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568 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "other" and experiment.library_strategy = "OTHER"

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devstage_curation >10

technology 5

devstage_curation_coarse 4

experiment.platform 2

experiment.library_source 2

experiment.library_strategy 1

  • OTHER · 568 ✖

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  • other · 568 ✖

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  • SINGLE · 568 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
9717 9717 ERR3842002 ERX3854564 ERS4268611 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     Shield 4Ei SAMEA6504165 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:05:06Z|ENA LAST UPDATE:2020 01 27T16:04:35Z|External Id:SAMEA6504165|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:05:06Z|INSDC last update:2020 01 27T16:04:35Z|INSDC status:public|Submitter Id:Shield 4Ei|common name:zebrafish|sample name:Shield 4Ei|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 17:26:02:557 2 Shield 4Ei LSU OTHER RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     10915827408.0 143629308.0 ena RUN Computational Biology Unit 27 01 2020 17:26:02:557 2 0:76 A:3900515347;C:2409375725;G:3041696977;T:1564127293;N:112066 76       3900515347 2409375725 3041696977 1564127293 112066 ERX3854564 ERS4268611 ERA2359340 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.64398   0.40944   0.98817   0.59337   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9718 9718 ERR3842001 ERX3854563 ERS4268611 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     Shield 4Ei SAMEA6504165 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:05:06Z|ENA LAST UPDATE:2020 01 27T16:04:35Z|External Id:SAMEA6504165|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:05:06Z|INSDC last update:2020 01 27T16:04:35Z|INSDC status:public|Submitter Id:Shield 4Ei|common name:zebrafish|sample name:Shield 4Ei|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 17:26:02:557 1 Shield 4Ei SSU OTHER RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     7154041880.0 94132130.0 ena RUN Computational Biology Unit 27 01 2020 17:26:02:557 1 0:76 A:2939474250;C:1489083073;G:1922522149;T:802890185;N:72223 76       2939474250 1489083073 1922522149 802890185 72223 ERX3854563 ERS4268611 ERA2359340 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.4369   0.25417   0.9867   0.60047   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9729 9729 ERR3489881 ERX3511296 ERS3556004 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     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|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:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 33 Shield 1 F20 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     975578636.0 12836561.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 33 0:76 A:398325549;C:237563934;G:230721299;T:108957698;N:10156 76       398325549 237563934 230721299 108957698 10156 ERX3511296 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.33102   0.19766   0.99918   0.12812   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9730 9730 ERR3489880 ERX3511295 ERS3556004 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     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|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:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 32 Shield 1 F19 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     931166668.0 12252193.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 32 0:76 A:271081669;C:253947035;G:272354427;T:133774815;N:8722 76       271081669 253947035 272354427 133774815 8722 ERX3511295 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.15598   0.10707   0.99902   0.47314   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9731 9731 ERR3489879 ERX3511294 ERS3556004 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     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|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:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 31 Shield 1 F18 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     1506513268.0 19822543.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 31 0:76 A:493273515;C:456544968;G:391677033;T:165002559;N:15193 76       493273515 456544968 391677033 165002559 15193 ERX3511294 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.01562   0.0053   0.99908   0.8127   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9732 9732 ERR3489878 ERX3511293 ERS3556004 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     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|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:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 30 Shield 1 F17 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     1259456496.0 16571796.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 30 0:76 A:471473123;C:333726472;G:302016190;T:152228002;N:12709 76       471473123 333726472 302016190 152228002 12709 ERX3511293 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.18339   0.12544   0.99928   0.22368   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9733 9733 ERR3489877 ERX3511292 ERS3556004 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     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|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:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 29 Shield 1 F16 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     1364615872.0 17955472.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 29 0:76 A:539462776;C:341141880;G:314571683;T:169426048;N:13485 76       539462776 341141880 314571683 169426048 13485 ERX3511292 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.11663   0.07319   0.99939   0.25377   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9734 9734 ERR3489876 ERX3511291 ERS3556004 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     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|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:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 28 Shield 1 F15 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     952605888.0 12534288.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 28 0:76 A:414133320;C:219437277;G:207418049;T:111607418;N:9824 76       414133320 219437277 207418049 111607418 9824 ERX3511291 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.17603   0.10972   0.99935   0.13311   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9735 9735 ERR3489875 ERX3511290 ERS3556004 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     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|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:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 27 Shield 1 F14 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     870952628.0 11459903.