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run_metadata

5,269 rows where experiment.library_layout = "PAIRED", experiment.library_strategy = "RNA-Seq" and tissue_curation = "Embryo Imprecise"

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technology 10

experiment.library_selection >10

devstage_curation >10

devstage_curation_coarse 5

experiment.platform 4

experiment.library_source 2

tissue_curation_coarse 1

tissue_curation 1

  • Embryo Imprecise · 5,269 ✖

experiment.library_strategy 1

  • RNA-Seq · 5,269 ✖

experiment.library_layout 1

  • PAIRED · 5,269 ✖
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
9419 9419 ERR273825 ERX248101 ERS092357 ERP001559 PRJEB3118 Zebrafish transcript profiling Zebrafish_transcript_profiling-sc-2012-06-28T15:47:32Z-82 Transcriptome Analysis Paired end sequence data from the Illumina Genome Analyzer was prepared from normal and mutant zebrafish embryos for transcript profiling. This includes pilot studies for transcript indexing within the sequence reads.         SAMEA1888984 SC ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 05 13T11:13:14Z|ENA LAST UPDATE:2018 03 08T15:36:21Z|External Id:SAMEA1888984|INSDC center name:SC|INSDC first public:2013 05 13T11:13:14Z|INSDC last update:2018 03 08T15:36:21Z|INSDC status:public|Submitter Id:hu2117 mutant vs wild type sc 2012 02 06T13:11:11Z 1107268|common name:zebrafish|sample description:3 prime end enriched mRNA from 3 morphological mutant hu2117 embryo samples and 3 matched sibling wild type samples. A 6 base indexing sequence is bases 5 to 10 of read 1 followed by polyT.|sample name:hu2117 mutant vs wild type sc 2012 02 06T13:11:11Z 1107268|scientific name:Danio rerio                 1 SC EXP 6316 8 2387558 Illumina sequencing of library 2387558 constructed from sample accession ERS092357 for study accession ERP001559. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001559 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 05 13|ENA LAST UPDATE:2018 11 16 6316_8.bam bam 12715227300.0 84768182.0 SC RUN 6316 8 0:75 1:75 A:3986328155;C:1983554902;G:2466211000;T:4277430579;N:1702664 75 75     3986328155 1983554902 2466211000 4277430579 1702664 ERX248101 ERS092357 ERA212579 SC Wellcome Sanger Institute 2 0.06657 0.60346 0.04569 0.19203 0.9767 0.82014 0.52373 0.4048 75 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-05-13 Undetermined Embryo Embryo Imprecise All anatomical structures
9420 9420 ERR273824 ERX248100 ERS092356 ERP001559 PRJEB3118 Zebrafish transcript profiling Zebrafish_transcript_profiling-sc-2012-06-28T15:47:32Z-82 Transcriptome Analysis Paired end sequence data from the Illumina Genome Analyzer was prepared from normal and mutant zebrafish embryos for transcript profiling. This includes pilot studies for transcript indexing within the sequence reads.         SAMEA1889000 SC ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 05 13T11:13:13Z|ENA LAST UPDATE:2018 03 08T15:36:25Z|External Id:SAMEA1889000|INSDC center name:SC|INSDC first public:2013 05 13T11:13:13Z|INSDC last update:2018 03 08T15:36:25Z|INSDC status:public|Submitter Id:e48 mutant vs wild type sc 2012 02 06T13:11:09Z 1107267|common name:zebrafish|sample description:3 prime end enriched mRNA from 3 morphological mutant e48 embryo samples and 3 matched sibling wild type samples. A 6 base indexing sequence is bases 5 to 10 of read 1 followed by polyT.|sample name:e48 mutant vs wild type sc 2012 02 06T13:11:09Z 1107267|scientific name:Danio rerio                 1 SC EXP 6316 7 2387557 Illumina sequencing of library 2387557 constructed from sample accession ERS092356 for study accession ERP001559. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001559 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 05 13|ENA LAST UPDATE:2018 11 16 6316_7.bam bam 17475932100.0 116506214.0 SC RUN 6316 7 0:75 1:75 A:5548228936;C:2693024343;G:3365940794;T:5867204994;N:1533033 75 75     5548228936 2693024343 3365940794 5867204994 1533033 ERX248100 ERS092356 ERA212579 SC Wellcome Sanger Institute 2 0.05939 0.59457 0.04089 0.19671 0.98068 0.838 0.46304 0.62741 75 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-05-13 Undetermined Embryo Embryo Imprecise All anatomical structures
9421 9421 ERR273823 ERX248099 ERS092354 ERP001559 PRJEB3118 Zebrafish transcript profiling Zebrafish_transcript_profiling-sc-2012-06-28T15:47:32Z-82 Transcriptome Analysis Paired end sequence data from the Illumina Genome Analyzer was prepared from normal and mutant zebrafish embryos for transcript profiling. This includes pilot studies for transcript indexing within the sequence reads.         SAMEA1889008 SC ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 05 13T11:13:13Z|ENA LAST UPDATE:2018 03 08T15:36:21Z|External Id:SAMEA1889008|INSDC center name:SC|INSDC first public:2013 05 13T11:13:13Z|INSDC last update:2018 03 08T15:36:21Z|INSDC status:public|Submitter Id:hu3332 mutant vs wild type sc 2012 02 06T13:11:07Z 1107265|common name:zebrafish|sample description:3 prime end enriched mRNA from 3 morphological mutant hu3332 embryo samples and 3 matched sibling wild type samples. A 6 base indexing sequence is bases 5 to 10 of read 1 followed by polyT.|sample name:hu3332 mutant vs wild type sc 2012 02 06T13:11:07Z 1107265|scientific name:Danio rerio                 1 SC EXP 6316 5 2387555 Illumina sequencing of library 2387555 constructed from sample accession ERS092354 for study accession ERP001559. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001559 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 05 13|ENA LAST UPDATE:2018 11 16 6316_5.bam bam 13995917850.0 93306119.0 SC RUN 6316 5 0:75 1:75 A:4367273029;C:2176748810;G:2714026832;T:4736121060;N:1748119 75 75     4367273029 2176748810 2714026832 4736121060 1748119 ERX248099 ERS092354 ERA212579 SC Wellcome Sanger Institute 2 0.06401 0.62019 0.04224 0.18728 0.97723 0.81071 0.461 0.55379 75 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-05-13 Undetermined Embryo Embryo Imprecise All anatomical structures
9422 9422 ERR273822 ERX248098 ERS092063 ERP001559 PRJEB3118 Zebrafish transcript profiling Zebrafish_transcript_profiling-sc-2012-06-28T15:47:32Z-82 Transcriptome Analysis Paired end sequence data from the Illumina Genome Analyzer was prepared from normal and mutant zebrafish embryos for transcript profiling. This includes pilot studies for transcript indexing within the sequence reads.         SAMEA1888996 SC ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 05 13T11:13:13Z|ENA LAST UPDATE:2018 03 08T15:36:13Z|External Id:SAMEA1888996|INSDC center name:SC|INSDC first public:2013 05 13T11:13:13Z|INSDC last update:2018 03 08T15:36:13Z|INSDC status:public|Submitter Id:sa0058 mutant vs wild type sc 2012 02 06T13:05:07Z 265521|common name:zebrafish|sample description:33 prime end enriched mRNA from 3 morphological mutant sa0058 embryo samples and 3 matched sibling wild type samples. A 6 base indexing sequence is bases 5 to 10 of read 1 followed by polyT.|sample name:sa0058 mutant vs wild type sc 2012 02 06T13:05:07Z 265521|scientific name:Danio rerio                 1 SC EXP 5287 7 449230 Illumina sequencing of library 449230 constructed from sample accession ERS092063 for study accession ERP001559. qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II   ERP001559 Illumina Genome Analyzer II paired end sequencing ENA FIRST PUBLIC:2013 05 13|ENA LAST UPDATE:2018 11 16 5287_7.bam bam 2216402460.0 20522245.0 SC RUN 5287 7 0:54 1:54 A:646882787;C:346392353;G:394060191;T:827745173;N:1321956 54 54     646882787 346392353 394060191 827745173 1321956 ERX248098 ERS092063 ERA212579 SC Wellcome Sanger Institute 2 0.02565 0.72009 0.01691 0.21429 0.98725 0.78944 0.62084 0.61278 54 54 T B mate1 technical by mapping diff illumina early_illumina 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-05-13 Undetermined Embryo Embryo Imprecise All anatomical structures
9892 9892 ERR4172795 ERX4136409 ERS4580819 ERP121885 PRJEB38455 RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E-MTAB-9113 Transcriptome Analysis RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22   Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion sibling 3 SAMEA6853229 Centre for Developmental Neurobiology King's College London ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853229|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 3|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E MTAB 9113:sibling 3 p sibling 3 p RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP121885 Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19 UCLGNS1141-gfp-sibs-3_S6_R1.fastq.gz UCLGNS1141-gfp-sibs-3_S6_R2.fastq.gz fastq fastq     E MTAB 9113:UCLGNS1141 gfp sibs 3 S6 R 0:81 1:81 A:1144578958;C:1113109875;G:1138809559;T:1117038434;N:213932 81 81     1144578958 1113109875 1138809559 1117038434 213932 ERX4136409 ERS4580819 ERA2625401 Centre for Developmental Neurobiology King Centre for Developmental Neurobiology King 2 0.96684 0.96492 0.03244 0.0317 0.71236 0.71514 0.45871 0.46189 81 81 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2020-05-22 Multi-stage Multi-stage Embryo Imprecise All anatomical structures
9893 9893 ERR4172794 ERX4136408 ERS4580818 ERP121885 PRJEB38455 RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E-MTAB-9113 Transcriptome Analysis RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22   Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion sibling 2 SAMEA6853228 Centre for Developmental Neurobiology King's College London ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853228|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 2|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E MTAB 9113:sibling 2 p sibling 2 p RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP121885 Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19 UCLGNS1141-gfp-sibs-2_S4_R1.fastq.gz UCLGNS1141-gfp-sibs-2_S4_R2.fastq.gz fastq fastq     E MTAB 9113:UCLGNS1141 gfp sibs 2 S4 R 0:81 1:81 A:1056280368;C:1036355469;G:1045429486;T:1035773622;N:189389 81 81     1056280368 1036355469 1045429486 1035773622 189389 ERX4136408 ERS4580818 ERA2625401 Centre for Developmental Neurobiology King Centre for Developmental Neurobiology King 2 0.95511 0.95696 0.02941 0.02903 0.71492 0.71628 0.45765 0.46537 81 81 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2020-05-22 Multi-stage Multi-stage Embryo Imprecise All anatomical structures
9894 9894 ERR4172793 ERX4136407 ERS4580817 ERP121885 PRJEB38455 RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E-MTAB-9113 Transcriptome Analysis RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22   Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion sibling 1 SAMEA6853227 Centre for Developmental Neurobiology King's College London ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853227|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 1|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E MTAB 9113:sibling 1 p sibling 1 p RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP121885 Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19 UCLGNS1141-gfp-sibs-1_S2_R1.fastq.gz UCLGNS1141-gfp-sibs-1_S2_R2.fastq.gz fastq fastq     E MTAB 9113:UCLGNS1141 gfp sibs 1 S2 R 0:81 1:81 A:1121176859;C:1093927654;G:1108608188;T:1101082277;N:209264 81 81     1121176859 1093927654 1108608188 1101082277 209264 ERX4136407 ERS4580817 ERA2625401 Centre for Developmental Neurobiology King Centre for Developmental Neurobiology King 2 0.95795 0.96004 0.02885 0.02854 0.71648 0.71756 0.44348 0.43956 81 81 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2020-05-22 Multi-stage Multi-stage Embryo Imprecise All anatomical structures
9895 9895 ERR4172792 ERX4136406 ERS4580816 ERP121885 PRJEB38455 RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E-MTAB-9113 Transcriptome Analysis RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22   Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion sfpq 3 SAMEA6853226 Centre for Developmental Neurobiology King's College London ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853226|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 3|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E MTAB 9113:sfpq 3 p sfpq 3 p RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion Experimental Factor: genotype:sfpq / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP121885 Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19 UCLGNS1141-gfp-neg_3_S5_R1.fastq.gz UCLGNS1141-gfp-neg_3_S5_R2.fastq.gz fastq fastq     E MTAB 9113:UCLGNS1141 gfp neg 3 S5 R 0:81 1:81 A:845849249;C:772302798;G:911660213;T:787409272;N:154042 81 81     845849249 772302798 911660213 787409272 154042 ERX4136406 ERS4580816 ERA2625401 Centre for Developmental Neurobiology King Centre for Developmental Neurobiology King 2 0.96298 0.95486 0.03415 0.03476 0.7167 0.73503 0.4665 0.45947 81 81 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2020-05-22 Multi-stage Multi-stage Embryo Imprecise All anatomical structures
