{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Cleavage\" and tissue_curation_coarse = \"Embryo Imprecise\"", "rows": [[9726, "ERR3841993", "ERX3854555", "ERS3555998", "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. 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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. 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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", null, null, "64 cell 2", "SAMEA5752539", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752539|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:2|common name:zebrafish|dev stage:64 cell|sample name:2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 3", "64 cell 2 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 9525478088.0, 125335238.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 3", "0:76", "A:4813606784;C:2048902072;G:2140220088;T:522714000;N:35144", 76, null, null, null, 4813606784, 2048902072, 2140220088, 522714000, 35144, "ERX3511266", "ERS3555998", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.59747, null, 0.26784, null, 0.996, null, 0.21193, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9760, "ERR3489850", "ERX3511265", "ERS3555997", "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", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|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:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 2", "64 cell 1 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 8544157652.0, 112423127.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 2", "0:76", "A:2633354802;C:2582123846;G:2505786164;T:822713754;N:179086", 76, null, null, null, 2633354802, 2582123846, 2505786164, 822713754, 179086, "ERX3511265", "ERS3555997", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.34707, null, 0.02129, null, 0.99797, null, 0.62478, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9761, "ERR3489849", "ERX3511264", "ERS3555997", "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", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|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:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 1", "64 cell 1 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", "run7_64_cell_SSU_12_13_14.fastq.gz", "fastq", 10139466432.0, 133414032.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 1", "0:76 1:0", "A:4628193785;C:2494821868;G:2485640988;T:530605907;N:203884", 76, 0, null, null, 4628193785, 2494821868, 2485640988, 530605907, 203884, "ERX3511264", "ERS3555997", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.06893, null, 0.02559, null, 0.99766, null, 0.90567, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9762, "ERR3413870", "ERX3437516", "ERS3555997", "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", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|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:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 03 07 2019 14:45:09:705 2", "64 cell 1 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, 8544157652.0, 112423127.0, "ena RUN Computational Biology Unit 03 07 2019 14:45:09:705 2", "0:76", "A:2633354802;C:2582123846;G:2505786164;T:822713754;N:179086", 76, null, null, null, 2633354802, 2582123846, 2505786164, 822713754, 179086, "ERX3437516", "ERS3555997", "ERA2028987", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.34696, null, 0.02086, null, 0.99795, null, 0.66261, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9763, "ERR3413869", "ERX3437515", "ERS3555997", "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", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|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:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 03 07 2019 14:45:09:705 1", "64 cell 1 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, 10139466432.0, 133414032.0, "ena RUN Computational Biology Unit 03 07 2019 14:45:09:705 1", "0:76", "A:4628193785;C:2494821868;G:2485640988;T:530605907;N:203884", 76, null, null, null, 4628193785, 2494821868, 2485640988, 530605907, 203884, "ERX3437515", "ERS3555997", "ERA2028987", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.06884, null, 0.02526, null, 0.99762, null, 0.89856, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9919, "ERR5167510", "ERX4972431", "ERS5593364", "ERP122761", "PRJEB39265", "RNA dynamics during zebrafish development", "ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183", "Other", "RNA dynamics during early zebrafish development", "ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", null, null, "cDNA WT 2hpf rep1", "JD T20 PDPN191089", null, "ENA FIRST PUBLIC:2022 07 05T12:06:34Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:34Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", null, null, null, null, null, null, null, null, "PromethION sequencing", "ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 21 01 2021 22:16:50:154 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "OXFORD_NANOPORE", "PromethION", null, "ERP122761", "PromethION sequencing", "ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", null, null, null, null, "ena RUN CENTER FOR GENOMIC REGULATION CRG 21 01 2021 22:16:50:154 1", null, null, null, null, null, null, null, null, null, null, null, "ERX4972431", null, "ERA3319053", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "ont", "ont", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-07-05", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [24550, "ERR964668", "ERX1041631", "ERS792102", "ERP011038", "PRJEB9889", "The Zebrafish transcriptome during early development", "ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22", "Other", "Zebrafish has emerged as a model organism to investigate vertebrate development  and human genetic diseases. However  currently zebrafish annotation is still ongoing and clearly not sufficed  therefore  providing opportunity for novel transcript finding.  With the introduction of massive parallel sequencing  whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study  we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.", null, null, null, "KI BN JKE DRERIO RNASEQ", "SAMEA3484817", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION", "ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484817|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 16cell|common name:zebrafish|dev stage:16 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 16cell|strain:Tuebingen", null, null, null, null, null, null, null, null, "AB SOLiD System 3.0 sequencing", "ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "ERP011038", "AB SOLiD System 3.0 sequencing", "ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16", "KI-BN-JKE-DRERIO-RNASEQ-20090709-16cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-16cell_F3_QV.qual.gz", "SOLiD_native SOLiD_native", 5278508300.0, 105570166.0, "ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 2", "0:50", "0:1410981717;1:1203936808;2:1415708111;3:1223403795;.:24477869", 50, null, null, null, null, null, null, null, null, "ERX1041631", "ERS792102", "ERA458495", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION", 1, 0.71371, null, 0.09346, null, 0.91539, null, 0.73015, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2015-07-15", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [24553, "ERR964672", "ERX1041635", "ERS792102", "ERP011038", "PRJEB9889", "The Zebrafish transcriptome during early development", "ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22", "Other", "Zebrafish has emerged as a model organism to investigate vertebrate development  and human genetic diseases. However  currently zebrafish annotation is still ongoing and clearly not sufficed  therefore  providing opportunity for novel transcript finding.  