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 27 0:76 A:357710338;C:221475453;G:191231014;T:100526675;N:9148 76       357710338 221475453 191231014 100526675 9148 ERX3511290 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.1248   0.06422   0.99896   0.34819   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9736 9736 ERR3489874 ERX3511289 ERS3556004 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     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|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:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 26 Shield 1 F13 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     981672620.0 12916745.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 26 0:76 A:434153198;C:223317075;G:198260771;T:125932145;N:9431 76       434153198 223317075 198260771 125932145 9431 ERX3511289 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.44603   0.25602   0.99874   0.18074   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9737 9737 ERR3489873 ERX3511288 ERS3556004 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     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|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:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 25 Shield 1 F12 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     1304618128.0 17166028.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 25 0:76 A:651341516;C:270458496;G:243929520;T:138874830;N:13766 76       651341516 270458496 243929520 138874830 13766 ERX3511288 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.64293   0.38159   0.99886   0.07313   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9738 9738 ERR3489872 ERX3511287 ERS3556004 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     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|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:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 24 Shield 1 F10 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     1336115948.0 17580473.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 24 0:76 A:608634206;C:295943144;G:286494431;T:145029697;N:14470 76       608634206 295943144 286494431 145029697 14470 ERX3511287 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.68758   0.47517   0.99898   0.02301   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9739 9739 ERR3489871 ERX3511286 ERS3556004 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     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|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:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 23 Shield 1 F9 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     1434402492.0 18873717.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 23 0:76 A:658705664;C:297967081;G:295595736;T:182118632;N:15379 76       658705664 297967081 295595736 182118632 15379 ERX3511286 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.74246   0.44235   0.99701   0.03112   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9740 9740 ERR3489870 ERX3511285 ERS3556007 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     Shield 4150NT SAMEA5752548 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752548|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:11|common name:zebrafish|dev stage:Shield|sample name:11|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 22 Shield 4150NT 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     24063208094.0 159358994.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 22 0:151 A:7153064588;C:5242791119;G:8513736630;T:3152547276;N:1068481 151       7153064588 5242791119 8513736630 3152547276 1068481 ERX3511285 ERS3556007 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.81267   0.27138   0.99868   0.91938   151   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9741 9741 ERR3489869 ERX3511284 ERS3556007 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     Shield 4150NT SAMEA5752548 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752548|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:11|common name:zebrafish|dev stage:Shield|sample name:11|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 21 Shield 4150NT 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 24     14987998619.0 99258269.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 21 0:151 A:4578051806;C:2616328922;G:5914185813;T:1878780090;N:651988 151       4578051806 2616328922 5914185813 1878780090 651988 ERX3511284 ERS3556007 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.77096   0.5278   0.99833   0.42635   151   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9742 9742 ERR3489868 ERX3511283 ERS3556003 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     64 cell 4Ei 10 SAMEA5752544 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752544|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:7|common name:zebrafish|dev stage:64 cell|sample name:7|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 20 64 cell 4Ei 10 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     5928054796.0 78000721.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 20 0:76 A:2109854905;C:1377083508;G:1616166285;T:824889630;N:60468 76       2109854905 1377083508 1616166285 824889630 60468 ERX3511283 ERS3556003 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.61525   0.45233   0.99379   0.57373   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9743 9743 ERR3489867 ERX3511282 ERS3556003 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     64 cell 4Ei 10 SAMEA5752544 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752544|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:7|common name:zebrafish|dev stage:64 cell|sample name:7|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 19 64 cell 4Ei 10 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     9772604780.0 128586905.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 19 0:76 A:3901301079;C:2223067879;G:2553338016;T:1094797648;N:100158 76       3901301079 2223067879 2553338016 1094797648 100158 ERX3511282 ERS3556003 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.52103   0.25046   0.9861   0.64575   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9744 9744 ERR3489866 ERX3511281 ERS3556002 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     64 cell 4Ei 0.1 SAMEA5752543 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752543|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:6|common name:zebrafish|dev stage:64 cell|sample name:6|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 18 64 cell 4Ei 0.1 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 09 26     6730725680.0 88562180.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 18 0:76 A:3805722011;C:1188715051;G:1382258076;T:353814168;N:216374 76       3805722011 1188715051 1382258076 353814168 216374 ERX3511281 ERS3556002 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.61922   0.37217   0.99527   0.29148   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9745 9745 ERR3489865 ERX3511280 ERS3556002 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     64 cell 4Ei 0.1 SAMEA5752543 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752543|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:6|common name:zebrafish|dev stage:64 cell|sample name:6|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 17 64 cell 4Ei 0.1 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 09 26     10616304872.0 139688222.