9896 9896 ERR4172791 ERX4136405 ERS4580815 ERP121885 PRJEB38455 RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E-MTAB-9113 Transcriptome Analysis RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22   Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion sfpq 2 SAMEA6853225 Centre for Developmental Neurobiology King's College London ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853225|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 2|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E MTAB 9113:sfpq 2 p sfpq 2 p RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion Experimental Factor: genotype:sfpq / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP121885 Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19 UCLGNS1141-gfp-neg-2_S3_R1.fastq.gz UCLGNS1141-gfp-neg-2_S3_R2.fastq.gz fastq fastq     E MTAB 9113:UCLGNS1141 gfp neg 2 S3 R 0:81 1:81 A:961156886;C:917011292;G:942713581;T:936109877;N:157724 81 81     961156886 917011292 942713581 936109877 157724 ERX4136405 ERS4580815 ERA2625401 Centre for Developmental Neurobiology King Centre for Developmental Neurobiology King 2 0.96276 0.96147 0.03436 0.03382 0.71892 0.72021 0.4581 0.46402 81 81 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2020-05-22 Multi-stage Multi-stage Embryo Imprecise All anatomical structures
9897 9897 ERR4172790 ERX4136404 ERS4580814 ERP121885 PRJEB38455 RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E-MTAB-9113 Transcriptome Analysis RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22   Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion sfpq 1 SAMEA6853224 Centre for Developmental Neurobiology King's College London ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853224|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 1|scientific name:Danio rerio                 Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E MTAB 9113:sfpq 1 p sfpq 1 p RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion Experimental Factor: genotype:sfpq / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP121885 Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19 UCLGNS1141-gfp-neg-1_S1_R1.fastq.gz UCLGNS1141-gfp-neg-1_S1_R2.fastq.gz fastq fastq     E MTAB 9113:UCLGNS1141 gfp neg 1 S1 R 0:81 1:81 A:1046317524;C:1014946275;G:1036910299;T:1023619857;N:185237 81 81     1046317524 1014946275 1036910299 1023619857 185237 ERX4136404 ERS4580814 ERA2625401 Centre for Developmental Neurobiology King Centre for Developmental Neurobiology King 2 0.96015 0.96173 0.03114 0.03098 0.7175 0.71865 0.46666 0.46399 81 81 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2020-05-22 Multi-stage Multi-stage Embryo Imprecise All anatomical structures
10285 10285 ERR7132868 ERX6700306 ERS8071630 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Oxy 6 SAMEA10418786 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418786|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Oxy 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:6|sample name:E MTAB 11086:Oxy 6|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Oxy 6 p Oxy 6 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:oxycod1|Experimental Factor: dose:1.14 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.B11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.B11.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2330698400.0 23306984.0 E MTAB 11086:SLX 19351.B11.HMLG7DRXX.s 2.r 0:50 1:50 A:619569172;C:544582535;G:551543197;T:614938437;N:65059 50 50     619569172 544582535 551543197 614938437 65059 ERX6700306 ERS8071630 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.9448 0.95044 0.1029 0.09965 0.67152 0.66864 0.46844 0.47553 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10286 10286 ERR7132867 ERX6700305 ERS8071629 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Oxy 5 SAMEA10418785 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418785|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Oxy 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:5|sample name:E MTAB 11086:Oxy 5|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Oxy 5 p Oxy 5 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:oxycod1|Experimental Factor: dose:1.14 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.H9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.H9.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2005314000.0 20053140.0 E MTAB 11086:SLX 19351.H9.HMLG7DRXX.s 2.r 0:50 1:50 A:533671597;C:466449227;G:473126638;T:532010412;N:56126 50 50     533671597 466449227 473126638 532010412 56126 ERX6700305 ERS8071629 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94406 0.94793 0.11192 0.10798 0.66184 0.66074 0.4603 0.4683 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10287 10287 ERR7132866 ERX6700304 ERS8071628 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Oxy 4 SAMEA10418784 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418784|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Oxy 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:4|sample name:E MTAB 11086:Oxy 4|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Oxy 4 p Oxy 4 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:oxycod1|Experimental Factor: dose:1.14 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.A9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.A9.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2036392600.0 20363926.0 E MTAB 11086:SLX 19351.A9.HMLG7DRXX.s 2.r 0:50 1:50 A:547586305;C:468797712;G:476477515;T:543474510;N:56558 50 50     547586305 468797712 476477515 543474510 56558 ERX6700304 ERS8071628 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94235 0.94873 0.11388 0.11054 0.67655 0.67294 0.47135 0.47234 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10288 10288 ERR7132865 ERX6700303 ERS8071627 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Oxy 3 SAMEA10418783 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418783|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Oxy 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:3|sample name:E MTAB 11086:Oxy 3|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Oxy 3 p Oxy 3 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:oxycod1|Experimental Factor: dose:1.14 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.B9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.B9.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2409819000.0 24098190.0 E MTAB 11086:SLX 19351.B9.HMLG7DRXX.s 2.r 0:50 1:50 A:641053989;C:561685242;G:569693271;T:637320302;N:66196 50 50     641053989 561685242 569693271 637320302 66196 ERX6700303 ERS8071627 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94407 0.94902 0.10789 0.10496 0.66478 0.66387 0.47154 0.47373 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10289 10289 ERR7132864 ERX6700302 ERS8071626 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Oxy 2 SAMEA10418782 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418782|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Oxy 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:2|sample name:E MTAB 11086:Oxy 2|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Oxy 2 p Oxy 2 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:oxycod1|Experimental Factor: dose:1.14 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.A11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.A11.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2068575200.0 20685752.0 E MTAB 11086:SLX 19351.A11.HMLG7DRXX.s 2.r 0:50 1:50 A:547986796;C:484533693;G:490663629;T:545334125;N:56957 50 50     547986796 484533693 490663629 545334125 56957 ERX6700302 ERS8071626 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94539 0.95188 0.10373 0.10116 0.66718 0.66584 0.46991 0.47611 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10290 10290 ERR7132863 ERX6700301 ERS8071625 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Oxy 1 SAMEA10418781 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418781|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Oxy 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:1|sample name:E MTAB 11086:Oxy 1|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Oxy 1 p Oxy 1 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:oxycod1|Experimental Factor: dose:1.14 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.G9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.G9.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2101607900.0 21016079.0 E MTAB 11086:SLX 19351.G9.HMLG7DRXX.s 2.r 0:50 1:50 A:557420271;C:491161431;G:497494262;T:555471610;N:60326 50 50     557420271 491161431 497494262 555471610 60326 ERX6700301 ERS8071625 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94378 0.94916 0.10779 0.10431 0.66507 0.66377 0.45477 0.4679 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10291 10291 ERR7132862 ERX6700300 ERS8071624 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Nic 6 SAMEA10418780 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418780|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Nic 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:6|sample name:E MTAB 11086:Nic 6|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Nic 6 p Nic 6 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:nicotine|Experimental Factor: dose:5 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.H11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.H11.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2236235700.0 22362357.0 E MTAB 11086:SLX 19351.H11.HMLG7DRXX.s 2.r 0:50 1:50 A:597573047;C:518264376;G:525314754;T:595021334;N:62189 50 50     597573047 518264376 525314754 595021334 62189 ERX6700300 ERS8071624 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94255 0.94893 0.11268 0.10955 0.66819 0.66687 0.46882 0.47485 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10292 10292 ERR7132861 ERX6700299 ERS8071623 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Nic 5 SAMEA10418779 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418779|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Nic 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:5|sample name:E MTAB 11086:Nic 5|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Nic 5 p Nic 5 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:nicotine|Experimental Factor: dose:5 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.D10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.D10.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 1904348300.0 19043483.0 E MTAB 11086:SLX 19351.D10.HMLG7DRXX.s 2.r 0:50 1:50 A:506678821;C:443756285;G:450118827;T:503742221;N:52146 50 50     506678821 443756285 450118827 503742221 52146 ERX6700299 ERS8071623 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94468 0.95019 0.10313 0.10023 0.66762 0.66513 0.47749 0.47611 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10293 10293 ERR7132860 ERX6700298 ERS8071622 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Nic 4 SAMEA10418778 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418778|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Nic 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:4|sample name:E MTAB 11086:Nic 4|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Nic 4 p Nic 4 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:nicotine|Experimental Factor: dose:5 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.C10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.C10.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2134565600.0 21345656.0 E MTAB 11086:SLX 19351.C10.HMLG7DRXX.s 2.r 0:50 1:50 A:568799307;C:496480840;G:503115671;T:566109163;N:60619 50 50     568799307 496480840 503115671 566109163 60619 ERX6700298 ERS8071622 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94279 0.94878 0.11466 0.1122 0.66291 0.66176 0.46991 0.47168 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10294 10294 ERR7132859 ERX6700297 ERS8071621 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Nic 3 SAMEA10418777 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418777|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Nic 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:3|sample name:E MTAB 11086:Nic 3|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Nic 3 p Nic 3 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:nicotine|Experimental Factor: dose:5 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.B10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.B10.