A:17404375;C:16997013;G:18318738;T:12210960;N:23996,34,35,,,17404375,16997013,18318738,12210960,23996,SRX363360,SRS490033,SRA104816,University of Bergen,ZEPROME consortium,2,0.55528,0.02138,9e-05,0.00135,0.99963,0.99991,9e-05,0.10169,34,35,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2014-02-10,Blastula,Embryo,Undetermined,Embryo Imprecise
40249,SRR3038049,SRX1494244,SRS1217111,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,IgG iCLIP zf ZGA rep3,GSM1976593,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti IgG|barcode sequence:NNNTGGCNN,IgG iCLIP zf ZGA rep3,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti IgG|barcode sequence:NNNTGGCNN,GSM1976593,GSM1976593: IgG iCLIP zf ZGA rep3; Danio rerio; OTHER,GSM1976593,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976593,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_IgG_zebrafishembryo_wt_1K_IgGcontrol_Dr_NNNTGGCNN_20140613_L4333_4.fq.gz,fastq,82722124.0,1088449.0,GSM1976593 r1,0:76,A:21959870;C:19048567;G:22289272;T:19403630;N:20785,76,,,,21959870,19048567,22289272,19403630,20785,SRX1494244,SRS1217111,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.08124,,0.02181,,0.98591,,0.59183,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
40250,SRR3038048,SRX1494243,SRS1217112,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,IgG iCLIP zf ZGA rep2,GSM1976592,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti IgG|barcode sequence:NNNCCACNN,IgG iCLIP zf ZGA rep2,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti IgG|barcode sequence:NNNCCACNN,GSM1976592,GSM1976592: IgG iCLIP zf ZGA rep2; Danio rerio; OTHER,GSM1976592,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976592,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_IgG_zebrafishembryo_wt_1K_IgGcontrol_Dr_NNNCCACNN_20140613_L4333_2.fq.gz,fastq,50195036.0,660461.0,GSM1976592 r1,0:76,A:14249581;C:12927029;G:12969451;T:10036400;N:12575,76,,,,14249581,12927029,12969451,10036400,12575,SRX1494243,SRS1217112,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.25447,,0.03871,,0.94556,,0.7523,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
40251,SRR3038047,SRX1494242,SRS1217113,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,IgG iCLIP zf ZGA rep1,GSM1976591,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti IgG|barcode sequence:NNNGGCGNN,IgG iCLIP zf ZGA rep1,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti IgG|barcode sequence:NNNGGCGNN,GSM1976591,GSM1976591: IgG iCLIP zf ZGA rep1; Danio rerio; OTHER,GSM1976591,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976591,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_IgG_zebrafishembryo_wt_1K_IgGcontrol_Dr_NNNGGCGNN_20140613_L4333_5.fq.gz,fastq,453449136.0,5966436.0,GSM1976591 r1,0:76,A:124726528;C:101139098;G:135573575;T:91900507;N:109428,76,,,,124726528,101139098,135573575,91900507,109428,SRX1494242,SRS1217113,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.51353,,0.10729,,0.88069,,0.7159,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
40255,SRR3038043,SRX1494238,SRS1217117,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,hnRNP A1 iCLIP zf ZGA rep4,GSM1976587,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNGGTCNN,hnRNP A1 iCLIP zf ZGA rep4,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNGGTCNN,GSM1976587,GSM1976587: hnRNP A1 iCLIP zf ZGA rep4; Danio rerio; OTHER,GSM1976587,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976587,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_hnRNPA1_zebrafishembryo_wt_1K_hnRNPA1_Dr_NNNGGTCNN_20140613_L4333_6.fq.gz,fastq,2884007568.0,37947468.0,GSM1976587 r1,0:76,A:936463452;C:557587142;G:746595510;T:642623181;N:738283,76,,,,936463452,557587142,746595510,642623181,738283,SRX1494238,SRS1217117,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.38306,,0.08291,,0.80568,,0.62132,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
40256,SRR3038042,SRX1494237,SRS1217118,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,hnRNP A1 iCLIP zf ZGA rep3,GSM1976586,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNCAATNN,hnRNP A1 iCLIP zf ZGA rep3,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNCAATNN,GSM1976586,GSM1976586: hnRNP A1 iCLIP zf ZGA rep3; Danio rerio; OTHER,GSM1976586,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976586,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_hnRNPA1_zebrafishembryo_wt_1K_hnRNPA1_Dr_NNNCAATNN_20140613_L4333_3.fq.gz,fastq,3875071508.0,50987783.0,GSM1976586 r1,0:76,A:1328984506;C:775814536;G:956147632;T:813109146;N:1015688,76,,,,1328984506,775814536,956147632,813109146,1015688,SRX1494237,SRS1217118,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.35787,,0.0904,,0.81874,,0.64706,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