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 17 0:76 A:4717003484;C:2600725234;G:2586105174;T:712124440;N:346540 76       4717003484 2600725234 2586105174 712124440 346540 ERX3511280 ERS3556002 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.30908   0.08252   0.94683   0.69548   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9746 9746 ERR3489864 ERX3511279 ERS3556006 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     Shield 3 SAMEA5752547 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752547|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:10|common name:zebrafish|dev stage:Shield|sample name:10|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 16 Shield 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     11777220072.0 154963422.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 16 0:76 A:3368038444;C:3190496935;G:3529701152;T:1688766119;N:217422 76       3368038444 3190496935 3529701152 1688766119 217422 ERX3511279 ERS3556006 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.70681   0.18846   0.99332   0.71978   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9747 9747 ERR3489863 ERX3511278 ERS3556006 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     Shield 3 SAMEA5752547 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752547|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:10|common name:zebrafish|dev stage:Shield|sample name:10|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 15 Shield 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     7920419952.0 104216052.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 15 0:76 A:2990167185;C:1767708808;G:2104830363;T:1057568560;N:145036 76       2990167185 1767708808 2104830363 1057568560 145036 ERX3511278 ERS3556006 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.5052   0.30841   0.99129   0.60948   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9748 9748 ERR3489862 ERX3511277 ERS3556005 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     Shield 2 SAMEA5752546 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752546|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:9|common name:zebrafish|dev stage:Shield|sample name:9|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 14 Shield 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 22     9775297004.0 128622329.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 14 0:76 A:4750565405;C:2540992255;G:1698817649;T:784832634;N:89061 76       4750565405 2540992255 1698817649 784832634 89061 ERX3511277 ERS3556005 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.74003   0.5616   0.99855   0.03607   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9749 9749 ERR3489861 ERX3511276 ERS3556005 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     Shield 2 SAMEA5752546 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752546|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:9|common name:zebrafish|dev stage:Shield|sample name:9|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 13 Shield 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     8210103300.0 108027675.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 13 0:76 A:3300825043;C:2576709678;G:1707115198;T:625376255;N:77126 76       3300825043 2576709678 1707115198 625376255 77126 ERX3511276 ERS3556005 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.2787   0.17583   0.99752   0.50171   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9750 9750 ERR3489860 ERX3511275 ERS3556004 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     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|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:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 12 Shield 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 22     2437679936.0 32074736.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 12 0:76 A:764355184;C:710492003;G:664031460;T:298777374;N:23915 76       764355184 710492003 664031460 298777374 23915 ERX3511275 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.0406   0.02417   0.99908   0.61299   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9751 9751 ERR3489859 ERX3511274 ERS3556004 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     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|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:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 11 Shield 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     3157243376.0 41542676.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 11 0:76 A:1443205052;C:715251024;G:633421305;T:365333650;N:32345 76       1443205052 715251024 633421305 365333650 32345 ERX3511274 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.47643   0.27944   0.99896   0.11464   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9752 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 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 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 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 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 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
9758 9758 ERR3489852 ERX3511267 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. 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 4 64 cell 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 22     11722578884.0 154244459.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 4 0:76 A:8175036829;C:1396062240;G:1882846539;T:268587131;N:46145 76       8175036829 1396062240 1882846539 268587131 46145 ERX3511267 ERS3555998 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.81133   0.41331   0.99823   0.03453   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9759 9759 ERR3489851 ERX3511266 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. 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 3 64 cell 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     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       4813606784 2048902072 2140220088 522714000 35144 ERX3511266 ERS3555998 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.59747   0.26784   0.996   0.21193   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9760 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 2 64 cell 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 22     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       2633354802 2582123846 2505786164 822713754 179086 ERX3511265 ERS3555997 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.34707   0.02129   0.99797   0.62478   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9761 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 1 64 cell 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 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     4628193785 2494821868 2485640988 530605907 203884 ERX3511264 ERS3555997 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.06893   0.02559   0.99766   0.90567   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9762 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 03 07 2019 14:45:09:705 2 64 cell 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 07 03     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       2633354802 2582123846 2505786164 822713754 179086 ERX3437516 ERS3555997 ERA2028987 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.34696   0.02086   0.99795   0.66261   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9763 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 03 07 2019 14:45:09:705 1 64 cell 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 07 03     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       4628193785 2494821868 2485640988 530605907 203884 ERX3437515 ERS3555997 ERA2028987 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.06884   0.02526   0.99762   0.89856   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