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2409355400.0 24093554.0 E MTAB 11086:SLX 19351.B10.HMLG7DRXX.s 2.r 0:50 1:50 A:643046449;C:559571909;G:567748411;T:638920943;N:67688 50 50     643046449 559571909 567748411 638920943 67688 ERX6700297 ERS8071621 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94305 0.94796 0.11097 0.10766 0.66149 0.65888 0.46643 0.47512 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10295 10295 ERR7132858 ERX6700296 ERS8071620 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Nic 2 SAMEA10418776 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418776|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Nic 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:2|sample name:E MTAB 11086:Nic 2|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Nic 2 p Nic 2 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:nicotine|Experimental Factor: dose:5 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.F10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.F10.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2046910800.0 20469108.0 E MTAB 11086:SLX 19351.F10.HMLG7DRXX.s 2.r 0:50 1:50 A:547096034;C:475610002;G:481041169;T:543104402;N:59193 50 50     547096034 475610002 481041169 543104402 59193 ERX6700296 ERS8071620 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94391 0.94965 0.10824 0.10557 0.66241 0.65963 0.47747 0.47375 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10296 10296 ERR7132857 ERX6700295 ERS8071619 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Nic 1 SAMEA10418775 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418775|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Nic 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:1|sample name:E MTAB 11086:Nic 1|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Nic 1 p Nic 1 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:nicotine|Experimental Factor: dose:5 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.G10.HMLG7DRXX.s_2.r_2.fq.gz SLX-19351.G10.HMLG7DRXX.s_2.r_1.fq.gz fastq fastq 2001312600.0 20013126.0 E MTAB 11086:SLX 19351.G10.HMLG7DRXX.s 2.r 0:50 1:50 A:535065614;C:463328218;G:468900497;T:533963156;N:55115 50 50     535065614 463328218 468900497 533963156 55115 ERX6700295 ERS8071619 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94179 0.9477 0.11455 0.11139 0.66697 0.66569 0.45749 0.47217 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10297 10297 ERR7132856 ERX6700294 ERS8071618 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Cnt 6 SAMEA10418774 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418774|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Cnt 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:6|sample name:E MTAB 11086:Cnt 6|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Cnt 6 p Cnt 6 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.C11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.C11.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2311609400.0 23116094.0 E MTAB 11086:SLX 19351.C11.HMLG7DRXX.s 2.r 0:50 1:50 A:616569709;C:538286683;G:545161394;T:611525546;N:66068 50 50     616569709 538286683 545161394 611525546 66068 ERX6700294 ERS8071618 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94486 0.95028 0.1097 0.10661 0.66703 0.6644 0.47311 0.47453 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10298 10298 ERR7132855 ERX6700293 ERS8071617 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Cnt 5 SAMEA10418773 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418773|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Cnt 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:5|sample name:E MTAB 11086:Cnt 5|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Cnt 5 p Cnt 5 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.G11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.G11.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 1590322800.0 15903228.0 E MTAB 11086:SLX 19351.G11.HMLG7DRXX.s 2.r 0:50 1:50 A:407583907;C:385496371;G:392945463;T:404250386;N:46673 50 50     407583907 385496371 392945463 404250386 46673 ERX6700293 ERS8071617 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94942 0.95571 0.10693 0.10576 0.69329 0.69063 0.46419 0.4826 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10299 10299 ERR7132854 ERX6700292 ERS8071616 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Cnt 4 SAMEA10418772 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418772|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Cnt 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:4|sample name:E MTAB 11086:Cnt 4|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Cnt 4 p Cnt 4 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.C9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.C9.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2079441500.0 20794415.0 E MTAB 11086:SLX 19351.C9.HMLG7DRXX.s 2.r 0:50 1:50 A:555430147;C:483109623;G:489773903;T:551069513;N:58314 50 50     555430147 483109623 489773903 551069513 58314 ERX6700292 ERS8071616 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94258 0.9491 0.10928 0.10545 0.66561 0.66279 0.46967 0.47237 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10300 10300 ERR7132853 ERX6700291 ERS8071615 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Cnt 3 SAMEA10418771 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418771|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Cnt 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:3|sample name:E MTAB 11086:Cnt 3|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Cnt 3 p Cnt 3 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.H10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.H10.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2606680900.0 26066809.0 E MTAB 11086:SLX 19351.H10.HMLG7DRXX.s 2.r 0:50 1:50 A:698010494;C:604285893;G:612505273;T:691805693;N:73547 50 50     698010494 604285893 612505273 691805693 73547 ERX6700291 ERS8071615 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94271 0.94917 0.11288 0.10987 0.67115 0.66827 0.4729 0.4736 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10301 10301 ERR7132852 ERX6700290 ERS8071614 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Cnt 2 SAMEA10418770 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418770|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Cnt 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:2|sample name:E MTAB 11086:Cnt 2|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Cnt 2 p Cnt 2 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.E11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.E11.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2248468400.0 22484684.0 E MTAB 11086:SLX 19351.E11.HMLG7DRXX.s 2.r 0:50 1:50 A:601914808;C:521501189;G:527610060;T:597380501;N:61842 50 50     601914808 521501189 527610060 597380501 61842 ERX6700290 ERS8071614 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94347 0.94939 0.11234 0.10984 0.66689 0.66342 0.46711 0.46831 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10302 10302 ERR7132851 ERX6700289 ERS8071613 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Cnt 1 SAMEA10418769 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418769|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Cnt 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:1|sample name:E MTAB 11086:Cnt 1|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Cnt 1 p Cnt 1 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.D11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.D11.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 1958517300.0 19585173.0 E MTAB 11086:SLX 19351.D11.HMLG7DRXX.s 2.r 0:50 1:50 A:523101436;C:454540970;G:459925156;T:520895141;N:54597 50 50     523101436 454540970 459925156 520895141 54597 ERX6700289 ERS8071613 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94413 0.95047 0.10482 0.10253 0.67044 0.66782 0.47233 0.4771 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10303 10303 ERR7132850 ERX6700288 ERS8071612 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Amp 6 SAMEA10418768 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418768|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Amp 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:6|sample name:E MTAB 11086:Amp 6|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Amp 6 p Amp 6 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:amphetamine|Experimental Factor: dose:25 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.E9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.E9.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 1712505000.0 17125050.0 E MTAB 11086:SLX 19351.E9.HMLG7DRXX.s 2.r 0:50 1:50 A:455641002;C:398314392;G:404466444;T:454036255;N:46907 50 50     455641002 398314392 404466444 454036255 46907 ERX6700288 ERS8071612 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94358 0.94966 0.10681 0.1037 0.66665 0.66373 0.46688 0.47225 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10304 10304 ERR7132849 ERX6700287 ERS8071611 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Amp 5 SAMEA10418767 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418767|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Amp 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:5|sample name:E MTAB 11086:Amp 5|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Amp 5 p Amp 5 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:amphetamine|Experimental Factor: dose:25 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.A10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.A10.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2007519200.0 20075192.0 E MTAB 11086:SLX 19351.A10.HMLG7DRXX.s 2.r 0:50 1:50 A:534568558;C:467539630;G:473805079;T:531550688;N:55245 50 50     534568558 467539630 473805079 531550688 55245 ERX6700287 ERS8071611 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94408 0.9499 0.10888 0.10604 0.66797 0.66458 0.46039 0.46669 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10305 10305 ERR7132848 ERX6700286 ERS8071610 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Amp 4 SAMEA10418766 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418766|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Amp 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:4|sample name:E MTAB 11086:Amp 4|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Amp 4 p Amp 4 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:amphetamine|Experimental Factor: dose:25 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.F11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.F11.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 1845345300.0 18453453.0 E MTAB 11086:SLX 19351.F11.HMLG7DRXX.s 2.r 0:50 1:50 A:490920758;C:430637266;G:435667744;T:488067453;N:52079 50 50     490920758 430637266 435667744 488067453 52079 ERX6700286 ERS8071610 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94484 0.9504 0.10472 0.10237 0.66618 0.66336 0.46903 0.47774 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10306 10306 ERR7132847 ERX6700285 ERS8071609 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Amp 3 SAMEA10418765 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418765|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Amp 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:3|sample name:E MTAB 11086:Amp 3|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Amp 3 p Amp 3 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:amphetamine|Experimental Factor: dose:25 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.F9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.F9.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2195415300.0 21954153.0 E MTAB 11086:SLX 19351.F9.HMLG7DRXX.s 2.r 0:50 1:50 A:583956682;C:511927452;G:518373455;T:581095379;N:62332 50 50     583956682 511927452 518373455 581095379 62332 ERX6700285 ERS8071609 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94571 0.95178 0.10567 0.10288 0.6688 0.66661 0.4677 0.47288 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10307 10307 ERR7132846 ERX6700284 ERS8071608 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Amp 2 SAMEA10418764 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418764|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Amp 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:2|sample name:E MTAB 11086:Amp 2|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Amp 2 p Amp 2 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:amphetamine|Experimental Factor: dose:25 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.D9.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.D9.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2093635000.0 20936350.0 E MTAB 11086:SLX 19351.D9.HMLG7DRXX.s 2.r 0:50 1:50 A:556451381;C:488314672;G:495691630;T:553118514;N:58803 50 50     556451381 488314672 495691630 553118514 58803 ERX6700284 ERS8071608 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94407 0.95012 0.11198 0.10872 0.66651 0.66352 0.46901 0.47198 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