40257,SRR3038041,SRX1494236,SRS1217119,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,hnRNP A1 iCLIP zf ZGA rep2,GSM1976585,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNTTGTNN,hnRNP A1 iCLIP zf ZGA rep2,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNTTGTNN,GSM1976585,GSM1976585: hnRNP A1 iCLIP zf ZGA rep2; Danio rerio; OTHER,GSM1976585,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976585,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_hnRNPA1_zebrafishembryo_wt_1K_hnRNPA1_Dr_NNNTTGTNN_20140613_L4333_1.fq.gz,fastq,3482039180.0,45816305.0,GSM1976585 r1,0:76,A:1093877493;C:647486562;G:914636686;T:825135975;N:902464,76,,,,1093877493,647486562,914636686,825135975,902464,SRX1494236,SRS1217119,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.29908,,0.07356,,0.83459,,0.62976,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
40258,SRR3038040,SRX1494235,SRS1217120,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,hnRNP A1 iCLIP zf ZGA rep1,GSM1976584,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNGGTTNN,hnRNP A1 iCLIP zf ZGA rep1,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNGGTTNN,GSM1976584,GSM1976584: hnRNP A1 iCLIP zf ZGA rep1; Danio rerio; OTHER,GSM1976584,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976584,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_hnRNPA1_zebrafishembryo_wt_1K_hnRNPA1_Dr_NNNGGTTNN_20140613_L4333_7.fq.gz,fastq,3547711920.0,46680420.0,GSM1976584 r1,0:76,A:1105542969;C:658172853;G:958654426;T:824422930;N:918742,76,,,,1105542969,658172853,958654426,824422930,918742,SRX1494235,SRS1217120,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.34257,,0.08694,,0.83055,,0.64965,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43058,SRR8354695,SRX5165478,SRS4174524,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS seq   RNA structure positive controls in vitro replicate 1,DMS seq   RNA positives ctrl in vitro B1 AG01489,,strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:1|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,DMS seq   RNA structure positive controls in vitro replicate 1,AG01489.1,AG01489.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,AG01489.1_R1.fastq.gz,fastq,75703530.0,2718404.0,AG01489.1 R1.fastq.gz,0:27.85 1:0,A:18206335;C:19464567;G:21319876;T:16712584;N:168,27,0,,,18206335,19464567,21319876,16712584,168,SRX5165478,SRS4174524,SRA825010,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.02389,,0.00591,,0.97654,,0.4758,,25,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-12-19,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43059,SRR8354696,SRX5165477,SRS4174523,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS seq   RNA structure positive controls in vitro replicate 2,DMS seq   RNA positives ctrl in vitro B2 AG01490,,strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:2|barcode:GTGT|BioSampleModel:Model organism or animal,,,,,,,,,DMS seq   RNA structure positive controls in vitro replicate 2,AG01490.1,AG01490.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,AG01490.1_R1.fastq.gz,fastq,295051199.0,10869746.0,AG01490.1 R1.fastq.gz,0:27.14 1:0,A:71900468;C:76519029;G:81589099;T:65042019;N:584,27,0,,,71900468,76519029,81589099,65042019,584,SRX5165477,SRS4174523,SRA825010,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.02362,,0.00528,,0.98173,,0.35096,,19,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-12-19,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43060,SRR8354697,SRX5165476,SRS4174522,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,Raw multiplex: DMS seq   RNA structure positive controls in vitro replicate 1;DMS seq   RNA structure positive controls in vitro replicate 2,Raw multiplex: DMS seq   RNA positives ctrl in vitro B1 AG01489;DMS seq   RNA positives ctrl in vitro B2 AG01490,,strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:1;2|barcode:TCTC;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: DMS seq   RNA structure positive controls in vitro replicate 1;DMS seq   RNA structure positive controls in vitro replicate 2,AG01489.1;AG01490.1,AG01489.1;AG01490.