25295 25295 SRR25764045 SRX21486723 SRS18719024 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 bud 10 hpf Ribo seq rep1 GSM7734770   source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|treatment:100 µg/ml CHX 100 µg/ml TIG|geo loc name:missing|collection date:missing WT bud 10 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 err… Gastrula 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 KAP… Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|treatment:100 µg/ml CHX 100 µg/ml TIG GSM7734770 GSM7734770: WT bud 10 hpf Ribo seq rep1; Danio rerio; OTHER GSM7734770 r1 GSM7734770 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 …   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   SRP457105     WT_ribo_bud_1.fastq.gz fastq 1476985703.0 55745002.0 GSM7734770 r1 0:26.50 A:266369385;C:466461341;G:473469631;T:270671671;N:13675 26       266369385 466461341 473469631 270671671 13675 SRX21486723 SRS18719024 SRA1700409 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.773   0.14121   0.82242   0.78464   30   B   usable mapping rate illumina nextseq 5prime rrna_depletion ribozero bulk unknown unknown   Germany 2023-08-28 Gastrula Embryo Whole Organism All anatomical structures
25296 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 err… 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 KAP… 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 …   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
35567 35567 SRR32928199 SRX28203119 SRS24552825 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.enzymatic.P01.F01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 6 100 100 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.enzymatic.P01.F01.fq.gz fastq 800436.0 9529.0 expt2.broad.48.enzymatic.P01.F01.fq.gz 0:84 A:247920;C:168170;G:180799;T:203153;N:394 84       247920 168170 180799 203153 394 SRX28203119 SRS24552825 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35568 35568 SRR32928200 SRX28203118 SRS24552823 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.enzymatic.P01.E01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 5 99 99 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.enzymatic.P01.E01.fq.gz fastq 496356.0 5909.0 expt2.broad.48.enzymatic.P01.E01.fq.gz 0:84 A:156600;C:99183;G:113282;T:127036;N:255 84       156600 99183 113282 127036 255 SRX28203118 SRS24552823 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35569 35569 SRR32928201 SRX28203117 SRS24552824 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.enzymatic.P01.D01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 4 98 98 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.enzymatic.P01.D01.fq.gz fastq 2053800.0 24450.0 expt2.broad.48.enzymatic.P01.D01.fq.gz 0:84 A:668634;C:393806;G:431279;T:559022;N:1059 84       668634 393806 431279 559022 1059 SRX28203117 SRS24552824 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35570 35570 SRR32928202 SRX28203116 SRS24552821 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.enzymatic.P01.C01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 3 97 97 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.enzymatic.P01.C01.fq.gz fastq 2159052.0 25703.0 expt2.broad.48.enzymatic.P01.C01.fq.gz 0:84 A:837784;C:348085;G:463530;T:508544;N:1109 84       837784 348085 463530 508544 1109 SRX28203116 SRS24552821 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35571 35571 SRR32928203 SRX28203115 SRS24552822 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.enzymatic.P01.B01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 2 96 96 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.enzymatic.P01.B01.fq.gz fastq 3287508.0 39137.0 expt2.broad.48.enzymatic.P01.B01.fq.gz 0:84 A:1090202;C:644484;G:702124;T:848812;N:1886 84       1090202 644484 702124 848812 1886 SRX28203115 SRS24552822 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35572 35572 SRR32928204 SRX28203114 SRS24552819 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.enzymatic.P01.A01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 1 95 95 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.enzymatic.P01.A01.fq.gz fastq 6623400.0 78850.0 expt2.broad.48.enzymatic.P01.A01.fq.gz 0:84 A:2915935;C:1012732;G:1256523;T:1434621;N:3589 84       2915935 1012732 1256523 1434621 3589 SRX28203114 SRS24552819 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35573 35573 SRR32928205 SRX28203113 SRS24552820 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.H02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:16|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 16 94 94 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.H02.fq.gz fastq 18079152.0 215228.0 expt2.broad.48.bead.P18.H02.fq.gz 0:84 A:6013555;C:3409380;G:3853431;T:4793252;N:9534 84       6013555 3409380 3853431 4793252 9534 SRX28203113 SRS24552820 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35574 35574 SRR32928206 SRX28203112 SRS24552818 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.H01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:15|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 15 93 93 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.H01.fq.gz fastq 13210764.0 157271.0 expt2.broad.48.bead.P18.H01.fq.gz 0:84 A:4207727;C:2577088;G:2821128;T:3597752;N:7069 84       4207727 2577088 2821128 3597752 7069 SRX28203112 SRS24552818 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35575 35575 SRR32928207 SRX28203111 SRS24552817 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.G02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:14|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 14 92 92 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.G02.fq.gz fastq 14834736.0 176604.0 expt2.broad.48.bead.P18.G02.fq.gz 0:84 A:5041294;C:2753273;G:3108141;T:3924037;N:7991 84       5041294 2753273 3108141 3924037 7991 SRX28203111 SRS24552817 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35576 35576 SRR32928310 SRX28203110 SRS24552815 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.G12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 7 212 212 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.enzymatic.P18.G12.fq.gz fastq 25010412.0 297743.0 expt3.96.enzymatic.P18.G12.fq.gz 0:84 A:10964374;C:4064284;G:5105517;T:4873835;N:2402 84       10964374 4064284 5105517 4873835 2402 SRX28203110 SRS24552815 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35577 35577 SRR32928208 SRX28203109 SRS24552816 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.F12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 6 211 211 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.enzymatic.P18.F12.fq.gz fastq 34833876.0 414689.0 expt3.96.enzymatic.P18.F12.fq.gz 0:84 A:15190499;C:5741220;G:7109697;T:6789172;N:3288 84       15190499 5741220 7109697 6789172 3288 SRX28203109 SRS24552816 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35578 35578 SRR32928209 SRX28203108 SRS24552814 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.   