10308 10308 ERR7132845 ERX6700283 ERS8071607 ERP132573 PRJEB48231 RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs E-MTAB-11086 Transcriptome Analysis RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf. ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24   Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Amp 1 SAMEA10418763 Cambridge Institute of Therapeutic Immunology & Infectious Disease ENA first public:2022 01 24|ENA last update:2022 01 24|External Id:SAMEA10418763|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease|INSDC first public:2022 01 24T16:27:32Z|INSDC last update:2022 01 24T16:27:32Z|INSDC status:public|Submitter Id:E MTAB 11086:Amp 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:pool of 7 embryos|organism part:whole organism|replicate:1|sample name:E MTAB 11086:Amp 1|sex:not available|strain:Tüpfel long fin TLF                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs E MTAB 11086:Amp 1 p Amp 1 p RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit. Experimental Factor: compound:amphetamine|Experimental Factor: dose:25 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP132573 Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs ENA FIRST PUBLIC:2022 01 24|ENA LAST UPDATE:2022 01 24 SLX-19351.E10.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.E10.HMLG7DRXX.s_2.r_2.fq.gz fastq fastq 2254130000.0 22541300.0 E MTAB 11086:SLX 19351.E10.HMLG7DRXX.s 2.r 0:50 1:50 A:599784010;C:525655199;G:531849347;T:596777643;N:63801 50 50     599784010 525655199 531849347 596777643 63801 ERX6700283 ERS8071607 ERA6757821 Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive Cambridge Institute of Therapeutic Immunology & Infectious Disease|European Nucleotide Archive 2 0.94449 0.95026 0.10608 0.10323 0.66758 0.66257 0.46869 0.47045 50 50 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United Kingdom 2022-01-24 Larval Larval Embryo Imprecise All anatomical structures
11245 11245 ERR10851251 ERX10296231 ERS14601258 ERP144652 PRJEB59599 Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E-MTAB-12577 Transcriptome Analysis Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17   Protocols: Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified WT3 cd41pflt1p48hpf SAMEA112483908 Department of Hematology cancer institute ErasmusMC ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483908|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:WT3 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 1|organism part:liver|sample name:E MTAB 12577:WT3 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP WT                 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E MTAB 12577:WT3 cd41pflt1p48hpf p WT3 cd41pflt1p48hpf p Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP144652 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17 WT3_cd41pflt1p48hpf_R1.fastq.gz WT3_cd41pflt1p48hpf_R2.fastq.gz fastq fastq 2865896816.0 14187608.0 E MTAB 12577:WT3 cd41pflt1p48hpf R 0:101 1:101 A:766433553;C:631932872;G:660672891;T:806849737;N:7763 101 101     766433553 631932872 660672891 806849737 7763 ERX10296231 ERS14601258 ERA20429817 Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive 2 0.90501 0.85042 0.09405 0.09335 0.87286 0.87943 0.48423 0.47904 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Netherlands 2023-02-17 Hatching Embryo Embryo Imprecise All anatomical structures
11246 11246 ERR10851250 ERX10296230 ERS14601257 ERP144652 PRJEB59599 Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E-MTAB-12577 Transcriptome Analysis Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17   Protocols: Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified WT2 cd41pflt1p48hpf SAMEA112483907 Department of Hematology cancer institute ErasmusMC ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483907|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:WT2 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 5|organism part:liver|sample name:E MTAB 12577:WT2 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP WT                 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E MTAB 12577:WT2 cd41pflt1p48hpf p WT2 cd41pflt1p48hpf p Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP144652 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17 WT2_cd41pflt1p48hpf_R1.fastq.gz WT2_cd41pflt1p48hpf_R2.fastq.gz fastq fastq 2929743360.0 14503680.0 E MTAB 12577:WT2 cd41pflt1p48hpf R 0:101 1:101 A:803775344;C:639485652;G:661899077;T:824575679;N:7608 101 101     803775344 639485652 661899077 824575679 7608 ERX10296230 ERS14601257 ERA20429817 Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive 2 0.94558 0.90768 0.09379 0.09399 0.79058 0.79833 0.48216 0.47743 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Netherlands 2023-02-17 Hatching Embryo Embryo Imprecise All anatomical structures
11247 11247 ERR10851249 ERX10296229 ERS14601256 ERP144652 PRJEB59599 Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E-MTAB-12577 Transcriptome Analysis Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17   Protocols: Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified WT1 cd41pflt1p48hpf SAMEA112483906 Department of Hematology cancer institute ErasmusMC ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483906|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:WT1 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 4|organism part:liver|sample name:E MTAB 12577:WT1 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP WT                 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E MTAB 12577:WT1 cd41pflt1p48hpf p WT1 cd41pflt1p48hpf p Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP144652 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17 WT1_cd41pflt1p48hpf_R1.fastq.gz WT1_cd41pflt1p48hpf_R2.fastq.gz fastq fastq 3248647426.0 16082413.0 E MTAB 12577:WT1 cd41pflt1p48hpf R 0:101 1:101 A:883030193;C:725566673;G:750551574;T:889489774;N:9212 101 101     883030193 725566673 750551574 889489774 9212 ERX10296229 ERS14601256 ERA20429817 Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive 2 0.91568 0.8915 0.09819 0.09602 0.86634 0.8706 0.48887 0.48731 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Netherlands 2023-02-17 Hatching Embryo Embryo Imprecise All anatomical structures
11248 11248 ERR10851248 ERX10296228 ERS14601255 ERP144652 PRJEB59599 Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E-MTAB-12577 Transcriptome Analysis Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17   Protocols: Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Het3 cd41pflt1p48hpf SAMEA112483905 Department of Hematology cancer institute ErasmusMC ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483905|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:Het3 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:Gata2b +/ |immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 3|organism part:liver|sample name:E MTAB 12577:Het3 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP Gata2b KO                 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E MTAB 12577:Het3 cd41pflt1p48hpf p Het3 cd41pflt1p48hpf p Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Experimental Factor: genotype:Gata2b +/ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP144652 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17 Het3_cd41pflt1p48hpf_R1.fastq.gz Het3_cd41pflt1p48hpf_R2.fastq.gz fastq fastq 2826011512.0 13990156.0 E MTAB 12577:Het3 cd41pflt1p48hpf R 0:101 1:101 A:777245323;C:622387331;G:640520737;T:785850577;N:7544 101 101     777245323 622387331 640520737 785850577 7544 ERX10296228 ERS14601255 ERA20429817 Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive 2 0.92716 0.90121 0.10896 0.10895 0.76739 0.77628 0.47007 0.46569 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Netherlands 2023-02-17 Hatching Embryo Embryo Imprecise All anatomical structures
11249 11249 ERR10851247 ERX10296227 ERS14601254 ERP144652 PRJEB59599 Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E-MTAB-12577 Transcriptome Analysis Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17   Protocols: Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Het2 cd41pflt1p48hpf SAMEA112483904 Department of Hematology cancer institute ErasmusMC ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483904|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:Het2 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:Gata2b +/ |immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 2|organism part:liver|sample name:E MTAB 12577:Het2 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP Gata2b KO                 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E MTAB 12577:Het2 cd41pflt1p48hpf p Het2 cd41pflt1p48hpf p Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Experimental Factor: genotype:Gata2b +/ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP144652 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17 Het2_cd41pflt1p48hpf_R1.fastq.gz Het2_cd41pflt1p48hpf_R2.fastq.gz fastq fastq 2999149954.0 14847277.0 E MTAB 12577:Het2 cd41pflt1p48hpf R 0:101 1:101 A:822247269;C:656610849;G:681974696;T:838308917;N:8223 101 101     822247269 656610849 681974696 838308917 8223 ERX10296227 ERS14601254 ERA20429817 Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive 2 0.94678 0.91473 0.10277 0.10053 0.76686 0.77684 0.46042 0.47202 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Netherlands 2023-02-17 Hatching Embryo Embryo Imprecise All anatomical structures
11250 11250 ERR10851246 ERX10296226 ERS14601253 ERP144652 PRJEB59599 Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E-MTAB-12577 Transcriptome Analysis Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17   Protocols: Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Het1 cd41pflt1p48hpf SAMEA112483903 Department of Hematology cancer institute ErasmusMC ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17|External Id:SAMEA112483903|INSDC center alias:Department of Hematology cancer institute ErasmusMC|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC first public:2023 02 17T00:21:53Z|INSDC last update:2023 02 17T00:21:53Z|INSDC status:public|Submitter Id:E MTAB 12577:Het1 cd41pflt1p48hpf|age:48|broker name:ArrayExpress|cell type:hematopoietic stem cell|common name:zebrafish|developmental stage:embryo|genotype:Gata2b +/ |immunophenotype:CD41:GFP+ Flt1:RFP+|individual:pools of 3 embryos 1|organism part:liver|sample name:E MTAB 12577:Het1 cd41pflt1p48hpf|scientific name:Danio rerio|strain:TgCD41:GFP TgFlt1:RFP Gata2b KO                 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 E MTAB 12577:Het1 cd41pflt1p48hpf p Het1 cd41pflt1p48hpf p Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 Embryos were dissociated using Collagenase 1 2 and 4 and sorted using a FACS Aria III in trizol RNA was isolated from trizol RNA was smarter amplified Experimental Factor: genotype:Gata2b +/ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP144652 Illumina NovaSeq 6000 paired end sequencing; Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41 ENA FIRST PUBLIC:2023 02 17|ENA LAST UPDATE:2023 02 17 Het1_cd41pflt1p48hpf_R1.fastq.gz Het1_cd41pflt1p48hpf_R2.fastq.gz fastq fastq 36682350994.0 181595797.0 E MTAB 12577:Het1 cd41pflt1p48hpf R 0:101 1:101 A:10130106739;C:7969045717;G:8373740062;T:10209360741;N:97735 101 101     10130106739 7969045717 8373740062 10209360741 97735 ERX10296226 ERS14601253 ERA20429817 Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive Department of Hematology cancer institute ErasmusMC|European Nucleotide Archive 2 0.94302 0.91104 0.11873 0.11597 0.7554 0.76579 0.48813 0.47764 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Netherlands 2023-02-17 Hatching Embryo Embryo Imprecise All anatomical structures