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,C7MYYANXX_JBDX127_009_R1.fastq.gz,fastq,1115150128.0,14673028.0,C7MYYANXX JBDX127 009 R1.fastq.gz,0:76,A:313482382;C:276309346;G:291633361;T:233659719;N:65320,76,,,,313482382,276309346,291633361,233659719,65320,SRX5165476,SRS4174522,SRA825010,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00546,,0.00047,,0.98602,,0.51535,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-12-19,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43111,SRR5893078,SRX3058767,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01043,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01043.6,AG01043.6,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.6_R1.fastq.gz,fastq,245591088.0,10387582.0,AG01043.6 R1.fastq.gz,0:23.64 1:0,A:66848740;C:56927652;G:60996703;T:60816631;N:1362,23,0,,,66848740,56927652,60996703,60816631,1362,SRX3058767,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.62265,,0.12438,,0.7696,,0.59474,,32,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43112,SRR5893079,SRX3058766,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01043,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01043.5,AG01043.5,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.5_R1.fastq.gz,fastq,935516222.0,39234795.0,AG01043.5 R1.fastq.gz,0:23.84 1:0,A:254864411;C:216185186;G:231676738;T:232716892;N:72995,23,0,,,254864411,216185186,231676738,232716892,72995,SRX3058766,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.6326,,0.12713,,0.76739,,0.59812,,27,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43113,SRR5893080,SRX3058765,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01043,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01043.4,AG01043.4,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.4_R1.fastq.gz,fastq,633932186.0,26698352.0,AG01043.4 R1.fastq.gz,0:23.74 1:0,A:172078766;C:147459021;G:157655737;T:156729321;N:9341,23,0,,,172078766,147459021,157655737,156729321,9341,SRX3058765,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.62892,,0.12689,,0.76915,,0.59625,,19,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43114,SRR5893081,SRX3058764,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01043,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01043.3,AG01043.3,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.3_R1.fastq.gz,fastq,545501906.0,22980935.0,AG01043.3 R1.fastq.gz,0:23.74 1:0,A:147643154;C:127194084;G:135926112;T:134737007;N:1549,23,0,,,147643154,127194084,135926112,134737007,1549,SRX3058764,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.63069,,0.12544,,0.76781,,0.60018,,26,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43125,SRR5893092,SRX3058753,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01043,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01043.1,AG01043.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.1_R1.fastq.gz,fastq,108747256.0,4575669.0,AG01043.1 R1.fastq.gz,0:23.77 1:0,A:29414532;C:25366431;G:27139739;T:26826074;N:480,23,0,,,29414532,25366431,27139739,26826074,480,SRX3058753,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.62913,,0.12566,,0.76946,,0.59653,,20,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43126,SRR5893093,SRX3058752,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01043,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01043.2,AG01043.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.2_R1.fastq.gz,fastq,37331204.0,1581621.0,AG01043.2 R1.fastq.gz,0:23.60 1:0,A:10098397;C:8686566;G:9362492;T:9181793;N:1956,23,0,,,10098397,8686566,9362492,9181793,1956,SRX3058752,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.60497,,0.12042,,0.77114,,0.5559,,21,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43145,SRR5893112,SRX3058733,SRS2404545,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01049,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01049.4,AG01049.4,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01049.4_R1.fastq.gz,fastq,693084196.0,30220927.0,AG01049.4 R1.fastq.gz,0:22.93 1:0,A:184260362;C:156379835;G:169790720;T:182650190;N:3089,22,0,,,184260362,156379835,169790720,182650190,3089,SRX3058733,SRS2404545,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.56552,,0.10478,,0.77329,,0.58948,,15,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43146,SRR5893113,SRX3058732,SRS2404545,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01049,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01049.3,AG01049.3,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01049.3_R1.fastq.gz,fastq,605892767.0,26434367.0,AG01049.3 R1.fastq.gz,0:22.92 1:0,A:160713810;C:136961096;G:148749325;T:159466624;N:1912,22,0,,,160713810,136961096,148749325,159466624,1912,SRX3058732,SRS2404545,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.5625,,0.10811,,0.77224,,0.58777,,23,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43147,SRR5893114,SRX3058731,SRS2404545,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01049,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01049.6,AG01049.6,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01049.6_R1.fastq.gz,fastq,394478885.0,17274979.0,AG01049.6 