expt1.12.bead.P1.H3.fq.gz   seq depth:NA|Experiment id:1|dissociation method:bead|replicate:22|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 22 22 22 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt1.12.bead.P1.H3.fq.gz fastq 1098724956.0 13080059.0 expt1.12.bead.P1.H3.fq.gz 0:84 A:504518768;C:161484922;G:183535740;T:248983693;N:201833 84       504518768 161484922 183535740 248983693 201833 SRX28203108 SRS24552814 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Segmentation Embryo Whole Organism All anatomical structures
35579 35579 SRR32928210 SRX28203107 SRS24552812 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.E12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 5 210 210 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.enzymatic.P18.E12.fq.gz fastq 27839784.0 331426.0 expt3.96.enzymatic.P18.E12.fq.gz 0:84 A:11930285;C:4560929;G:5811743;T:5534159;N:2668 84       11930285 4560929 5811743 5534159 2668 SRX28203107 SRS24552812 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35580 35580 SRR32928211 SRX28203106 SRS24552811 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.D12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 4 209 209 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.enzymatic.P18.D12.fq.gz fastq 27695556.0 329709.0 expt3.96.enzymatic.P18.D12.fq.gz 0:84 A:12091110;C:4491745;G:5609269;T:5500850;N:2582 84       12091110 4491745 5609269 5500850 2582 SRX28203106 SRS24552811 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35581 35581 SRR32928212 SRX28203105 SRS24552813 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.C12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 3 208 208 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.enzymatic.P18.C12.fq.gz fastq 24844932.0 295773.0 expt3.96.enzymatic.P18.C12.fq.gz 0:84 A:10700258;C:4111418;G:5035794;T:4994990;N:2472 84       10700258 4111418 5035794 4994990 2472 SRX28203105 SRS24552813 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35582 35582 SRR32928213 SRX28203104 SRS24552810 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.B12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 2 207 207 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.enzymatic.P18.B12.fq.gz fastq 10780812.0 128343.0 expt3.96.enzymatic.P18.B12.fq.gz 0:84 A:4635118;C:1860640;G:2120826;T:2163173;N:1055 84       4635118 1860640 2120826 2163173 1055 SRX28203104 SRS24552810 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.33865   0.22704   0.93659   0.55528   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35583 35583 SRR32928214 SRX28203103 SRS24552809 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.   expt3.96.enzymatic.P18.A12.fq.gz   seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 1 206 206 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.enzymatic.P18.A12.fq.gz fastq 10534272.0 125408.0 expt3.96.enzymatic.P18.A12.fq.gz 0:84 A:4632079;C:1746502;G:2069269;T:2085448;N:974 84       4632079 1746502 2069269 2085448 974 SRX28203103 SRS24552809 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.33522   0.19264   0.93624   0.50295   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35584 35584 SRR32928215 SRX28203102 SRS24552808 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.H11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 8 205 205 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.bead.P18.H11.fq.gz fastq 235038972.0 2798083.0 expt3.96.bead.P18.H11.fq.gz 0:84 A:85855798;C:40354173;G:45974107;T:62832438;N:22456 84       85855798 40354173 45974107 62832438 22456 SRX28203102 SRS24552808 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.61865   0.46937   0.80791   0.46334   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35585 35585 SRR32928216 SRX28203101 SRS24552807 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.G11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 7 204 204 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.bead.P18.G11.fq.gz fastq 280436688.0 3338532.0 expt3.96.bead.P18.G11.fq.gz 0:84 A:105066150;C:48021700;G:54614521;T:72707589;N:26728 84       105066150 48021700 54614521 72707589 26728 SRX28203101 SRS24552807 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.59159   0.43599   0.80842   0.46679   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35586 35586 SRR32928217 SRX28203100 SRS24552806 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.F11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 6 203 203 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.bead.P18.F11.fq.gz fastq 286313832.0 3408498.0 expt3.96.bead.P18.F11.fq.gz 0:84 A:106784155;C:49395267;G:55919780;T:74187078;N:27552 84       106784155 49395267 55919780 74187078 27552 SRX28203100 SRS24552806 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.60245   0.44424   0.81124   0.48908   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35587 35587 SRR32928218 SRX28203099 SRS24552804 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.E11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 5 202 202 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.bead.P18.E11.fq.gz fastq 307881252.0 3665253.0 expt3.96.bead.P18.E11.fq.gz 0:84 A:115701302;C:52449337;G:59620790;T:80080256;N:29567 84       115701302 52449337 59620790 80080256 29567 SRX28203099 SRS24552804 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.5787   0.44122   0.81854   0.50262   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35588 35588 SRR32928219 SRX28203098 SRS24552803 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.D11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 4 201 201 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.bead.P18.D11.fq.gz fastq 300632640.0 3578960.0 expt3.96.bead.P18.D11.fq.gz 0:84 A:113779580;C:51205126;G:58283346;T:77335567;N:29021 84       113779580 51205126 58283346 77335567 29021 SRX28203098 SRS24552803 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.57846   0.43882   0.81925   0.50496   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35589 35589 SRR32928220 SRX28203097 SRS24552805 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.   expt1.12.bead.P1.G5.fq.gz   seq depth:NA|Experiment id:1|dissociation method:bead|replicate:21|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 21 21 21 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt1.12.bead.P1.G5.fq.gz fastq 561441468.0 6683827.0 expt1.12.bead.P1.G5.fq.gz 0:84 A:234940814;C:88191402;G:96728695;T:141478801;N:101756 84       234940814 88191402 96728695 141478801 101756 SRX28203097 SRS24552805 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.50019   0.4034   0.85959   0.49922   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Segmentation Embryo Whole Organism All anatomical structures