11723 11723 ERR11422840 ERX10830011 ERS15422295 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 hom ttn1 het 1 SAMEA113427169 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427169|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 het 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 / ; ttn.1 +/ |individual:pool of 3 embryos 1|organism part:embryo|replicate:1|sample name:E MTAB 12934:srpk3 hom ttn1 het 1|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 hom ttn1 het 1 p srpk3 hom ttn1 het 1 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 / ; ttn.1 +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.C4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.C4.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 5201588100.0 17338627.0 E MTAB 12934:SLX 21419.C4.HV2TTDRXY.s 2.r 0:150 1:150 A:1395812979;C:1209220590;G:1233107747;T:1363200419;N:246365 150 150     1395812979 1209220590 1233107747 1363200419 246365 ERX10830011 ERS15422295 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11724 11724 ERR11422856 ERX10830027 ERS15422311 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 wt ttn1 het 8 SAMEA113427185 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427185|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 het 8|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/ |individual:pool of 3 embryos 8|organism part:embryo|replicate:8|sample name:E MTAB 12934:srpk3 wt ttn1 het 8|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 wt ttn1 het 8 p srpk3 wt ttn1 het 8 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 +/+; ttn.1 +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.C5.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.C5.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 6243031800.0 20810106.0 E MTAB 12934:SLX 21419.C5.HV2TTDRXY.s 2.r 0:150 1:150 A:1678428066;C:1448795147;G:1483028868;T:1632478253;N:301466 150 150     1678428066 1448795147 1483028868 1632478253 301466 ERX10830027 ERS15422311 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11725 11725 ERR11422863 ERX10830034 ERS15422318 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 wt ttn1 wt 7 SAMEA113427192 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427192|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 wt 7|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/+|individual:pool of 3 embryos 7|organism part:embryo|replicate:7|sample name:E MTAB 12934:srpk3 wt ttn1 wt 7|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 wt ttn1 wt 7 p srpk3 wt ttn1 wt 7 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 +/+; ttn.1 +/+ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.G3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.G3.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 7924538100.0 26415127.0 E MTAB 12934:SLX 21419.G3.HV2TTDRXY.s 2.r 0:150 1:150 A:2128544326;C:1844570027;G:1875605207;T:2075443615;N:374925 150 150     2128544326 1844570027 1875605207 2075443615 374925 ERX10830034 ERS15422318 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11726 11726 ERR11422862 ERX10830033 ERS15422317 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 wt ttn1 wt 6 SAMEA113427191 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427191|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 wt 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/+|individual:pool of 3 embryos 6|organism part:embryo|replicate:6|sample name:E MTAB 12934:srpk3 wt ttn1 wt 6|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 wt ttn1 wt 6 p srpk3 wt ttn1 wt 6 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 +/+; ttn.1 +/+ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.D5.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.D5.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 8652848700.0 28842829.0 E MTAB 12934:SLX 21419.D5.HV2TTDRXY.s 2.r 0:150 1:150 A:2323784475;C:2011287942;G:2055678520;T:2261686116;N:411647 150 150     2323784475 2011287942 2055678520 2261686116 411647 ERX10830033 ERS15422317 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11727 11727 ERR11422852 ERX10830023 ERS15422307 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 wt ttn1 het 1 SAMEA113427181 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427181|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 het 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/ |individual:pool of 3 embryos 1|organism part:embryo|replicate:1|sample name:E MTAB 12934:srpk3 wt ttn1 het 1|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 wt ttn1 het 1 p srpk3 wt ttn1 het 1 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 +/+; ttn.1 +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.E3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.E3.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 5595162300.0 18650541.0 E MTAB 12934:SLX 21419.E3.HV2TTDRXY.s 2.r 0:150 1:150 A:1500582422;C:1301393746;G:1326420086;T:1466508237;N:257809 150 150     1500582422 1301393746 1326420086 1466508237 257809 ERX10830023 ERS15422307 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11728 11728 ERR11422841 ERX10830012 ERS15422296 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 hom ttn1 het 10 SAMEA113427170 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427170|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 het 10|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 / ; ttn.1 +/ |individual:pool of 3 embryos 10|organism part:embryo|replicate:10|sample name:E MTAB 12934:srpk3 hom ttn1 het 10|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 hom ttn1 het 10 p srpk3 hom ttn1 het 10 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 / ; ttn.1 +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.F2.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.F2.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 6163159800.0 20543866.0 E MTAB 12934:SLX 21419.F2.HV2TTDRXY.s 2.r 0:150 1:150 A:1651051246;C:1435397149;G:1465377920;T:1611039390;N:294095 150 150     1651051246 1435397149 1465377920 1611039390 294095 ERX10830012 ERS15422296 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11729 11729 ERR11422858 ERX10830029 ERS15422313 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 wt ttn1 wt 2 SAMEA113427187 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427187|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 wt 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/+|individual:pool of 3 embryos 2|organism part:embryo|replicate:2|sample name:E MTAB 12934:srpk3 wt ttn1 wt 2|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 wt ttn1 wt 2 p srpk3 wt ttn1 wt 2 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 +/+; ttn.1 +/+ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.E4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.E4.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 4948755000.0 16495850.0 E MTAB 12934:SLX 21419.E4.HV2TTDRXY.s 2.r 0:150 1:150 A:1328315519;C:1150664187;G:1172962823;T:1296576134;N:236337 150 150     1328315519 1150664187 1172962823 1296576134 236337 ERX10830029 ERS15422313 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11730 11730 ERR11422853 ERX10830024 ERS15422308 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 wt ttn1 het 2 SAMEA113427182 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427182|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 het 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/ |individual:pool of 3 embryos 2|organism part:embryo|replicate:2|sample name:E MTAB 12934:srpk3 wt ttn1 het 2|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 wt ttn1 het 2 p srpk3 wt ttn1 het 2 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 +/+; ttn.1 +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.A5.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.A5.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 5172515100.0 17241717.0 E MTAB 12934:SLX 21419.A5.HV2TTDRXY.s 2.r 0:150 1:150 A:1390660856;C:1200693628;G:1226597252;T:1354312680;N:250684 150 150     1390660856 1200693628 1226597252 1354312680 250684 ERX10830024 ERS15422308 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11731 11731 ERR11422842 ERX10830013 ERS15422297 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 hom ttn1 het 2 SAMEA113427171 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427171|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 het 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 / ; ttn.1 +/ |individual:pool of 3 embryos 2|organism part:embryo|replicate:2|sample name:E MTAB 12934:srpk3 hom ttn1 het 2|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 hom ttn1 het 2 p srpk3 hom ttn1 het 2 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 / ; ttn.1 +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.B3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.B3.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 7596727500.0 25322425.0 E MTAB 12934:SLX 21419.B3.HV2TTDRXY.s 2.r 0:150 1:150 A:2040744877;C:1765753859;G:1800431343;T:1989434039;N:363382 150 150     2040744877 1765753859 1800431343 1989434039 363382 ERX10830013 ERS15422297 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11732 11732 ERR11422854 ERX10830025 ERS15422309 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 wt ttn1 het 3 SAMEA113427183 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427183|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 het 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/ |individual:pool of 3 embryos 3|organism part:embryo|replicate:3|sample name:E MTAB 12934:srpk3 wt ttn1 het 3|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 wt ttn1 het 3 p srpk3 wt ttn1 het 3 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 +/+; ttn.1 +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.B4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.B4.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 4147455600.0 13824852.0 E MTAB 12934:SLX 21419.B4.HV2TTDRXY.s 2.r 0:150 1:150 A:1111933168;C:965101703;G:986324158;T:1083898570;N:198001 150 150     1111933168 965101703 986324158 1083898570 198001 ERX10830025 ERS15422309 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11733 11733 ERR11422855 ERX10830026 ERS15422310 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 wt ttn1 het 7 SAMEA113427184 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427184|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 het 7|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/ |individual:pool of 3 embryos 7|organism part:embryo|replicate:7|sample name:E MTAB 12934:srpk3 wt ttn1 het 7|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 wt ttn1 het 7 p srpk3 wt ttn1 het 7 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 +/+; ttn.1 +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.C3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.C3.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 7815347400.0 26051158.0 E MTAB 12934:SLX 21419.C3.HV2TTDRXY.s 2.r 0:150 1:150 A:2105543787;C:1810060936;G:1848658748;T:2050709339;N:374590 150 150     2105543787 1810060936 1848658748 2050709339 374590 ERX10830026 ERS15422310 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11734 11734 ERR11422847 ERX10830018 ERS15422302 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 hom ttn1 wt 4 SAMEA113427176 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427176|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 wt 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 / ; ttn.1 +/+|individual:pool of 3 embryos 4|organism part:embryo|replicate:4|sample name:E MTAB 12934:srpk3 hom ttn1 wt 4|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 hom ttn1 wt 4 p srpk3 hom ttn1 wt 4 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 / ; ttn.1 +/+ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.F4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.F4.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 5552048400.0 18506828.0 E MTAB 12934:SLX 21419.F4.HV2TTDRXY.s 2.r 0:150 1:150 A:1494691750;C:1287655327;G:1313223405;T:1456215647;N:262271 150 150     1494691750 1287655327 1313223405 1456215647 262271 ERX10830018 ERS15422302 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11735 11735 ERR11422843 ERX10830014 ERS15422298 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 hom ttn1 het 7 SAMEA113427172 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427172|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 het 7|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 / ; ttn.1 +/ |individual:pool of 3 embryos 7|organism part:embryo|replicate:7|sample name:E MTAB 12934:srpk3 hom ttn1 het 7|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 hom ttn1 het 7 p srpk3 hom ttn1 het 7 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 / ; ttn.1 +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.G2.