R1.fastq.gz,0:22.84 1:0,A:105227778;C:88892938;G:96681477;T:103674703;N:1989,22,0,,,105227778,88892938,96681477,103674703,1989,SRX3058731,SRS2404545,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.55998,,0.10523,,0.77279,,0.58664,,29,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43148,SRR5893115,SRX3058730,SRS2404545,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01049,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01049.5,AG01049.5,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01049.5_R1.fastq.gz,fastq,886753255.0,38566196.0,AG01049.5 R1.fastq.gz,0:22.99 1:0,A:235539511;C:199422326;G:217573523;T:234156689;N:61206,22,0,,,235539511,199422326,217573523,234156689,61206,SRX3058730,SRS2404545,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.56676,,0.10782,,0.77331,,0.58475,,25,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43151,SRR5893118,SRX3058727,SRS2404545,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01049,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01049.2,AG01049.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01049.2_R1.fastq.gz,fastq,37381210.0,1641906.0,AG01049.2 R1.fastq.gz,0:22.77 1:0,A:9910821;C:8448316;G:9246060;T:9775054;N:959,22,0,,,9910821,8448316,9246060,9775054,959,SRX3058727,SRS2404545,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.54348,,0.10292,,0.77467,,0.59127,,21,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
43152,SRR5893119,SRX3058726,SRS2404545,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT sphere in vivo,dmsseq AG01049,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT sphere in vivo,AG01049.1,AG01049.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01049.1_R1.fastq.gz,fastq,113060119.0,4927027.0,AG01049.1 R1.fastq.gz,0:22.95 1:0,A:29961989;C:25583869;G:27802427;T:29711326;N:508,22,0,,,29961989,25583869,27802427,29711326,508,SRX3058726,SRS2404545,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.56357,,0.10878,,0.77143,,0.59024,,23,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
44645,SRR6268203,SRX3374371,SRS2671594,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,oocyte A+ 4h,GSM2845357,,source name:zebrafish oocyte|developmental stage:4h|tissue:oocyte,oocyte A+ 4h,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish oocyte,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:4h|tissue:oocyte,GSM2845357,GSM2845357: oocyte A+ 4h; Danio rerio; OTHER,GSM2845357,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845357,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,AR21-SL41.fastq.gz,fastq,474802240.0,2967514.0,GSM2845357 r1,0:160 1:0,A:145810423;C:111330144;G:93000312;T:124660574;N:787,160,0,,,145810423,111330144,93000312,124660574,787,SRX3374371,SRS2671594,SRA629220,GEO,Broad Institute,1,2e-05,,0.0,,0.99997,,0.0,,160,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Blastula,Embryo,Oocyte,Reproductive System
44648,SRR6268200,SRX3374368,SRS2671593,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,oocyte A  4h,GSM2845354,,source name:zebrafish oocyte|developmental stage:4h|tissue:oocyte,oocyte A  4h,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish oocyte,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:4h|tissue:oocyte,GSM2845354,GSM2845354: oocyte A  4h; Danio rerio; OTHER,GSM2845354,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845354,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,AR18-SL39.fastq.gz,fastq,533958880.0,3337243.0,GSM2845354 r1,0:160 1:0,A:163118236;C:125487590;G:106580813;T:138769793;N:2448,160,0,,,163118236,125487590,106580813,138769793,2448,SRX3374368,SRS2671593,SRA629220,GEO,Broad Institute,1,1e-05,,0.0,,0.99997,,0.0,,160,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Blastula,Embryo,Oocyte,Reproductive System
44655,SRR6268193,SRX3374361,SRS2671586,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,rep A  4h,GSM2845347,,source name:zebrafish embryos|developmental stage:4hpf|tissue:embryo,rep A  4h,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:4hpf|tissue:embryo,GSM2845347,GSM2845347: rep A  4h; Danio rerio; OTHER,GSM2845347,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845347,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,4hpf-1.fastq.gz,fastq,443483200.0,2771770.0,GSM2845347 r1,0:160 1:0,A:139383281;C:100368800;G:84425873;T:119267938;N:37308,160,0,,,139383281,100368800,84425873,119267938,37308,SRX3374361,SRS2671586,SRA629220,GEO,Broad Institute,1,2e-05,,0.0,,0.99995,,0.5,,160,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