35590 35590 SRR32928221 SRX28203096 SRS24552802 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.   expt1.12.bead.P1.A5.fq.gz   seq depth:NA|Experiment id:1|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 3 3 3 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt1.12.bead.P1.A5.fq.gz fastq 490718256.0 5841884.0 expt1.12.bead.P1.A5.fq.gz 0:84 A:207644706;C:75241234;G:85463387;T:122279492;N:89437 84       207644706 75241234 85463387 122279492 89437 SRX28203096 SRS24552802 SRA2104467 University of Washington|Genome Sciences University of Washington 1 0.50293   0.39872   0.85916   0.50964   84   B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Segmentation Embryo Whole Organism All anatomical structures
35591 35591 SRR32928222 SRX28203095 SRS24552801 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.C11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 3 200 200 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.bead.P18.C11.fq.gz fastq 269049312.0 3202968.0 expt3.96.bead.P18.C11.fq.gz 0:84 A:100635643;C:45939296;G:52190404;T:70258145;N:25824 84       100635643 45939296 52190404 70258145 25824 SRX28203095 SRS24552801 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35592 35592 SRR32928223 SRX28203094 SRS24552799 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.B11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 2 199 199 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.bead.P18.B11.fq.gz fastq 123292428.0 1467767.0 expt3.96.bead.P18.B11.fq.gz 0:84 A:45529584;C:21218529;G:24007853;T:32524700;N:11762 84       45529584 21218529 24007853 32524700 11762 SRX28203094 SRS24552799 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35593 35593 SRR32928224 SRX28203093 SRS24552800 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.   expt3.96.bead.P18.A11.fq.gz   seq depth:NA|Experiment id:3|dissociation method:bead|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 1 198 198 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt3.96.bead.P18.A11.fq.gz fastq 277357248.0 3301872.0 expt3.96.bead.P18.A11.fq.gz 0:84 A:105979207;C:47015802;G:54386470;T:69949155;N:26614 84       105979207 47015802 54386470 69949155 26614 SRX28203093 SRS24552800 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35594 35594 SRR32928225 SRX28203092 SRS24552798 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.H03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 8 197 197 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.deep.72.enzymatic.P01.H03.fq.gz fastq 3437364.0 40921.0 expt2.deep.72.enzymatic.P01.H03.fq.gz 0:84 A:1374051;C:578097;G:717673;T:766942;N:601 84       1374051 578097 717673 766942 601 SRX28203092 SRS24552798 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35595 35595 SRR32928226 SRX28203091 SRS24552797 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.G03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 7 196 196 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.deep.72.enzymatic.P01.G03.fq.gz fastq 8559096.0 101894.0 expt2.deep.72.enzymatic.P01.G03.fq.gz 0:84 A:3252394;C:1515721;G:1860485;T:1929016;N:1480 84       3252394 1515721 1860485 1929016 1480 SRX28203091 SRS24552797 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35596 35596 SRR32928227 SRX28203090 SRS24552795 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.F03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 6 195 195 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.deep.72.enzymatic.P01.F03.fq.gz fastq 86570988.0 1030607.0 expt2.deep.72.enzymatic.P01.F03.fq.gz 0:84 A:39076701;C:15258279;G:16117195;T:16103299;N:15514 84       39076701 15258279 16117195 16103299 15514 SRX28203090 SRS24552795 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35597 35597 SRR32928228 SRX28203089 SRS24552796 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.E03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 5 194 194 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.deep.72.enzymatic.P01.E03.fq.gz fastq 21496020.0 255905.0 expt2.deep.72.enzymatic.P01.E03.fq.gz 0:84 A:7897723;C:3941227;G:4608642;T:5044562;N:3866 84       7897723 3941227 4608642 5044562 3866 SRX28203089 SRS24552796 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35598 35598 SRR32928229 SRX28203088 SRS24552794 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.D03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 4 193 193 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.deep.72.enzymatic.P01.D03.fq.gz fastq 38955504.0 463756.0 expt2.deep.72.enzymatic.P01.D03.fq.gz 0:84 A:18141798;C:6097971;G:8057753;T:6650850;N:7132 84       18141798 6097971 8057753 6650850 7132 SRX28203088 SRS24552794 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35599 35599 SRR32928230 SRX28203087 SRS24552793 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.C03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 3 192 192 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.deep.72.enzymatic.P01.C03.fq.gz fastq 51870336.0 617504.0 expt2.deep.72.enzymatic.P01.C03.fq.gz 0:84 A:17090212;C:9836274;G:12030231;T:12904330;N:9289 84       17090212 9836274 12030231 12904330 9289 SRX28203087 SRS24552793 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35600 35600 SRR32928231 SRX28203086 SRS24552791 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.B03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 2 191 191 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.deep.72.enzymatic.P01.B03.fq.gz fastq 14069832.0 167498.0 expt2.deep.72.enzymatic.P01.B03.fq.gz 0:84 A:5389848;C:2403134;G:3075076;T:3199255;N:2519 84       5389848 2403134 3075076 3199255 2519 SRX28203086 SRS24552791 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35601 35601 SRR32928232 SRX28203085 SRS24552792 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.   expt1.12.bead.P1.G4.fq.gz   seq depth:NA|Experiment id:1|dissociation method:bead|replicate:20|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 20 20 20 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt1.12.bead.P1.G4.fq.gz fastq 515444412.0 6136243.0 expt1.12.bead.P1.G4.fq.gz 0:84 A:215225166;C:80082472;G:88915670;T:131127655;N:93449 84       215225166 80082472 88915670 131127655 93449 SRX28203085 SRS24552792 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Segmentation Embryo Whole Organism All anatomical structures
35602 35602 SRR32928233 SRX28203084 SRS24552790 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.enzymatic.P01.A03.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf enzymatic dissociation replicate 1 190 190 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.deep.72.enzymatic.P01.A03.fq.gz fastq 218177316.0 2597349.0 expt2.deep.72.enzymatic.P01.A03.fq.gz 0:84 A:102730118;C:32493129;G:39547427;T:43367265;N:39377 84       102730118 32493129 39547427 43367265 39377 SRX28203084 SRS24552790 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures
35603 35603 SRR32928234 SRX28203083 SRS24552789 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.G01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:13|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 13 91 91 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.G01.fq.gz fastq 14202468.0 169077.0 expt2.broad.48.bead.P18.G01.fq.gz 0:84 A:4692822;C:2685182;G:2975257;T:3841545;N:7662 84       4692822 2685182 2975257 3841545 7662 SRX28203083 SRS24552789 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35604 35604 SRR32928235 SRX28203082 SRS24552787 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.   expt1.12.bead.P1.D3.fq.gz   seq depth:NA|Experiment id:1|dissociation method:bead|replicate:10|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 10 10 10 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt1.12.bead.P1.D3.fq.gz fastq 629856780.0 7498295.0 expt1.12.bead.P1.D3.fq.gz 0:84 A:273859568;C:96165073;G:108875157;T:150842309;N:114673 84       273859568 96165073 108875157 150842309 114673 SRX28203082 SRS24552787 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Segmentation Embryo Whole Organism All anatomical structures
35605 35605 SRR32928236 SRX28203081 SRS24552788 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.F02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:12|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 12 90 90 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.F02.fq.gz fastq 16051728.0 191092.0 expt2.broad.48.bead.P18.F02.fq.gz 0:84 A:5221193;C:3079215;G:3420876;T:4321889;N:8555 84       5221193 3079215 3420876 4321889 8555 SRX28203081 SRS24552788 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35606 35606 SRR32928237 SRX28203080 SRS24552786 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.F01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:11|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 11 89 89 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.F01.fq.gz fastq 19022388.0 226457.0 expt2.broad.48.bead.P18.F01.fq.gz 0:84 A:6375349;C:3646304;G:4032366;T:4958089;N:10280 84       6375349 3646304 4032366 4958089 10280 SRX28203080 SRS24552786 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35607 35607 SRR32928238 SRX28203079 SRS24552785 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.E02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:10|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 10 88 88 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.E02.fq.gz fastq 17436720.0 207580.0 expt2.broad.48.bead.P18.E02.fq.gz 0:84 A:5912075;C:3260546;G:3682832;T:4572094;N:9173 84       5912075 3260546 3682832 4572094 9173 SRX28203079 SRS24552785 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35608 35608 SRR32928239 SRX28203078 SRS24552783 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.E01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:9|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 9 87 87 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.E01.fq.gz fastq 12759768.0 151902.0 expt2.broad.48.bead.P18.E01.fq.gz 0:84 A:4143321;C:2424389;G:2695567;T:3489773;N:6718 84       4143321 2424389 2695567 3489773 6718 SRX28203078 SRS24552783 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35609 35609 SRR32928240 SRX28203077 SRS24552784 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.D02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 8 86 86 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.D02.fq.gz fastq 17226132.0 205073.0 expt2.broad.48.bead.P18.D02.fq.gz 0:84 A:5722683;C:3229414;G:3698323;T:4566519;N:9193 84       5722683 3229414 3698323 4566519 9193 SRX28203077 SRS24552784 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35610 35610 SRR32928241 SRX28203076 SRS24552782 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.D01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 7 85 85 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.D01.fq.gz fastq 14390124.0 171311.0 expt2.broad.48.bead.P18.D01.fq.gz 0:84 A:4584304;C:2823369;G:3092301;T:3882609;N:7541 84       4584304 2823369 3092301 3882609 7541 SRX28203076 SRS24552782 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35611 35611 SRR32928242 SRX28203075 SRS24552781 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.C02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 6 84 84 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.C02.fq.gz fastq 18592560.0 221340.0 expt2.broad.48.bead.P18.C02.fq.gz 0:84 A:6370777;C:3468105;G:3988886;T:4754942;N:9850 84       6370777 3468105 3988886 4754942 9850 SRX28203075 SRS24552781 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35612 35612 SRR32928243 SRX28203074 SRS24552780 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.C01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 5 83 83 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.C01.fq.gz fastq 12557076.0 149489.0 expt2.broad.48.bead.P18.C01.fq.gz 0:84 A:3977371;C:2443832;G:2711905;T:3417301;N:6667 84       3977371 2443832 2711905 3417301 6667 SRX28203074 SRS24552780 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35613 35613 SRR32928244 SRX28203073 SRS24552779 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.B02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 4 82 82 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.B02.fq.gz fastq 14289828.0 170117.0 expt2.broad.48.bead.P18.B02.fq.gz 0:84 A:4795697;C:2698305;G:3083373;T:3704963;N:7490 84       4795697 2698305 3083373 3704963 7490 SRX28203073 SRS24552779 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35614 35614 SRR32928245 SRX28203072 SRS24552778 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.B01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 3 81 81 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.B01.fq.gz fastq 6255144.0 74466.0 expt2.broad.48.bead.P18.B01.fq.gz 0:84 A:1953811;C:1213806;G:1335743;T:1748533;N:3251 84       1953811 1213806 1335743 1748533 3251 SRX28203072 SRS24552778 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35615 35615 SRR32928246 SRX28203071 SRS24552777 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.   expt1.12.bead.P1.C5.fq.gz   seq depth:NA|Experiment id:1|dissociation method:bead|replicate:9|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 9 9 9 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt1.12.bead.P1.C5.fq.gz fastq 461470968.0 5493702.0 expt1.12.bead.P1.C5.fq.gz 0:84 A:188895160;C:72428601;G:79983141;T:120080226;N:83840 84       188895160 72428601 79983141 120080226 83840 SRX28203071 SRS24552777 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Segmentation Embryo Whole Organism All anatomical structures