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.G2.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 6130593900.0 20435313.0 E MTAB 12934:SLX 21419.G2.HV2TTDRXY.s 2.r 0:150 1:150 A:1646268883;C:1426071699;G:1453474221;T:1604484627;N:294470 150 150     1646268883 1426071699 1453474221 1604484627 294470 ERX10830014 ERS15422298 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11736 11736 ERR11422857 ERX10830028 ERS15422312 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 wt ttn1 het 9 SAMEA113427186 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427186|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 het 9|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/ |individual:pool of 3 embryos 9|organism part:embryo|replicate:9|sample name:E MTAB 12934:srpk3 wt ttn1 het 9|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 wt ttn1 het 9 p srpk3 wt ttn1 het 9 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 +/+; ttn.1 +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.A3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.A3.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 7955802600.0 26519342.0 E MTAB 12934:SLX 21419.A3.HV2TTDRXY.s 2.r 0:150 1:150 A:2139048525;C:1844468923;G:1881094685;T:2090808427;N:382040 150 150     2139048525 1844468923 1881094685 2090808427 382040 ERX10830028 ERS15422312 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11737 11737 ERR11422844 ERX10830015 ERS15422299 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 hom ttn1 het 8 SAMEA113427173 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427173|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 het 8|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 / ; ttn.1 +/ |individual:pool of 3 embryos 8|organism part:embryo|replicate:8|sample name:E MTAB 12934:srpk3 hom ttn1 het 8|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 hom ttn1 het 8 p srpk3 hom ttn1 het 8 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 / ; ttn.1 +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.H2.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.H2.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 4707444000.0 15691480.0 E MTAB 12934:SLX 21419.H2.HV2TTDRXY.s 2.r 0:150 1:150 A:1266769556;C:1091810198;G:1114454117;T:1234185729;N:224400 150 150     1266769556 1091810198 1114454117 1234185729 224400 ERX10830015 ERS15422299 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11738 11738 ERR11422850 ERX10830021 ERS15422305 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 hom ttn1 wt 7 SAMEA113427179 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427179|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 wt 7|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 / ; ttn.1 +/+|individual:pool of 3 embryos 7|organism part:embryo|replicate:7|sample name:E MTAB 12934:srpk3 hom ttn1 wt 7|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 hom ttn1 wt 7 p srpk3 hom ttn1 wt 7 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 / ; ttn.1 +/+ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.G4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.G4.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 6262379700.0 20874599.0 E MTAB 12934:SLX 21419.G4.HV2TTDRXY.s 2.r 0:150 1:150 A:1681113096;C:1456657472;G:1485545256;T:1638760380;N:303496 150 150     1681113096 1456657472 1485545256 1638760380 303496 ERX10830021 ERS15422305 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11739 11739 ERR11422846 ERX10830017 ERS15422301 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 hom ttn1 wt 1 SAMEA113427175 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427175|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 wt 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 / ; ttn.1 +/+|individual:pool of 3 embryos 1|organism part:embryo|replicate:1|sample name:E MTAB 12934:srpk3 hom ttn1 wt 1|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 hom ttn1 wt 1 p srpk3 hom ttn1 wt 1 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 / ; ttn.1 +/+ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.A4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.A4.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 6071901300.0 20239671.0 E MTAB 12934:SLX 21419.A4.HV2TTDRXY.s 2.r 0:150 1:150 A:1629141748;C:1412963306;G:1441970376;T:1587528201;N:297669 150 150     1629141748 1412963306 1441970376 1587528201 297669 ERX10830017 ERS15422301 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11740 11740 ERR11422860 ERX10830031 ERS15422315 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 wt ttn1 wt 4 SAMEA113427189 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427189|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 wt 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/+|individual:pool of 3 embryos 4|organism part:embryo|replicate:4|sample name:E MTAB 12934:srpk3 wt ttn1 wt 4|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 wt ttn1 wt 4 p srpk3 wt ttn1 wt 4 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 +/+; ttn.1 +/+ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.H4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.H4.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 8552416200.0 28508054.0 E MTAB 12934:SLX 21419.H4.HV2TTDRXY.s 2.r 0:150 1:150 A:2292742388;C:1992671634;G:2031906776;T:2234679447;N:415955 150 150     2292742388 1992671634 2031906776 2234679447 415955 ERX10830031 ERS15422315 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11741 11741 ERR11422851 ERX10830022 ERS15422306 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 hom ttn1 wt 8 SAMEA113427180 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427180|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 wt 8|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 / ; ttn.1 +/+|individual:pool of 3 embryos 8|organism part:embryo|replicate:8|sample name:E MTAB 12934:srpk3 hom ttn1 wt 8|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 hom ttn1 wt 8 p srpk3 hom ttn1 wt 8 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 / ; ttn.1 +/+ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.D4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.D4.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 4693977900.0 15646593.0 E MTAB 12934:SLX 21419.D4.HV2TTDRXY.s 2.r 0:150 1:150 A:1260530822;C:1090058889;G:1111595821;T:1231573984;N:218384 150 150     1260530822 1090058889 1111595821 1231573984 218384 ERX10830022 ERS15422306 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11742 11742 ERR11422849 ERX10830020 ERS15422304 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 hom ttn1 wt 6 SAMEA113427178 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427178|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 wt 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 / ; ttn.1 +/+|individual:pool of 3 embryos 6|organism part:embryo|replicate:6|sample name:E MTAB 12934:srpk3 hom ttn1 wt 6|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 hom ttn1 wt 6 p srpk3 hom ttn1 wt 6 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 / ; ttn.1 +/+ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.E2.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.E2.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 8212296300.0 27374321.0 E MTAB 12934:SLX 21419.E2.HV2TTDRXY.s 2.r 0:150 1:150 A:2208490788;C:1905530286;G:1945454560;T:2152431537;N:389129 150 150     2208490788 1905530286 1945454560 2152431537 389129 ERX10830020 ERS15422304 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11743 11743 ERR11422845 ERX10830016 ERS15422300 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 hom ttn1 het 9 SAMEA113427174 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427174|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 het 9|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 / ; ttn.1 +/ |individual:pool of 3 embryos 9|organism part:embryo|replicate:9|sample name:E MTAB 12934:srpk3 hom ttn1 het 9|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 hom ttn1 het 9 p srpk3 hom ttn1 het 9 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 / ; ttn.1 +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.H3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.H3.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 6498128700.0 21660429.0 E MTAB 12934:SLX 21419.H3.HV2TTDRXY.s 2.r 0:150 1:150 A:1747443944;C:1508729516;G:1535387292;T:1706266342;N:301606 150 150     1747443944 1508729516 1535387292 1706266342 301606 ERX10830016 ERS15422300 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11744 11744 ERR11422861 ERX10830032 ERS15422316 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 wt ttn1 wt 5 SAMEA113427190 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427190|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 wt 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/+|individual:pool of 3 embryos 5|organism part:embryo|replicate:5|sample name:E MTAB 12934:srpk3 wt ttn1 wt 5|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 wt ttn1 wt 5 p srpk3 wt ttn1 wt 5 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 +/+; ttn.1 +/+ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.B5.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.B5.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 5670094800.0 18900316.0 E MTAB 12934:SLX 21419.B5.HV2TTDRXY.s 2.r 0:150 1:150 A:1520345271;C:1320386106;G:1349261719;T:1479832706;N:268998 150 150     1520345271 1320386106 1349261719 1479832706 268998 ERX10830032 ERS15422316 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11745 11745 ERR11422848 ERX10830019 ERS15422303 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 hom ttn1 wt 5 SAMEA113427177 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427177|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 hom ttn1 wt 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 / ; ttn.1 +/+|individual:pool of 3 embryos 5|organism part:embryo|replicate:5|sample name:E MTAB 12934:srpk3 hom ttn1 wt 5|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 hom ttn1 wt 5 p srpk3 hom ttn1 wt 5 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 / ; ttn.1 +/+ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.D3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.D3.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 4627365300.0 15424551.0 E MTAB 12934:SLX 21419.D3.HV2TTDRXY.s 2.r 0:150 1:150 A:1240390225;C:1077656611;G:1099301867;T:1209799382;N:217215 150 150     1240390225 1077656611 1099301867 1209799382 217215 ERX10830019 ERS15422303 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11746 11746 ERR11422859 ERX10830030 ERS15422314 ERP147133 PRJEB62042 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E-MTAB-12934 Transcriptome Analysis RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos. ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09   Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. srpk3 wt ttn1 wt 3 SAMEA113427188 QMUL ENA FIRST PUBLIC:2024 02 09T16:00:07Z|ENA LAST UPDATE:2024 02 09T16:00:07Z|External Id:SAMEA113427188|INSDC center name:QMUL|INSDC first public:2024 02 09T16:00:07Z|INSDC last update:2024 02 09T16:00:07Z|INSDC status:public|Submitter Id:E MTAB 12934:srpk3 wt ttn1 wt 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:srpk3 +/+; ttn.1 +/+|individual:pool of 3 embryos 3|organism part:embryo|replicate:3|sample name:E MTAB 12934:srpk3 wt ttn1 wt 3|scientific name:Danio rerio|sex:not available|strain:Tüpfel long fin                 RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein E MTAB 12934:srpk3 wt ttn1 wt 3 p srpk3 wt ttn1 wt 3 p RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina. Experimental Factor: genotype:srpk3 +/+; ttn.1 +/+ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP147133 Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein ENA FIRST PUBLIC:2024 02 09|ENA LAST UPDATE:2024 02 09 SLX-21419.F3.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.F3.HV2TTDRXY.s_2.r_2.fq.gz fastq fastq 6046705800.0 20155686.0 E MTAB 12934:SLX 21419.F3.HV2TTDRXY.s 2.r 0:150 1:150 A:1628067770;C:1402636688;G:1430886037;T:1584821803;N:293502 150 150     1628067770 1402636688 1430886037 1584821803 293502 ERX10830030 ERS15422314 ERA23329494 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2024-02-09 Larval Larval Embryo Imprecise All anatomical structures
11753 11753 ERR11758614 ERX11157721 ERS16172939 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. fli1tp1 24hpf SAMEA114192246 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+ tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed tp1:eGFP                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:fli1tp1 24hpf p fli1tp1 24hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 FliTp124hpf_S25_L001_R1_001.fastq.gz FliTp124hpf_S25_L001_R2_001.fastq.gz fastq fastq 226833768.0 1800268.0 E MTAB 13196:FliTp124hpf S25 L001 0:28 1:98 A:65319978;C:50920193;G:49999849;T:60474280;N:119468 28 98     65319978 50920193 49999849 60474280 119468 ERX11157721 ERS16172939 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00122 0.88236 0.00056 0.09684 0.9978 0.89309 0.424 0.44186 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11754 11754 ERR11758619 ERX11157721 ERS16172939 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. fli1tp1 24hpf SAMEA114192246 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+ tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed tp1:eGFP                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:fli1tp1 24hpf p fli1tp1 24hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 FliTp124hpf_S27_L001_R1_001.fastq.gz FliTp124hpf_S27_L001_R2_001.fastq.gz fastq fastq 261098334.0 2072209.0 E MTAB 13196:FliTp124hpf S27 L001 0:28 1:98 A:76098436;C:58031830;G:57099955;T:69729759;N:138354 28 98     76098436 58031830 57099955 69729759 138354 ERX11157721 ERS16172939 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00109 0.87641 0.00062 0.0976 0.99837 0.90065 0.45555 0.48712 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11755 11755 ERR11758589 ERX11157721 ERS16172939 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. fli1tp1 24hpf SAMEA114192246 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+ tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed tp1:eGFP                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:fli1tp1 24hpf p fli1tp1 24hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 FliTp124hpf_S16_L005_R1_001.fastq.gz FliTp124hpf_S16_L005_R2_001.fastq.gz fastq fastq 1168367130.0 9272755.0 E MTAB 13196:FliTp124hpf S16 L005 0:28 1:98 A:323651598;C:269884286;G:268030176;T:306695030;N:106040 28 98     323651598 269884286 268030176 306695030 106040 ERX11157721 ERS16172939 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00491 0.90853 0.00131 0.07851 0.99019 0.84331 0.41536 0.48076 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11756 11756 ERR11758638 ERX11157721 ERS16172939 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. fli1tp1 24hpf SAMEA114192246 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+ tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed tp1:eGFP                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:fli1tp1 24hpf p fli1tp1 24hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 FliTp124hpf_S22_L001_R1_001.fastq.gz FliTp124hpf_S22_L001_R2_001.fastq.gz fastq fastq 864786636.0 6863386.0 E MTAB 13196:FliTp124hpf S22 L001 0:28 1:98 A:241767760;C:198370882;G:198049093;T:226508751;N:90150 28 98     241767760 198370882 198049093 226508751 90150 ERX11157721 ERS16172939 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00375 0.89002 0.00114 0.0769 0.99237 0.84563 0.41796 0.48995 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11757 11757 ERR11758599 ERX11157721 ERS16172939 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. fli1tp1 24hpf SAMEA114192246 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+ tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed tp1:eGFP                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:fli1tp1 24hpf p fli1tp1 24hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 FliTp124hpf_S15_L005_R1_001.fastq.gz FliTp124hpf_S15_L005_R2_001.fastq.gz fastq fastq 1795799502.0 14252377.0 E MTAB 13196:FliTp124hpf S15 L005 0:28 1:98 A:500590460;C:413239086;G:410401125;T:471402890;N:165941 28 98     500590460 413239086 410401125 471402890 165941 ERX11157721 ERS16172939 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00492 0.91242 0.0012 0.08044 0.99007 0.84668 0.42778 0.49291 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11758 11758 ERR11758601 ERX11157721 ERS16172939 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. fli1tp1 24hpf SAMEA114192246 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+ tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed tp1:eGFP                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:fli1tp1 24hpf p fli1tp1 24hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 FliTp124hpf_S26_L001_R1_001.fastq.gz FliTp124hpf_S26_L001_R2_001.fastq.gz fastq fastq 266141358.0 2112233.0 E MTAB 13196:FliTp124hpf S26 L001 0:28 1:98 A:76996100;C:59592346;G:58963461;T:70457732;N:131719 28 98     76996100 59592346 58963461 70457732 131719 ERX11157721 ERS16172939 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00106 0.88422 0.00046 0.09358 0.99782 0.89449 0.47826 0.48948 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11759 11759 ERR11758630 ERX11157721 ERS16172939 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. fli1tp1 24hpf SAMEA114192246 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+ tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed tp1:eGFP                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:fli1tp1 24hpf p fli1tp1 24hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 FliTp124hpf_S14_L005_R1_001.fastq.gz FliTp124hpf_S14_L005_R2_001.fastq.gz fastq fastq 1812847428.0 14387678.0 E MTAB 13196:FliTp124hpf S14 L005 0:28 1:98 A:502956890;C:417865079;G:416595454;T:475266679;N:163326 28 98     502956890 417865079 416595454 475266679 163326 ERX11157721 ERS16172939 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00483 0.91317 0.00123 0.07918 0.99036 0.84143 0.40704 0.4819 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11760 11760 ERR11758603 ERX11157721 ERS16172939 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. fli1tp1 24hpf SAMEA114192246 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+ tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed tp1:eGFP                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:fli1tp1 24hpf p fli1tp1 24hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 FliTp124hpf_S13_L005_R1_001.fastq.gz FliTp124hpf_S13_L005_R2_001.fastq.gz fastq fastq 1544281830.0 12256205.0 E MTAB 13196:FliTp124hpf S13 L005 0:28 1:98 A:428008915;C:356252081;G:354333187;T:405545992;N:141655 28 98     428008915 356252081 354333187 405545992 141655 ERX11157721 ERS16172939 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00507 0.91025 0.00138 0.07858 0.98987 0.84295 0.41793 0.4891 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11761 11761 ERR11758613 ERX11157721 ERS16172939 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. fli1tp1 24hpf SAMEA114192246 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+ tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed tp1:eGFP                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:fli1tp1 24hpf p fli1tp1 24hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 FliTp124hpf_S21_L001_R1_001.fastq.gz FliTp124hpf_S21_L001_R2_001.fastq.gz fastq fastq 761441436.0 6043186.0 E MTAB 13196:FliTp124hpf S21 L001 0:28 1:98 A:212876877;C:174700212;G:174244892;T:199537401;N:82054 28 98     212876877 174700212 174244892 199537401 82054 ERX11157721 ERS16172939 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00334 0.88899 0.00106 0.07762 0.99322 0.84476 0.42792 0.48783 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11762 11762 ERR11758645 ERX11157721 ERS16172939 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. fli1tp1 24hpf SAMEA114192246 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+ tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed tp1:eGFP                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:fli1tp1 24hpf p fli1tp1 24hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 FliTp124hpf_S23_L001_R1_001.fastq.gz FliTp124hpf_S23_L001_R2_001.fastq.gz fastq fastq 873938772.0 6936022.0 E MTAB 13196:FliTp124hpf S23 L001 0:28 1:98 A:245075115;C:199879929;G:199312177;T:229576663;N:94888 28 98     245075115 199879929 199312177 229576663 94888 ERX11157721 ERS16172939 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00361 0.88671 0.00104 0.07855 0.99255 0.84723 0.41141 0.4885 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11763 11763 ERR11758598 ERX11157721 ERS16172939 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. fli1tp1 24hpf SAMEA114192246 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+ tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed tp1:eGFP                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:fli1tp1 24hpf p fli1tp1 24hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 FliTp124hpf_S28_L001_R1_001.fastq.gz FliTp124hpf_S28_L001_R2_001.fastq.gz fastq fastq 164465532.0 1305282.0 E MTAB 13196:FliTp124hpf S28 L001 0:28 1:98 A:47319366;C:37063279;G:36394680;T:43602586;N:85621 28 98     47319366 37063279 36394680 43602586 85621 ERX11157721 ERS16172939 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00117 0.88222 0.00058 0.09358 0.99799 0.89217 0.54867 0.48545 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11764 11764 ERR11758593 ERX11157721 ERS16172939 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. fli1tp1 24hpf SAMEA114192246 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+ tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed tp1:eGFP                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:fli1tp1 24hpf p fli1tp1 24hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 FliTp124hpf_S24_L001_R1_001.fastq.gz FliTp124hpf_S24_L001_R2_001.fastq.gz fastq fastq 558365976.0 4431476.0 E MTAB 13196:FliTp124hpf S24 L001 0:28 1:98 A:156054630;C:128109738;G:127885708;T:146256146;N:59754 28 98     156054630 128109738 127885708 146256146 59754 ERX11157721 ERS16172939 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00345 0.8879 0.00104 0.07718 0.99322 0.84364 0.38266 0.49193 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11765 11765 ERR11758635 ERX11157720 ERS16172938 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. etv2 wt 22hpf SAMEA114192245 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:etv2 wt 22hpf p etv2 wt 22hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 Etv2Kaede_WT_S6_L001_R1_001.fastq.gz Etv2Kaede_WT_S6_L001_R2_001.fastq.gz fastq fastq 1144014102.0 9079477.0 E MTAB 13196:Etv2Kaede WT S6 L001 0:28 1:98 A:316366230;C:260322813;G:259447166;T:307680623;N:197270 28 98     316366230 260322813 259447166 307680623 197270 ERX11157720 ERS16172938 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00336 0.89267 0.00137 0.13734 0.99545 0.81957 0.3734 0.53458 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11766 11766 ERR11758622 ERX11157720 ERS16172938 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. etv2 wt 22hpf SAMEA114192245 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:etv2 wt 22hpf p etv2 wt 22hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 Etv2Kaede_WT_S8_L001_R2_001.fastq.gz Etv2Kaede_WT_S8_L001_R1_001.fastq.gz fastq fastq 919270926.0 7295801.0 E MTAB 13196:Etv2Kaede WT S8 L001 0:28 1:98 A:259787542;C:207541571;G:206711907;T:245072713;N:157193 28 98     259787542 207541571 206711907 245072713 157193 ERX11157720 ERS16172938 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00358 0.88757 0.00137 0.15368 0.99551 0.83378 0.36405 0.53733 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11767 11767 ERR11758644 ERX11157720 ERS16172938 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. etv2 wt 22hpf SAMEA114192245 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:etv2 wt 22hpf p etv2 wt 22hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 Etv2Kaede_WT_S5_L001_R2_001.fastq.gz Etv2Kaede_WT_S5_L001_R1_001.fastq.gz fastq fastq 877658166.0 6965541.0 E MTAB 13196:Etv2Kaede WT S5 L001 0:28 1:98 A:243057461;C:199464116;G:198654377;T:236322700;N:159512 28 98     243057461 199464116 198654377 236322700 159512 ERX11157720 ERS16172938 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00328 0.88916 0.00127 0.13782 0.99559 0.81925 0.38227 0.53623 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11768 11768 ERR11758628 ERX11157720 ERS16172938 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. etv2 wt 22hpf SAMEA114192245 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:etv2 wt 22hpf p etv2 wt 22hpf p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 Etv2Kaede_WT_S7_L001_R1_001.fastq.gz Etv2Kaede_WT_S7_L001_R2_001.fastq.gz fastq fastq 930443598.0 7384473.0 E MTAB 13196:Etv2Kaede WT S7 L001 0:28 1:98 A:258539610;C:211017108;G:209074684;T:251641766;N:170430 28 98     258539610 211017108 209074684 251641766 170430 ERX11157720 ERS16172938 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00355 0.88938 0.00148 0.14297 0.99569 0.83358 0.35626 0.53314 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Pharyngula Embryo Embryo Imprecise All anatomical structures
11769 11769 ERR11758631 ERX11157719 ERS16172937 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. etv2 15s SAMEA114192244 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:etv2 15s p etv2 15s p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 Etv2_Traver_S10_L001_R2_001.fastq.gz Etv2_Traver_S10_L001_R1_001.fastq.gz fastq fastq 1947733326.0 15458201.0 E MTAB 13196:Etv2 Traver S10 L001 0:28 1:98 A:532150077;C:434208725;G:472140578;T:508906834;N:327112 28 98     532150077 434208725 472140578 508906834 327112 ERX11157719 ERS16172937 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00677 0.92596 0.00142 0.07895 0.98526 0.85123 0.42802 0.53518 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Segmentation Embryo Embryo Imprecise All anatomical structures
11770 11770 ERR11758646 ERX11157719 ERS16172937 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. etv2 15s SAMEA114192244 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:etv2 15s p etv2 15s p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 Etv2_Traver_S28_L001_R2_001.fastq.gz Etv2_Traver_S28_L001_R1_001.fastq.gz fastq fastq 1091426920.0 8801830.0 E MTAB 13196:Etv2 Traver S28 L001 0:26 1:98 A:302665480;C:247712584;G:269795015;T:271081940;N:171901 26 98     302665480 247712584 269795015 271081940 171901 ERX11157719 ERS16172937 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00585 0.90012 0.00149 0.07225 0.98746 0.84916 0.39007 0.54873 26 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Segmentation Embryo Embryo Imprecise All anatomical structures
11771 11771 ERR11758602 ERX11157719 ERS16172937 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. etv2 15s SAMEA114192244 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:etv2 15s p etv2 15s p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 Etv2_Traver_S25_L001_R2_001.fastq.gz Etv2_Traver_S25_L001_R1_001.fastq.gz fastq fastq 983616732.0 7932393.0 E MTAB 13196:Etv2 Traver S25 L001 0:26 1:98 A:272974243;C:222949925;G:242884450;T:244652916;N:155198 26 98     272974243 222949925 242884450 244652916 155198 ERX11157719 ERS16172937 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00571 0.90139 0.00143 0.07484 0.98756 0.85019 0.40119 0.54977 26 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Segmentation Embryo Embryo Imprecise All anatomical structures
11772 11772 ERR11758647 ERX11157719 ERS16172937 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. etv2 15s SAMEA114192244 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:etv2 15s p etv2 15s p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 Etv2_Traver_S27_L001_R2_001.fastq.gz Etv2_Traver_S27_L001_R1_001.fastq.gz fastq fastq 1162223232.0 9372768.0 E MTAB 13196:Etv2 Traver S27 L001 0:26 1:98 A:322910431;C:262934167;G:286614718;T:289578468;N:185448 26 98     322910431 262934167 286614718 289578468 185448 ERX11157719 ERS16172937 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00563 0.89924 0.00128 0.07464 0.98762 0.85064 0.38525 0.53889 26 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Segmentation Embryo Embryo Imprecise All anatomical structures
11773 11773 ERR11758634 ERX11157719 ERS16172937 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. etv2 15s SAMEA114192244 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:etv2 15s p etv2 15s p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 Etv2_Traver_S12_L001_R2_001.fastq.gz Etv2_Traver_S12_L001_R1_001.fastq.gz fastq fastq 1979462268.0 15710018.0 E MTAB 13196:Etv2 Traver S12 L001 0:28 1:98 A:539088187;C:442520328;G:480420115;T:517077908;N:355730 28 98     539088187 442520328 480420115 517077908 355730 ERX11157719 ERS16172937 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00707 0.9236 0.00137 0.07727 0.98451 0.85021 0.41845 0.56136 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Segmentation Embryo Embryo Imprecise All anatomical structures
11774 11774 ERR11758642 ERX11157719 ERS16172937 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. etv2 15s SAMEA114192244 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:etv2 15s p etv2 15s p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 Etv2_Traver_S9_L001_R2_001.fastq.gz Etv2_Traver_S9_L001_R1_001.fastq.gz fastq fastq 1809560214.0 14361589.0 E MTAB 13196:Etv2 Traver S9 L001 0:28 1:98 A:493206820;C:403886293;G:438502430;T:473641472;N:323199 28 98     493206820 403886293 438502430 473641472 323199 ERX11157719 ERS16172937 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00668 0.92354 0.00141 0.0785 0.98543 0.84938 0.43326 0.52002 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Segmentation Embryo Embryo Imprecise All anatomical structures
11775 11775 ERR11758623 ERX11157719 ERS16172937 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. etv2 15s SAMEA114192244 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:etv2 15s p etv2 15s p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 Etv2_Traver_S26_L001_R2_001.fastq.gz Etv2_Traver_S26_L001_R1_001.fastq.gz fastq fastq 1074533780.0 8665595.0 E MTAB 13196:Etv2 Traver S26 L001 0:26 1:98 A:298569273;C:243430874;G:265536499;T:266825982;N:171152 26 98     298569273 243430874 265536499 266825982 171152 ERX11157719 ERS16172937 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00579 0.90109 0.00136 0.07564 0.98788 0.85017 0.3554 0.54362 26 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Segmentation Embryo Embryo Imprecise All anatomical structures
11776 11776 ERR11758596 ERX11157719 ERS16172937 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. etv2 15s SAMEA114192244 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:etv2 15s p etv2 15s p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 Etv2_Traver_S11_L001_R2_001.fastq.gz Etv2_Traver_S11_L001_R1_001.fastq.gz fastq fastq 2167279758.0 17200633.0 E MTAB 13196:Etv2 Traver S11 L001 0:28 1:98 A:591928396;C:482735357;G:524267488;T:567952272;N:396245 28 98     591928396 482735357 524267488 567952272 396245 ERX11157719 ERS16172937 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00635 0.92351 0.00136 0.07835 0.9865 0.85204 0.41521 0.53672 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Segmentation Embryo Embryo Imprecise All anatomical structures
11777 11777 ERR11758595 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S36_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S36_L001_R1_001.fastq.gz fastq fastq 211593816.0 1679316.0 E MTAB 13196:drl h2b dendra tb S36 L001 0:28 1:98 A:62689430;C:45809168;G:45709128;T:57272091;N:113999 28 98     62689430 45809168 45709128 57272091 113999 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00192 0.91331 0.00072 0.14588 0.99675 0.89292 0.51304 0.63144 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11778 11778 ERR11758629 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S37_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S37_L001_R1_001.fastq.gz fastq fastq 980164836.0 7779086.0 E MTAB 13196:drl h2b dendra tb S37 L001 0:28 1:98 A:281375011;C:216067640;G:222839674;T:259781180;N:101331 28 98     281375011 216067640 222839674 259781180 101331 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00817 0.89718 0.00237 0.12153 0.98912 0.82643 0.46403 0.64954 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11779 11779 ERR11758618 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S39_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S39_L001_R1_001.fastq.gz fastq fastq 12118302.0 96177.0 E MTAB 13196:drl h2b dendra tb S39 L001 0:28 1:98 A:3543790;C:2662872;G:2728134;T:3182383;N:1123 28 98     3543790 2662872 2728134 3182383 1123 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00786 0.88963 0.0025 0.12543 0.99403 0.88635 0.50098 0.64694 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11780 11780 ERR11758643 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S5_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S5_L005_R1_001.fastq.gz fastq fastq 2061022698.0 16357323.0 E MTAB 13196:drl h2b dendra tb S5 L005 0:28 1:98 A:587730953;C:457631700;G:470283474;T:545196979;N:179592 28 98     587730953 457631700 470283474 545196979 179592 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.01192 0.91661 0.00336 0.12397 0.98518 0.82568 0.45692 0.65555 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11781 11781 ERR11758610 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S38_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S38_L001_R1_001.fastq.gz fastq fastq 924603120.0 7338120.0 E MTAB 13196:drl h2b dendra tb S38 L001 0:28 1:98 A:265987815;C:203824483;G:210024160;T:244670646;N:96016 28 98     265987815 203824483 210024160 244670646 96016 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00773 0.89881 0.00242 0.12145 0.98944 0.82948 0.50529 0.66568 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11782 11782 ERR11758641 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S6_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S6_L005_R1_001.fastq.gz fastq fastq 1954661562.0 15513187.0 E MTAB 13196:drl h2b dendra tb S6 L005 0:28 1:98 A:558769608;C:433724557;G:445550100;T:516443984;N:173313 28 98     558769608 433724557 445550100 516443984 173313 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.0125 0.91697 0.00373 0.12359 0.98447 0.82558 0.4881 0.6456 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11783 11783 ERR11758591 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S35_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S35_L001_R1_001.fastq.gz fastq fastq 4717188.0 37438.0 E MTAB 13196:drl h2b dendra tb S35 L001 0:28 1:98 A:1419430;C:1014265;G:1016661;T:1264642;N:2190 28 98     1419430 1014265 1016661 1264642 2190 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.0012 0.65482 0.00054 0.10783 0.99953 0.97157 0.625 0.63689 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11784 11784 ERR11758606 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S34_L001_R1_001.fastq.gz drl_h2b-dendra_tb_S34_L001_R2_001.fastq.gz fastq fastq 303645636.0 2409886.0 E MTAB 13196:drl h2b dendra tb S34 L001 0:28 1:98 A:90748559;C:65369482;G:65969002;T:81405258;N:153335 28 98     90748559 65369482 65969002 81405258 153335 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00228 0.91262 0.00099 0.14666 0.99638 0.89006 0.47177 0.63109 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11785 11785 ERR11758640 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S40_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S40_L001_R1_001.fastq.gz fastq fastq 661361022.0 5248897.0 E MTAB 13196:drl h2b dendra tb S40 L001 0:28 1:98 A:190087869;C:145985661;G:150124621;T:175095762;N:67109 28 98     190087869 145985661 150124621 175095762 67109 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00785 0.89784 0.00251 0.12159 0.98948 0.83055 0.46095 0.64951 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11786 11786 ERR11758605 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S7_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S7_L005_R1_001.fastq.gz fastq fastq 25157790.0 199665.0 E MTAB 13196:drl h2b dendra tb S7 L005 0:28 1:98 A:7330053;C:5600451;G:5635840;T:6589498;N:1948 28 98     7330053 5600451 5635840 6589498 1948 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.01201 0.91385 0.00341 0.12826 0.98595 0.85161 0.49226 0.64953 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11787 11787 ERR11758600 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S8_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S8_L005_R1_001.fastq.gz fastq fastq 1422735804.0 11291554.0 E MTAB 13196:drl h2b dendra tb S8 L005 0:28 1:98 A:405788442;C:317299433;G:322206476;T:377317416;N:124037 28 98     405788442 317299433 322206476 377317416 124037 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.01226 0.91547 0.0037 0.12565 0.9849 0.83662 0.48279 0.64531 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11788 11788 ERR11758616 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S33_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S33_L001_R1_001.fastq.gz fastq fastq 328918212.0 2610462.0 E MTAB 13196:drl h2b dendra tb S33 L001 0:28 1:98 A:98036464;C:71090137;G:71650807;T:87969481;N:171323 28 98     98036464 71090137 71650807 87969481 171323 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00197 0.89969 0.00087 0.14269 0.99681 0.89134 0.49763 0.63651 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise 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");;