With the introduction of massive parallel sequencing  whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study  we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.", null, null, null, "KI BN JKE DRERIO RNASEQ", "SAMEA3484817", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION", "ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484817|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 16cell|common name:zebrafish|dev stage:16 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 16cell|strain:Tuebingen", null, null, null, null, null, null, null, null, "AB SOLiD System 3.0 sequencing", "ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 6", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "ERP011038", "AB SOLiD System 3.0 sequencing", "ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16", "KI-BN-JKE-DRERIO-RNASEQ-20091014-16cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-16cell_F3_QV.qual.gz", "SOLiD_native SOLiD_native", 2719433200.0, 54388664.0, "ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 6", "0:50", "0:699731678;1:628745158;2:754903505;3:633574679;.:2478180", 50, null, null, null, null, null, null, null, null, "ERX1041635", "ERS792102", "ERA458495", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION", 1, 0.73214, null, 0.09566, null, 0.90836, null, 0.74043, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2015-07-15", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [59499, "SRR11924325", "SRX8469997", "SRS6770648", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "small RNA 32 cell", "GSM4591064", null, "source name:32 cell stage|tissue:32 cell stage|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt", "small RNA 32 cell", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "32 cell stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction  one  ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen  and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short  the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs  adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module  without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.", null, "tissue:32 cell stage|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt", "GSM4591064", "GSM4591064: small RNA 32 cell; Danio rerio; OTHER", "GSM4591064", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction  one  ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen  and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short  the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs  adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module  without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.", "GEO Accession:GSM4591064", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent S5", null, "SRP265951", null, null, "small_RNA_32_cell_stage.fastq", "fastq", 275040056.0, 6091077.0, "GSM4591064 r1", "0:45.15", "A:69136092;C:69806677;G:72527986;T:63569301;N:0", 45, null, null, null, 69136092, 69806677, 72527986, 63569301, 0, "SRX8469997", "SRS6770648", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.67676, null, 0.30881, null, 0.86636, null, 0.63482, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [59509, "SRR11924311", "SRX8469986", "SRS6770637", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "32 cell 3", "GSM4591054", null, "source name:32 cell stage|tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "32 cell 3", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "32 cell stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591054", "GSM4591054: 32 cell 3; Danio rerio; OTHER", "GSM4591054", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591054", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "32_cell_3.bam GSE151797_Reference_sequence.fa", "bam bam", 306452866.0, 9472058.0, "GSM4591054 r1", "0:32.35", "A:62923439;C:99486553;G:78734118;T:65308756;N:0", 32, null, null, null, 62923439, 99486553, 78734118, 65308756, 0, "SRX8469986", "SRS6770637", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.69616, null, 0.21356, null, 0.91885, null, 0.77399, null, 44, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [59510, "SRR11924310", "SRX8469985", "SRS6770636", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "32 cell 2", "GSM4591053", null, "source name:32 cell stage|tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "32 cell 2", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "32 cell stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591053", "GSM4591053: 32 cell 2; Danio rerio; OTHER", "GSM4591053", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591053", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "32_cell_2.bam GSE151797_Reference_sequence.fa", "bam bam", 231900531.0, 6985149.0, "GSM4591053 r1", "0:33.20", "A:46033127;C:77390842;G:61355372;T:47121190;N:0", 33, null, null, null, 46033127, 77390842, 61355372, 47121190, 0, "SRX8469985", "SRS6770636", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.83429, null, 0.25864, null, 0.9137, null, 0.78928, null, 39, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [59511, "SRR11924308", "SRX8469984", "SRS6770635", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "32 cell 1", "GSM4591052", null, "source name:32 cell stage|tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "32 cell 1", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "32 cell stage", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591052", "GSM4591052: 32 cell 1; Danio rerio; OTHER", "GSM4591052", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591052", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "32_cell_1.bam GSE151797_Reference_sequence.fa", "bam bam", 252107732.0, 7470443.0, "GSM4591052 r1", "0:33.75", "A:53056857;C:79089015;G:65131744;T:54830116;N:0", 33, null, null, null, 53056857, 79089015, 65131744, 54830116, 0, "SRX8469984", "SRS6770635", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.78874, null, 0.25062, null, 0.89645, null, 0.73533, null, 48, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"]], "truncated": false, "filtered_table_rows_count": 20, "expanded_columns": [], "expandable_columns": 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