35616 35616 SRR32928247 SRX28203070 SRS24552776 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.A02.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 2 80 80 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.A02.fq.gz fastq 16441656.0 195734.0 expt2.broad.48.bead.P18.A02.fq.gz 0:84 A:5495147;C:3127531;G:3493145;T:4317176;N:8657 84       5495147 3127531 3493145 4317176 8657 SRX28203070 SRS24552776 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35617 35617 SRR32928248 SRX28203069 SRS24552775 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.48.bead.P18.A01.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 1 79 79 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.48.bead.P18.A01.fq.gz fastq 14319564.0 170471.0 expt2.broad.48.bead.P18.A01.fq.gz 0:84 A:4614154;C:2749141;G:3043759;T:3904988;N:7522 84       4614154 2749141 3043759 3904988 7522 SRX28203069 SRS24552775 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Hatching Embryo Whole Organism All anatomical structures
35618 35618 SRR32928249 SRX28203068 SRS24552774 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.24.enzymatic.P01.H05.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 8 78 78 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.24.enzymatic.P01.H05.fq.gz fastq 9110220.0 108455.0 expt2.broad.24.enzymatic.P01.H05.fq.gz 0:84 A:3384792;C:1565195;G:1973031;T:2182427;N:4775 84       3384792 1565195 1973031 2182427 4775 SRX28203068 SRS24552774 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Pharyngula Embryo Whole Organism All anatomical structures
35619 35619 SRR32928250 SRX28203067 SRS24552773 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.24.enzymatic.P01.G05.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 7 77 77 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.24.enzymatic.P01.G05.fq.gz fastq 4093068.0 48727.0 expt2.broad.24.enzymatic.P01.G05.fq.gz 0:84 A:1283703;C:801390;G:874961;T:1130908;N:2106 84       1283703 801390 874961 1130908 2106 SRX28203067 SRS24552773 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Pharyngula Embryo Whole Organism All anatomical structures
35620 35620 SRR32928251 SRX28203066 SRS24552772 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.24.enzymatic.P01.F05.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 6 76 76 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.24.enzymatic.P01.F05.fq.gz fastq 15414840.0 183510.0 expt2.broad.24.enzymatic.P01.F05.fq.gz 0:84 A:6868692;C:2274988;G:2950304;T:3312556;N:8300 84       6868692 2274988 2950304 3312556 8300 SRX28203066 SRS24552772 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Pharyngula Embryo Whole Organism All anatomical structures
35621 35621 SRR32928252 SRX28203065 SRS24552771 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.24.enzymatic.P01.E05.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 5 75 75 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.24.enzymatic.P01.E05.fq.gz fastq 7552440.0 89910.0 expt2.broad.24.enzymatic.P01.E05.fq.gz 0:84 A:2833004;C:1314546;G:1543833;T:1856906;N:4151 84       2833004 1314546 1543833 1856906 4151 SRX28203065 SRS24552771 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Pharyngula Embryo Whole Organism All anatomical structures
35622 35622 SRR32928253 SRX28203064 SRS24552770 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.24.enzymatic.P01.D05.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 4 74 74 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.24.enzymatic.P01.D05.fq.gz fastq 18449592.0 219638.0 expt2.broad.24.enzymatic.P01.D05.fq.gz 0:84 A:8110605;C:2781954;G:3613141;T:3933803;N:10089 84       8110605 2781954 3613141 3933803 10089 SRX28203064 SRS24552770 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Pharyngula Embryo Whole Organism All anatomical structures
35623 35623 SRR32928254 SRX28203063 SRS24552769 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.24.enzymatic.P01.C05.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 3 73 73 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.24.enzymatic.P01.C05.fq.gz fastq 5944344.0 70766.0 expt2.broad.24.enzymatic.P01.C05.fq.gz 0:84 A:2038886;C:1067891;G:1274553;T:1559956;N:3058 84       2038886 1067891 1274553 1559956 3058 SRX28203063 SRS24552769 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Pharyngula Embryo Whole Organism All anatomical structures
35624 35624 SRR32928255 SRX28203062 SRS24552768 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.24.enzymatic.P01.B05.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 2 72 72 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.24.enzymatic.P01.B05.fq.gz fastq 8608320.0 102480.0 expt2.broad.24.enzymatic.P01.B05.fq.gz 0:84 A:3054837;C:1594241;G:1754868;T:2199803;N:4571 84       3054837 1594241 1754868 2199803 4571 SRX28203062 SRS24552768 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Pharyngula Embryo Whole Organism All anatomical structures
35625 35625 SRR32928256 SRX28203061 SRS24552767 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.   expt2.broad.24.enzymatic.P01.A05.fq.gz   seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 24hpf enzymatic dissociation replicate 1 71 71 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.broad.24.enzymatic.P01.A05.fq.gz fastq 3979164.0 47371.0 expt2.broad.24.enzymatic.P01.A05.fq.gz 0:84 A:1268971;C:764759;G:844472;T:1098812;N:2150 84       1268971 764759 844472 1098812 2150 SRX28203061 SRS24552767 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Pharyngula Embryo Whole Organism All anatomical structures
35626 35626 SRR32928257 SRX28203060 SRS24552766 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.   expt1.12.bead.P1.C4.fq.gz   seq depth:NA|Experiment id:1|dissociation method:bead|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 8 8 8 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt1.12.bead.P1.C4.fq.gz fastq 451683456.0 5377184.0 expt1.12.bead.P1.C4.fq.gz 0:84 A:188077465;C:71524093;G:79688471;T:112311489;N:81938 84       188077465 71524093 79688471 112311489 81938 SRX28203060 SRS24552766 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Segmentation Embryo Whole Organism All anatomical structures
35627 35627 SRR32928258 SRX28203059 SRS24552765 SRP575522 PRJNA1244443 An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing PRJNA1244443 Other Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.     Sci plexRNAseq of a 72hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.   expt2.deep.72.bead.P18.H05.fq.gz   seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:16|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:72 hpf|dev stage:72 hpf|collection date:2024 02 01|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal                 sciPlex RNAseq of whole Danio rerio embryos: expt2 deep sequencing of limited cells 72hpf bead dissociation replicate 16 189 189 Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.     OTHER TRANSCRIPTOMIC SINGLE CELL other SINGLE ILLUMINA NextSeq 2000   SRP575522     expt2.deep.72.bead.P18.H05.fq.gz fastq 100072896.0 1191344.0 expt2.deep.72.bead.P18.H05.fq.gz 0:84 A:37670921;C:17233514;G:20449798;T:24701130;N:17533 84       37670921 17233514 20449798 24701130 17533 SRX28203059 SRS24552765 SRA2104467 University of Washington|Genome Sciences University of Washington                       B   usable mapping rate illumina nextseq_v2 unknown other unknown sc single_cell_generic generic-scrnaseq-only   United States 2025-03-31 Larval Larval Whole Organism All anatomical structures

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