44656,SRR6268192,SRX3374360,SRS2671587,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,rep A  3h,GSM2845346,,source name:zebrafish embryos|developmental stage:3hpf|tissue:embryo,rep A  3h,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:3hpf|tissue:embryo,GSM2845346,GSM2845346: rep A  3h; Danio rerio; OTHER,GSM2845346,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845346,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,3hpf.fastq.gz,fastq,557489280.0,3484308.0,GSM2845346 r1,0:160 1:0,A:174273480;C:125862121;G:107763308;T:149536497;N:53874,160,0,,,174273480,125862121,107763308,149536497,53874,SRX3374360,SRS2671587,SRA629220,GEO,Broad Institute,1,6e-05,,0.0,,0.99981,,0.22222,,160,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
44666,SRR6268182,SRX3374350,SRS2671577,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,techrep A+ 5h.2,GSM2845336,,source name:zebrafish embryos|developmental stage:5hpf|tissue:embryo,techrep A+ 5h.2,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:5hpf|tissue:embryo,GSM2845336,GSM2845336: techrep A+ 5h.2; Danio rerio; OTHER,GSM2845336,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845336,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,AR18_S18.fastq.gz,fastq,188186880.0,1120160.0,GSM2845336 r1,0:168 1:0,A:64287530;C:38206555;G:34905552;T:50786665;N:578,168,0,,,64287530,38206555,34905552,50786665,578,SRX3374350,SRS2671577,SRA629220,GEO,Broad Institute,1,0.0,,0.0,,1.0,,,,168,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
44667,SRR6268181,SRX3374349,SRS2671578,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,techrep A+ 4h.2,GSM2845335,,source name:zebrafish embryos|developmental stage:4hpf|tissue:embryo,techrep A+ 4h.2,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:4hpf|tissue:embryo,GSM2845335,GSM2845335: techrep A+ 4h.2; Danio rerio; OTHER,GSM2845335,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845335,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,AR17_S17.fastq.gz,fastq,184770096.0,1099822.0,GSM2845335 r1,0:168 1:0,A:63618247;C:37087101;G:34147549;T:49916639;N:560,168,0,,,63618247,37087101,34147549,49916639,560,SRX3374349,SRS2671578,SRA629220,GEO,Broad Institute,1,1e-05,,0.0,,1.0,,,,168,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
44668,SRR6268180,SRX3374348,SRS2671576,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,techrep A+ 3h.2,GSM2845334,,source name:zebrafish embryos|developmental stage:3hpf|tissue:embryo,techrep A+ 3h.2,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:3hpf|tissue:embryo,GSM2845334,GSM2845334: techrep A+ 3h.2; Danio rerio; OTHER,GSM2845334,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845334,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,AR16_S16.fastq.gz,fastq,196416864.0,1169148.0,GSM2845334 r1,0:168 1:0,A:68358077;C:39754902;G:34495844;T:53807445;N:596,168,0,,,68358077,39754902,34495844,53807445,596,SRX3374348,SRS2671576,SRA629220,GEO,Broad Institute,1,2e-05,,0.0,,1.0,,,,168,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
44678,SRR6268170,SRX3374338,SRS2671566,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,techrep A+ 5h.1,GSM2845324,,source name:zebrafish embryos|developmental stage:5hpf|tissue:embryo,techrep A+ 5h.1,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:5hpf|tissue:embryo,GSM2845324,GSM2845324: techrep A+ 5h.1; Danio rerio; OTHER,GSM2845324,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845324,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,AR06_S6.fastq.gz,fastq,190078560.0,1131420.0,GSM2845324 r1,0:168 1:0,A:65220545;C:38085617;G:34999757;T:51772096;N:545,168,0,,,65220545,38085617,34999757,51772096,545,SRX3374338,SRS2671566,SRA629220,GEO,Broad Institute,1,2e-05,,0.0,,0.99997,,1.0,,168,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures
44679,SRR6268169,SRX3374337,SRS2671565,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,techrep A+ 4h.1,GSM2845323,,source name:zebrafish embryos|developmental stage:4hpf|tissue:embryo,techrep A+ 4h.1,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:4hpf|tissue:embryo,GSM2845323,GSM2845323: techrep A+ 4h.1; Danio rerio; OTHER,GSM2845323,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845323,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,AR05_S5.fastq.gz,fastq,185419080.0,1103685.0,GSM2845323 r1,0:168 1:0,A:63320889;C:37435097;G:34226069;T:50436440;N:585,168,0,,,63320889,37435097,34226069,50436440,585,SRX3374337,SRS2671565,SRA629220,GEO,Broad Institute,1,2e-05,,0.0,,0.99997,,0.0,,168,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures